NCBI Conserved Domain Search

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 159.41 E-value: 3.24e-48

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYAD 436
Cdd:cd22434     1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNAQYLLQNSVKQYSG 74

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411861 [Multi-domain] Cd Length: 70 Bit Score: 134.69 E-value: 6.91e-39

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 120 DCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22433     1 DCELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQIGGKPDKVVECIREILELL 70

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411860 [Multi-domain] Cd Length: 64 Bit Score: 116.13 E-value: 4.80e-32

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463  42 MVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKII 105
Cdd:cd22432     1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGPERILTISADRETVLGILTEIL 64

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411867 [Multi-domain] Cd Length: 68 Bit Score: 87.29 E-value: 2.18e-21

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22439     1 QTTQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLAQYLI 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 85.03 E-value: 1.41e-20

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN 429
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 78.11 E-value: 4.21e-18

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd00105     2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411949 Cd Length: 76 Bit Score: 75.86 E-value: 3.92e-17

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22521     6 SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411950 [Multi-domain] Cd Length: 75 Bit Score: 74.76 E-value: 7.73e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 358 DLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNS 430
Cdd:cd22522     3 DASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGSPANISLAQYLINAR 75

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 74.18 E-value: 9.25e-17

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQEC--CPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22437     1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDqlLPGSSERIVTITGSFDQVVKAVALILEKL 69

ROKNT (NUC014) domain; This presumed domain is found at the N-terminus of RNP K-like proteins that also contains KH domains pfam00013.

Pssm-ID: 429813 Cd Length: 39 Bit Score: 72.71 E-value: 1.63e-16

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2462624463   4 EQPEETFPNTETNGefgKRPAEDMEEEQAFKRSRNTDEMV 43
Cdd:pfam08067   3 QQEEETFSNTESNG---KRPAEDMEEEQAFKRSRNSDEMV 39

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 71.94 E-value: 7.20e-16

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463  364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPleGSEDRIITITGTQDQIQNAQYLLQNSV 431
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGPPENVEKAAELILEIL 68

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 70.74 E-value: 1.83e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 366 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22462     1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLIE 63

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 70.32 E-value: 2.58e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNAQYL 426
Cdd:cd22437     2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKIspkDQLLPGSSERIVTITGSFDQVVKAVAL 64

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411942 [Multi-domain] Cd Length: 71 Bit Score: 68.60 E-value: 9.61e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 431
Cdd:cd22514     1 TSVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKIsdrGDFVSGTRNRKVTITGPQDAVQMAQYLLEQKL 71

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411807 [Multi-domain] Cd Length: 71 Bit Score: 68.37 E-value: 1.16e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKID---EPLEGSEDRIITITGTQDQIQNAQYLLQNSV 431
Cdd:cd09031     2 VIELEVPENLVGAILGKGGKTLVEIQELTGARIQISkkgEFVPGTRNRKVTITGTPAAVQAAQYLIEQRI 71

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 67.25 E-value: 2.76e-14

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 418
Cdd:cd22459     8 CPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSSEA 56

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 66.97 E-value: 4.47e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd22520     4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411951 Cd Length: 68 Bit Score: 66.46 E-value: 6.07e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22523     8 IPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLI 65

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 64.97 E-value: 1.92e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 431
Cdd:cd22396     1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLIDQIV 68

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 64.37 E-value: 3.11e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22463     2 SKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIvqDRYPLEETQKILRISGTEEQLKRAQSLVE 68

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411806 [Multi-domain] Cd Length: 72 Bit Score: 64.21 E-value: 3.57e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd02396     4 LRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTISGSPEAITKCVEQICCVMLE 72

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 64.15 E-value: 4.32e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK 432
Cdd:cd22404     5 VTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLINALIK 69

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 64.04 E-value: 6.27e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISESP 193
Cdd:cd22519     8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESP 78

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.

Pssm-ID: 411857 [Multi-domain] Cd Length: 82 Bit Score: 63.12 E-value: 1.12e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSED--RIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22429     1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDlvRLITITGTKKEVDAAKSLILEKVSE 73

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 61.45 E-value: 2.69e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESgaSIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22411     3 KVPIFKQFHKNIIGKGGATIKKIREET--NTRIDLPEENSDSDVITITGKKEDVEKARERIL 62

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411806 [Multi-domain] Cd Length: 72 Bit Score: 61.52 E-value: 3.16e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd02396     2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVaSEMLPNSTERAVTISGSPEAITKCVEQI 66

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 61.40 E-value: 4.36e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNAQ 424
Cdd:cd22435     8 VPNYAAGSIIGKGGQTIAQLQKETGARIKLsknNDFYPGTTERVCLIQGEVEAVNAVL 65

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 60.35 E-value: 7.23e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEY 111
Cdd:cd22438     1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCPERIVTVTGTTDAVFKAFELICRKLEED 67

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 60.35 E-value: 9.23e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462624463 375 AGSIIGKGGQRIKQIRHESGASIKIDEplEGSEDRIITITGTQDQIQNA 423
Cdd:cd22438    10 VGSIIGKKGETIKKFREESGARINISD--GSCPERIVTVTGTTDAVFKA 56

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411826 [Multi-domain] Cd Length: 67 Bit Score: 59.97 E-value: 1.17e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 366 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22398     2 MEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPDQVQHA 59

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 59.51 E-value: 1.77e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDriITITGTQDQIQNAQYLLQNSVK 432
Cdd:cd02394     3 FTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDE--IRIEGSPEGVKKAKAEILELVD 68

fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 59.16 E-value: 2.19e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKID--EPLEGSEdRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22399     1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDrnPPPNPNE-KLFIIRGNPQQIEHAKQLIR 65

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411884 [Multi-domain] Cd Length: 69 Bit Score: 58.85 E-value: 2.44e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22456     6 IPHSLIGSIIGKGGARIKEIQDGSGARLVAsKEFLPLSTERILEVQGTPDAIHNA 60

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 59.17 E-value: 2.59e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 124 RLLIHQSLAGGIIGVKGAKIKELRENTQTTIK-LFQEC---CPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22460     3 RLLVASSQAGSLIGKGGAIIKQIREESGASVRiLPEEElppCASPDDRVVQISGEAQAVKKALELVSSRL 72

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 58.69 E-value: 3.02e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22395     6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKA 59

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 58.79 E-value: 3.50e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEG--SEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22460     6 VASSQAGSLIGKGGAIIKQIREESGASVRIlpeEELPPCasPDDRVVQISGEAQAVKKALELV 68

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411885 [Multi-domain] Cd Length: 64 Bit Score: 58.24 E-value: 3.84e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22457     3 ISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIaKAPHDETGERMFTITGTPEANDRALRLL 63

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 58.32 E-value: 4.09e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 121 CELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQ--ECCPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22435     2 CSLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKnnDFYPGTTERVCLIQGEVEAVNAVLDFILEKI 72

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 57.68 E-value: 5.75e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 122 ELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQEcCPHSTDRVVLIGGKPDRVVECIKIILD 187
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGTPEAVEAAKALIEE 65

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411946 [Multi-domain] Cd Length: 78 Bit Score: 57.83 E-value: 7.89e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISES 192
Cdd:cd22518     9 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLES 78

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411830 [Multi-domain] Cd Length: 66 Bit Score: 57.26 E-value: 1.09e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22402     1 ETTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPAdSPDAPERKVTITGPPEAQWKAQLCI 65

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER and flowering locus K homology domain protein (FLK). PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. The model corresponds to the KH3 domain of PEPPER and FLK.

Pssm-ID: 411889 Cd Length: 69 Bit Score: 57.18 E-value: 1.20e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN 429
Cdd:cd22461     2 VSQQMQIPLSYADAIIGTAGANISYIRRTSGATITIQETRGAPGEMTVEIHGTQSQVQTAQQLIQN 67

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 56.53 E-value: 1.82e-10

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463  120 DCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQeccPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEKAAELILEIL 68

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 56.55 E-value: 1.85e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSV 431
Cdd:cd22454     4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 56.18 E-value: 2.63e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQI 420
Cdd:cd22520     2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVaGDLLPNSTERAVTVSGVPDAI 59

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411861 [Multi-domain] Cd Length: 70 Bit Score: 55.34 E-value: 4.94e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 374 LAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22433    12 QAGCIIGRAGFKIKELREKTGATIKVySECCPRSTDRVVQIGGKPDKVVEC 62

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 54.99 E-value: 5.94e-10

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463   43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKI 104
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELI 64

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

Pssm-ID: 411886 [Multi-domain] Cd Length: 65 Bit Score: 54.38 E-value: 1.11e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22458     1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRL-IPISNSSQQTIHLSGTDKQIALA 59

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 54.38 E-value: 1.11e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22451     2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQV--PKKDDPSGKIRITGARDGVEAATAKILNISDE 68

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 54.16 E-value: 1.14e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 366 TQVTI--PKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG--SEDRIITITGTQDQIQNA 423
Cdd:cd22436     1 KQVKIlvPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESinLQERVVTVTGEPEANRKA 62

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411884 [Multi-domain] Cd Length: 69 Bit Score: 54.22 E-value: 1.37e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECI 182
Cdd:cd22456     2 IRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNAT 61

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 53.82 E-value: 1.82e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE-GSEDRIITITGTQDQIQNA 423
Cdd:cd22400     6 VPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENaGAAEKAITIYGTPEGCSSA 60

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411883 Cd Length: 70 Bit Score: 53.84 E-value: 1.89e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462624463 375 AGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22455    12 AAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKA 60

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 53.44 E-value: 2.14e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463  44 ELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILSISADIETIGEILKKII 105
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSEseGNERIVTITGTPEAVEAAKALIE 64

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411883 Cd Length: 70 Bit Score: 53.45 E-value: 2.15e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALR--TDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22455     1 LTLRALVSSKEAAVIIGKGGENIARLRatTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411907 [Multi-domain] Cd Length: 71 Bit Score: 53.41 E-value: 2.65e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22479     1 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGSPEAVQKAKMMLDDIVSR 70

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411906 [Multi-domain] Cd Length: 75 Bit Score: 53.49 E-value: 2.91e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22478     3 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK 73

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 53.64 E-value: 3.03e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 362 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQI 420
Cdd:cd22519     4 PPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVaGDMLPNSTERAVTISGTPDAI 63

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411831 [Multi-domain] Cd Length: 66 Bit Score: 52.63 E-value: 4.19e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQ 424
Cdd:cd22403     1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLprDQTPDEGDEVPVEIIGNFYATQSAQ 62

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 52.30 E-value: 5.15e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQEcCPHSTDRVVLIGGKPDRVVECIKIIL 186
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKE-GEGSGERVVTITGTPEAVEKAKELIE 63

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 52.32 E-value: 6.68e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 121 CELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKlFQECCPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22454     4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVIT-FERVNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411806 [Multi-domain] Cd Length: 72 Bit Score: 52.27 E-value: 6.87e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-----PDSSgpERILSISADIETIGEILKKI 104
Cdd:cd02396     2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVasemlPNST--ERAVTISGSPEAITKCVEQI 66

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411945 Cd Length: 70 Bit Score: 51.57 E-value: 1.18e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22517     4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCPERITTITGSTDAVFRAFSMIAFKLEE 69

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 51.57 E-value: 1.26e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE--DRIITITGTQDQIQNAQ 424
Cdd:cd22428     5 IEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGElpERVLLIQGNPVQAQRAE 67

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 51.07 E-value: 1.49e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 371 PKDLAGSIIGKGGQRIKQIRHESGASI---KIDEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22401     7 HNNLCGRLIGKDGRNIKKIMEDTNTKItisSLQDLTSYNPERTITIKGSLEAMSEAESLI 66

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411943 Cd Length: 70 Bit Score: 51.17 E-value: 1.81e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22515     4 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEE 69

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins; The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance.

Pssm-ID: 411892 [Multi-domain] Cd Length: 66 Bit Score: 50.94 E-value: 1.92e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 366 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22464     1 AKISVDASLAGAIIGKGGVNSKQICRETGVKLSIRDHERDPNLKNVELEGSFEQIKEA 58

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 50.30 E-value: 3.02e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 120 DCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLfQECCPHSTDRVVLIGGKPDR 177
Cdd:cd22459     1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV-EDGVPGTEERVITISSSEAP 57

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411941 [Multi-domain] Cd Length: 73 Bit Score: 50.51 E-value: 3.22e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 375 AGSIIGKGGQRIKQIRHESGASIKIDEPLE---GSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22513    13 AGSVIGKGGATINDFQAQSGARIQLSRAQEffpGTTDRVLLVSGSLNEVLTALNLI 68

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411908 [Multi-domain] Cd Length: 71 Bit Score: 49.90 E-value: 3.95e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22480     1 ITEEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMPERPCVLTGTPESIEQAKRLL 64

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 49.48 E-value: 5.07e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRIITITGTQDQIQNA 423
Cdd:cd22408     1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEV--PPNDSDSETITLRGPADKLGAA 57

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 49.62 E-value: 5.74e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEdrIITITGTQDQIQNAQYLLQ 428
Cdd:cd22406     6 SVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSD--EIKITGTKEGIEKARHEIQ 67

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411946 [Multi-domain] Cd Length: 78 Bit Score: 48.97 E-value: 1.28e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 362 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI-DEPLEGSEDRIITITGTQDQI 420
Cdd:cd22518     5 PPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVaGDMLPNSTERAITIAGIPQSI 64

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 48.37 E-value: 1.56e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNAS--VSVPDSSGP---ERILSISADIETI 97
Cdd:cd22437     1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANikISPKDQLLPgssERIVTITGSFDQV 58

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 48.38 E-value: 1.56e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 122 ELRLLIHQSLAGGIIGVKGAKIKELRENTQT--TIKLFQECCPHSTDRVVLIGGKPDRVVE 180
Cdd:cd22401     1 PLKILAHNNLCGRLIGKDGRNIKKIMEDTNTkiTISSLQDLTSYNPERTITIKGSLEAMSE 61

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 48.30 E-value: 1.60e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-------PDSSgpERILSISADIETIGEILKKII 105
Cdd:cd22435     4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLsknndfyPGTT--ERVCLIQGEVEAVNAVLDFIL 69

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411924 Cd Length: 76 Bit Score: 48.09 E-value: 2.30e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEP-LEGSEDRIITITGTQDqiqnAQYLLQNSVKQYADVEGF 440
Cdd:cd22496     4 TVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPeTPDSKVRMVIITGPPE----AQFKAQGRIYGKLKEENF 76

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411917 [Multi-domain] Cd Length: 69 Bit Score: 47.62 E-value: 2.41e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 369 TIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSED---RIITITGTQDQIQNAQYLLQ 428
Cdd:cd22489     5 TIPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNTDpnvRIFTIRGVPQQIEHARQLID 67

third type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411855 [Multi-domain] Cd Length: 79 Bit Score: 47.99 E-value: 2.86e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKI---DEPLEGSEDR---IITITGTQDQIQNAQYLLQ 428
Cdd:cd22427     5 IFQVPRDLVGKVIGKNGRVIQEIVDKSGvVRVKIegdNEDGPRPREEglvPFIFVGTREAIANAKLLLE 73

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 47.76 E-value: 3.10e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdEPLEGSE--DRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22498     6 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKI-APAEGPDakLRMVIITGPPEAQFKAQGRIYGKLKE 75

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411945 Cd Length: 70 Bit Score: 47.33 E-value: 3.48e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2462624463 376 GSIIGKGGQRIKQIRHESGASIKIDEplEGSEDRIITITGTQDQIQNA 423
Cdd:cd22517    14 GSIIGKKGETVKRIREESSARITISE--GSCPERITTITGSTDAVFRA 59

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411941 [Multi-domain] Cd Length: 73 Bit Score: 47.43 E-value: 3.61e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLF--QECCPHSTDRVVLIGGKPDRVVECIKIILD 187
Cdd:cd22513     4 AKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSraQEFFPGTTDRVLLVSGSLNEVLTALNLILE 70

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 47.41 E-value: 4.67e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 361 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI------DEPLEGSEDRI--ITITGTQDQIQNAQYLLQNSVK 432
Cdd:cd22447     1 SPKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIpprdadAAPADEDDDTMveVTITGDEFNVQHAKQRIEEIIS 80

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 46.82 E-value: 5.93e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDrIITITGTQDQIQNAQYLLQNSVKQYAD 436
Cdd:cd22417     2 TLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDD-EITITGYEKNAEAAKDAILKIVQELES 72

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 46.48 E-value: 6.71e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPhstDRVVLIGGKPDRVVECIKII 185
Cdd:cd22438     1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCP---ERIVTVTGTTDAVFKAFELI 60

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 51.20 E-value: 8.81e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 362 PIITTqVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDeplegsEDRIITITGT-QDQIQNA 423
Cdd:PRK11824  553 PRIET-IKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATdGEAAEAA 608

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 45.77 E-value: 9.14e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 376 GSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22452    14 GRIIGPGGSNINQIREKSGCFINV--PKKNKESDVITLRGTKEGVEKAEEMIK 64

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411944 Cd Length: 77 Bit Score: 45.86 E-value: 1.38e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22516    11 IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIFKAFAMIAYKFEE 76

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 45.68 E-value: 1.39e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILSISA 92
Cdd:cd22459     2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGvpGTEERVITISS 53

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 45.37 E-value: 1.41e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD--SSGPERILSISADIETI 97
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKegEGSGERVVTITGTPEAV 55

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411943 Cd Length: 70 Bit Score: 45.77 E-value: 1.41e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEplEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22515     1 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNAIFKAFAMIIDKLEE 69

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411860 [Multi-domain] Cd Length: 64 Bit Score: 45.25 E-value: 1.53e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 122 ELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQEccpHSTDRVVLIGGKPDRVVECIKIIL 186
Cdd:cd22432     3 ELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS---SGPERILTISADRETVLGILTEIL 64

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 45.68 E-value: 1.53e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  44 ELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-----PDSSGPERILSISADIETIGEILKKI 104
Cdd:cd22401     1 PLKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITIsslqdLTSYNPERTITIKGSLEAMSEAESLI 66

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411930 [Multi-domain] Cd Length: 71 Bit Score: 45.52 E-value: 1.62e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVK 432
Cdd:cd22502     2 SKKVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTGDRIITIRGGTESTRQATQLINALIK 69

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411943 Cd Length: 70 Bit Score: 45.39 E-value: 1.90e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPhstDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd22515     4 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP---ERIITLAGPTNAIFKAFAMIIDKLEE 69

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411944 Cd Length: 77 Bit Score: 45.09 E-value: 2.65e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2462624463 376 GSIIGKGGQRIKQIRHESGASIKIDEplEGSEDRIITITGTQDQIQNA 423
Cdd:cd22516    21 GSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGPTDAIFKA 66

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411945 Cd Length: 70 Bit Score: 45.02 E-value: 2.72e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPhstDRVVLIGGKPDRVVECIKII 185
Cdd:cd22517     4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCP---ERITTITGSTDAVFRAFSMI 63

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 44.56 E-value: 2.76e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 378 IIGKGGQRIKQIRHESGASIKIdePLEGSEDR-IITITGTQDQIQNAQYLL 427
Cdd:cd22413    17 LIGRGGANIRKIRDNTGARIIF--PTARDEDQeLITIIGTKEAVEKAKEEL 65

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 44.39 E-value: 3.53e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 366 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDeplegsEDRIITITGT-QDQIQNAQYLLQNSVK 432
Cdd:cd02393     6 TTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE------DDGTVTIFATdKESAEAAKAMIEDIVA 67

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 44.53 E-value: 3.55e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  46 RILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGP-------ERILSISADIETIGEILKKI 104
Cdd:cd22460     3 RLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELppcaspdDRVVQISGEAQAVKKALELV 68

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 44.20 E-value: 4.06e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIDeplEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22430     6 IDSSLVGAVIGRGGSKIRELEESTGSKIKII---KGGQEAEVKIFGSDEAQQKAKELIDELVGR 66

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411860 [Multi-domain] Cd Length: 64 Bit Score: 43.32 E-value: 6.52e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRIITITGTQDQI 420
Cdd:cd22432     2 VELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSV--PDSSGPERILTISADRETV 56

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411925 Cd Length: 77 Bit Score: 43.93 E-value: 6.65e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIdEPLEGSE--DRIITITGTQDQIQNAQ 424
Cdd:cd22497     9 IPTQAVGAIIGKKGQHIKQLARFAGASIKI-APAEGPDvsERMVIITGPPEAQFKAQ 64

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 42.94 E-value: 1.15e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2462624463  42 MVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS 82
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDE 41

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411944 Cd Length: 77 Bit Score: 42.40 E-value: 2.45e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 116 GSDFDCELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPhstDRVVLIGGKPDRVVECIKII 185
Cdd:cd22516     4 GLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCP---ERIVTITGPTDAIFKAFAMI 70

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411909 [Multi-domain] Cd Length: 71 Bit Score: 41.92 E-value: 2.58e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22481     5 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMiqDGPQNTGADKPLRITGDPYKVQQAKEMV 67

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 41.87 E-value: 3.00e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV---PDSSGPERILSI 90
Cdd:cd22400     2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIhrkENAGAAEKAITI 50

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411915 Cd Length: 72 Bit Score: 41.87 E-value: 3.26e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 369 TIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSED---RIITITGTQDQIQNAQYLLQNSV 431
Cdd:cd22487     7 IVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADpnmKLFTIRGSPQQIDYARQLIEEKI 72

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 41.83 E-value: 3.28e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRIITITGTQDQIQNAQYLLQNSVKQY 434
Cdd:cd22416     2 VTEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISI--PPAELQSDIIKITGPPANVERAKAALLERVKEL 70

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 41.92 E-value: 3.43e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 127 IHQSLAGGIIGVKGAKIKELRENTQTTIKLfQECCPHSTDRVVLIGGKPDRV 178
Cdd:cd22434     8 IPKDLAGSIIGKGGQRIRQIRHESGASIKI-DEPLPGSEDRIITITGTQDQI 58

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 41.49 E-value: 3.73e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 362 PIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDE-PLEGSedriITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22449     2 NGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFEDkTGEGN----VEIKGSKKNVEEAKKRILSQIDE 70

second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411854 [Multi-domain] Cd Length: 63 Bit Score: 40.98 E-value: 4.33e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA-SIKIDEplegsEDRIITITG-TQDQIQNAQYLLQ 428
Cdd:cd22426     2 FIEEFKVDPDLIGLAIGSHGSNIQQARKIPGVeSIDVDE-----EDGTFRIYGeTPEAVEKARALLE 63

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 41.45 E-value: 4.39e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 122 ELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTD-RVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22436     2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLQeRVVTVTGEPEANRKAVSLILQKI 70

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 41.55 E-value: 4.44e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-----PDSSgpERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22520     2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVagdllPNST--ERAVTVSGVPDAIIQCVRQICAVILE 72

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 41.02 E-value: 4.66e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462624463 370 IPKDLAGSIIGKGGQRIKQIRHESGASIKIdePLEGSEDRiITITGTQDQ 419
Cdd:cd22419     7 VPSALFKFIIGKKGETKKRLESETKTQIRI--PRQGKEGD-IVITGKDRS 53

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 41.07 E-value: 5.39e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463  44 ELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV---PDSSG-PERILSISADIETIGE----ILKKI 104
Cdd:cd22436     2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQIsqkPESINlQERVVTVTGEPEANRKavslILQKI 70

second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411825 [Multi-domain] Cd Length: 69 Bit Score: 41.07 E-value: 5.95e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22397     1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMiqDGPQPTGQDKPLRITGDPQKVQRAKELVM 66

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 40.65 E-value: 6.39e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 135 IIGVKGAKIKELRENTQTTIKLFQEccpHSTDRVVLIGGKPDRVVECIKIIL 186
Cdd:cd22411    14 IIGKGGATIKKIREETNTRIDLPEE---NSDSDVITITGKKEDVEKARERIL 62

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411912 Cd Length: 68 Bit Score: 40.66 E-value: 7.24e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdEPLEGSE-DRIITITGTQDQIQNAQYLLQN 429
Cdd:cd22484     4 DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF-KPDDGTTpERIAQITGPPDRCQHAAEIITD 66

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411939 [Multi-domain] Cd Length: 78 Bit Score: 41.13 E-value: 7.25e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGAsikIDEPLEGSEDRIIT---------ITGTQDQIQNAQYLLQ 428
Cdd:cd22511     6 VQVPRNLVGKVIGKNGKVIQEIVDKSGV---VRVRVEGDNDKKNPreegmvpfiFVGTKENISNAQALLE 72

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411914 Cd Length: 70 Bit Score: 40.70 E-value: 7.93e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIdEPLEG-SEDRIITITGTQDQIQNAQYLL 427
Cdd:cd22486     4 SIEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQF-KPDDGiSPERVAQVMGPPDRCQHAAHII 66

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 40.93 E-value: 8.20e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-----PDSSgpERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22519     6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVagdmlPNST--ERAVTISGTPDAIIQCVKQICVVMLE 76

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.

Pssm-ID: 411931 Cd Length: 83 Bit Score: 40.89 E-value: 9.17e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITG----TQDQIQNAQYLLQNSVKQYADV 437
Cdd:cd22503     2 SKKLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNGERMITIRGgtesTRYAVQLINALIQDPAKELEDL 78

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 39.97 E-value: 1.31e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 363 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGAsIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22412     1 IVEVEVEIPAKLHNSLIGAKGRLIRSIMEECGG-VHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLL 65

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 39.50 E-value: 1.40e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDriITITGTQDQIQNA 423
Cdd:cd22407     1 TERLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDE--IVVSGEKEGVAQA 57

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411916 Cd Length: 69 Bit Score: 39.70 E-value: 1.59e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 369 TIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSED---RIITITGTQDQIQNAQYLLQ 428
Cdd:cd22488     5 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQPPPNGDpnfKLFIIRGSPQQIDHAKQLIE 67

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411830 [Multi-domain] Cd Length: 66 Bit Score: 39.54 E-value: 1.72e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 124 RLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPD 176
Cdd:cd22402     4 YLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPERKVTITGPPE 56

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411867 [Multi-domain] Cd Length: 68 Bit Score: 39.52 E-value: 1.85e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 131 LAGGIIGVKGAKIKELRENTQTTIKLfQECCPHSTDRVVLIGGKPdrvvECIKIILDLISES 192
Cdd:cd22439    12 LIGCIIGKGGTKINEIRQLSGATIKI-ANSEDGSTERSVTITGTP----EAVSLAQYLINAR 68

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 43.50 E-value: 2.11e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463  55 GAVIGKGGKNIKALRTDYNASVSVPD--------SSGP------ERILSISADIEtIGEIL----KKIIP 106
Cdd:PRK11824  566 RDVIGPGGKTIREITEETGAKIDIEDdgtvkiaaTDGEaaeaakERIEGITAEPE-VGEIYegkvVRIVD 634

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 39.61 E-value: 2.17e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2462624463  54 AGAVIGKGGKNIKALRTDYNASVSV--PDSSGPERILSISADIETI 97
Cdd:cd22434    13 AGSIIGKGGQRIRQIRHESGASIKIdePLPGSEDRIITITGTQDQI 58

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411830 [Multi-domain] Cd Length: 66 Bit Score: 39.16 E-value: 2.35e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462624463  41 EMVELRILLQSknAGAVIGKGGKNIKALRTDYNASVSV--PDSSG-PERILSIS 91
Cdd:cd22402     1 ETTYLYIPNKA--VGAIIGTKGSHIRYIKRFSGASIKIapADSPDaPERKVTIT 52

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411919 Cd Length: 74 Bit Score: 39.27 E-value: 2.45e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd22491     2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENAGAAEKPITIHATPEGCSAACRMILEIMQK 70

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411911 [Multi-domain] Cd Length: 83 Bit Score: 39.51 E-value: 3.24e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22483     8 EILIPASKVGLVIGKGGETIKQLQERTGVKMIMiqDGPLPTGADKPLRITGDPFKVQQAREMVLEIIRE 76

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411883 Cd Length: 70 Bit Score: 38.82 E-value: 3.54e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 122 ELRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKlFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd22455     2 TLRALVSSKEAAVIIGKGGENIARLRATTGVKAG-VSKVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411938 [Multi-domain] Cd Length: 78 Bit Score: 39.18 E-value: 3.74e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESG-ASIKI----DEPLEGSEDRI-ITITGTQDQIQNAQYLLQ 428
Cdd:cd22510     6 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIegdnENKLPREDGMVpFVFVGTKESIGNVQVLLE 72

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411946 [Multi-domain] Cd Length: 78 Bit Score: 38.95 E-value: 3.98e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463  43 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV-----PDSSgpERILSISADIETIGEILKKIIPTLEE 110
Cdd:cd22518     7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVagdmlPNST--ERAITIAGIPQSIIECVKQICVVMLE 77

KH domain;

Pssm-ID: 463779 Cd Length: 73 Bit Score: 38.61 E-value: 4.35e-04

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2462624463  37 RNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT 70
Cdd:pfam13083  23 EEEEKTVVLELNVAGEDMGKVIGKQGRTLDALRT 56

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 38.38 E-value: 4.78e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSV--PDSSGPERILSISADIE 95
Cdd:cd22462     1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVlkPDSATGERIVLISGTPD 53

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411826 [Multi-domain] Cd Length: 67 Bit Score: 38.39 E-value: 5.01e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463 130 SLAGGIIGVKGAKIKELRENTQTTIKlFQECCPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22398     9 FAVGVVIGKGGEMIKKIQNETGARVQ-FKPDDGNSPDRICVITGPPDQVQHAARMIQELI 67

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411918 Cd Length: 76 Bit Score: 38.53 E-value: 5.27e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISE 191
Cdd:cd22490     2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHSTPEGCSAACKMILEIMQK 70

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411940 [Multi-domain] Cd Length: 78 Bit Score: 38.40 E-value: 5.92e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGAsikIDEPLEGSEDRIIT---------ITGTQDQIQNAQYLL 427
Cdd:cd22512     6 IQVPRNLVGKVIGKNGKLIQEIVDKSGV---VRVRIEAENDKNIPqeegmvpfvFVGTKDSITNATVLL 71

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 38.54 E-value: 6.18e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 361 GPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI------DEPLEGSEDRIITITGTQD 418
Cdd:cd22446     4 SPKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIpkrneeGNYDEDDDDETVEISIEGD 67

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411921 Cd Length: 97 Bit Score: 38.50 E-value: 8.39e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463  39 TDEMVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILSISADIETI----GEILKKI 104
Cdd:cd22493     1 TADEVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQdltlyNPERTITVKGSIEACcraeQEIMKKV 75

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];

Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 41.53 E-value: 9.59e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462624463  55 GAVIGKGGKNIKALRTDYNASVSVPDS-----SGP---------ERILSISADIEtIGEIL----KKIIP 106
Cdd:COG1185   561 RDVIGPGGKVIRKIIEETGAKIDIEDDgtvkiAATdgeaaekaiERIEGITAEPE-VGEIYegkvVRIMD 629

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 37.70 E-value: 9.74e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQT--TIKLFQECCPHSTDRVVLIGG 173
Cdd:cd22494     2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTkiTISSLQDLTIYNPERTITVKG 54

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 37.70 E-value: 9.74e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 374 LAGSIIGKGGQRIKQIRHESGASIKIdEPLEG----SEDRIITITGTQDQIQNAQ 424
Cdd:cd22494    10 LVGRLIGKEGRNLKKIEQDTGTKITI-SSLQDltiyNPERTITVKGSIEACSSAE 63

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411928 Cd Length: 78 Bit Score: 37.80 E-value: 1.16e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 364 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYADVE 438
Cdd:cd22500     2 LEAHIKVPSSAAGRVIGKGGKTVNELQNLTSAEVIVprDQTPDENEEVIVKIIGHFFASQTAQRKIREIVQQVKQQE 78

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];

Pssm-ID: 441442 Cd Length: 76 Bit Score: 37.34 E-value: 1.24e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2462624463  35 RSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT 70
Cdd:COG1837    22 TEEEGERTVVLELRVAPEDLGKVIGKQGRTAKAIRT 57

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 37.12 E-value: 1.29e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 131 LAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTdRVVLIGGKPDRVVECIKII 185
Cdd:cd22395    10 LVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNF-QICSIEGTQQQIDKALKLI 63

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411923 Cd Length: 77 Bit Score: 37.33 E-value: 1.37e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463  45 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILSISADIETIG----EILKKIIPTLE 109
Cdd:cd22495     2 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAkaeeEIMKKIRESYE 75

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411910 [Multi-domain] Cd Length: 73 Bit Score: 37.20 E-value: 1.67e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGAS-IKIDEPLEGSE-DRIITITGTQDQIQNAQYLLQNSVKQ 433
Cdd:cd22482     5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNvDKPLRIIGDPYKVQQACEMVMDILRE 73

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411920 Cd Length: 76 Bit Score: 37.10 E-value: 1.72e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22492     2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIM 68

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411909 [Multi-domain] Cd Length: 71 Bit Score: 36.91 E-value: 1.87e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 125 LLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECC-PHSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22481     6 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPqNTGADKPLRITGDPYKVQQAKEMVLELI 71

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one.

Pssm-ID: 411925 Cd Length: 77 Bit Score: 36.99 E-value: 2.08e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 125 LLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPD 176
Cdd:cd22497     7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPDVSERMVIITGPPE 58

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411913 Cd Length: 68 Bit Score: 36.09 E-value: 3.68e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462624463 367 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQN 429
Cdd:cd22485     4 DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIND 66

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 36.16 E-value: 3.78e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2462624463  55 GAVIGKGGKNIKALRTDYNASVSVPDS----SGPERILSIS 91
Cdd:cd22428    17 GLIIGRQGATIKQIQKETGARIDFKDEgsggELPERVLLIQ 57

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411949 Cd Length: 76 Bit Score: 36.19 E-value: 3.84e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462624463 125 LLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQEcCPHSTDRVVLIGGKP 175
Cdd:cd22521     9 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP-VEGSTDRQVTITGSA 58

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411929 Cd Length: 66 Bit Score: 35.82 E-value: 4.06e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462624463 366 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI--DEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22501     2 AHIKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVprDQTPDENDQVVVKITGHFYASQLAQRKIQ 66

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 35.69 E-value: 4.66e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463  55 GAVIGKGGKNIKALRTDYNASVSV-PDSSG-PERILSISA---DIETIGEILKKII 105
Cdd:cd22396    13 GLIIGRGGEQINRLQAESGAKIQIaPDSGGlPERPCTLTGtpdAIETAKRLIDQIV 68

putative RNA-processing protein; Provisional

Pssm-ID: 237494 [Multi-domain] Cd Length: 180 Bit Score: 37.93 E-value: 4.84e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDeplegSEDRIITITGTQDQ 419
Cdd:PRK13763    7 VKIPKDRIGVLIGKKGETKKEIEERTGVKLEID-----SETGEVIIEPTDGE 53

ATPase; Provisional

Pssm-ID: 184311 [Multi-domain] Cd Length: 602 Bit Score: 39.05 E-value: 5.38e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462624463 368 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSEDRIITI 413
Cdd:PRK13764  485 VYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVrpldEEPGEEAEEGEEVT 534

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411923 Cd Length: 77 Bit Score: 35.79 E-value: 5.43e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQT--TIKLFQECCPHSTDRVVLIGGKPDRVVECIKIILDLISES 192
Cdd:cd22495     2 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTkiTISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRES 73

type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins; The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).

Pssm-ID: 411790 Cd Length: 75 Bit Score: 35.52 E-value: 5.49e-03

                          10        20        30
                  ....*....|....*....|....*....|..
gi 2462624463  39 TDEMVELRILLQSKNAGAVIGKGGKNIKALRT 70
Cdd:cd22533    26 GEKTTVYELRVAPEDVGRVIGKQGRTAKAIRT 57

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 35.39 E-value: 6.00e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462624463 378 IIGKGGQRIKQIRHESGASIKIDEPLEGSEDR-IITITGTQDQIQNA-QYLL 427
Cdd:cd22422    16 MLGRNGSNIKHIMQRTGAQIHFPDPNNPPQRKsTVFISGSIDSVYLArQQLM 67

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 35.37 E-value: 6.13e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462624463  39 TDEMVelrilLQSKNAGAVIGKGGKNIKALR--TDYNASVSVPDSSGPERILSISADIETIGEILKKIIPT 107
Cdd:cd22454     5 TIEVV-----IPNADVGKVIGKGGETIKRIEalTDTVITFERVNGGSPNREVQITGSPDNVAAAKRLIEDT 70

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 35.26 E-value: 6.32e-03

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2462624463  55 GAVIGKGGKNIKALRTDYNASVSVPDSSGPE 85
Cdd:cd22417    13 PKIIGRKGAVITKLRDDHDVNIQFPDKGDEN 43

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 34.95 E-value: 6.45e-03

                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIK 155
Cdd:cd22430     2 LCFKIDSSLVGAVIGRGGSKIRELEESTGSKIK 34

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 34.94 E-value: 6.98e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462624463 365 TTQVTIPKDLAGSIIGKGGQRIKQIRhESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 428
Cdd:cd22410     3 TKDIIIEQRFHRTIIGQKGEKIREIR-DKFPQVQITFPDPGSKSDVVTLRGPKDEVDKCYKYLK 65

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 35.10 E-value: 8.06e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462624463 123 LRLLIHQSLAGGIIGVKGAKIKELRENTQTTIKLFQECCP-HSTDRVVLIGGKPDRVVECIKIILDLI 189
Cdd:cd22463     4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPlEETQKILRISGTEEQLKRAQSLVEGLI 71

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 34.85 E-value: 8.32e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462624463 127 IHQSLAGGIIGVKGAKIKELRENTQTTIKlfqecCPHSTDR--VVLIGGKPDRVVECIKIILDLIS 190
Cdd:cd02394     8 IDPKFHGHIIGKGGANIKRIREESGVSIR-----IPDDEANsdEIRIEGSPEGVKKAKAEILELVD 68