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Conserved domains on  [gi|1865183900|ref|XP_035183246|]
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alkylated DNA repair protein alkB homolog 8 isoform X3 [Oxyura jamaicensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 1-81 1.42e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


:

Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.77  E-value: 1.42e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   1 MNLVIANAGLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKELMLGDsgQNVVLYSNFVE 80
Cdd:cd12431     2 QHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKELELPQ--QNVPLYLSFVE 79


                  .
gi 1865183900  81 K 81
Cdd:cd12431    80 K 80
2OG-FeII_Oxy super family cl21496
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 95-257 5.80e-19

2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.


The actual alignment was detected with superfamily member pfam13532:

Pssm-ID: 473886  Cd Length: 191  Bit Score: 85.06  E-value: 5.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900  95 GLVVIEKVVSPEEE----RRMLESIDWIGDED--------AQNAQKTLkhRKVKHfGYEFRYDNNNVDKDKPLPGGLPEI 162
Cdd:pfam13532   1 GLVLLPGFLSPEEAaellRELLEEGPFRQPTTqggrpmsvRMTNCGQL--GWVTD-GPGYRYSGVDPVTGEPWPPFPEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 163 CSLfLEKCLKQ-GYIKHKPDQLTVNQYEPGQGIPPHID-THSAFEDEIISLSLGAEIVMDFKHPDGH--TVAVMLPRCSL 238
Cdd:pfam13532  78 LQL-AERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRSdpTISLRLESGDV 156

                         170
                  ....*....|....*....
gi 1865183900 239 LVMSGESRYLWtHGITPRK 257
Cdd:pfam13532 157 LVMGGESRLAY-HGVPPIR 174
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 342-468 6.84e-19

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


:

Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 83.50  E-value: 6.84e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 342 YEEIATHFSSTRhspwpRIVEFLrSLPEGSIVADVGCGNGKYLGI--NKDLYMIGCDRSKNLVDICGEK------KFQAF 413
Cdd:COG2226     1 FDRVAARYDGRE-----ALLAAL-GLRPGARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1865183900 414 VGDALSVPIRSGSCDACISIAVIHHFstaERRLAAIRELARLLRPGGTALIYVWA 468
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
 
Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 1-81 1.42e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.77  E-value: 1.42e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   1 MNLVIANAGLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKELMLGDsgQNVVLYSNFVE 80
Cdd:cd12431     2 QHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKELELPQ--QNVPLYLSFVE 79


                  .
gi 1865183900  81 K 81
Cdd:cd12431    80 K 80
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
95-257 5.80e-19

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 85.06  E-value: 5.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900  95 GLVVIEKVVSPEEE----RRMLESIDWIGDED--------AQNAQKTLkhRKVKHfGYEFRYDNNNVDKDKPLPGGLPEI 162
Cdd:pfam13532   1 GLVLLPGFLSPEEAaellRELLEEGPFRQPTTqggrpmsvRMTNCGQL--GWVTD-GPGYRYSGVDPVTGEPWPPFPEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 163 CSLfLEKCLKQ-GYIKHKPDQLTVNQYEPGQGIPPHID-THSAFEDEIISLSLGAEIVMDFKHPDGH--TVAVMLPRCSL 238
Cdd:pfam13532  78 LQL-AERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRSdpTISLRLESGDV 156

                         170
                  ....*....|....*....
gi 1865183900 239 LVMSGESRYLWtHGITPRK 257
Cdd:pfam13532 157 LVMGGESRLAY-HGVPPIR 174
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 342-468 6.84e-19

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 83.50  E-value: 6.84e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 342 YEEIATHFSSTRhspwpRIVEFLrSLPEGSIVADVGCGNGKYLGI--NKDLYMIGCDRSKNLVDICGEK------KFQAF 413
Cdd:COG2226     1 FDRVAARYDGRE-----ALLAAL-GLRPGARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1865183900 414 VGDALSVPIRSGSCDACISIAVIHHFstaERRLAAIRELARLLRPGGTALIYVWA 468
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 375-464 1.92e-18

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 80.40  E-value: 1.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 375 DVGCGNGKYLGINKDLYM--IGCDRSKNLVDICGEKKFQAF----VGDALSVPIRSGSCDACISIAVIHHFstaERRLAA 448
Cdd:pfam08241   2 DVGCGTGLLTELLARLGArvTGVDISPEMLELAREKAPREGltfvVGDAEDLPFPDNSFDLVLSSEVLHHV---EDPERA 78

                          90
                  ....*....|....*.
gi 1865183900 449 IRELARLLRPGGTALI 464
Cdd:pfam08241  79 LREIARVLKPGGILII 94
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
89-257 2.64e-13

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 69.03  E-value: 2.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900  89 PTNLP-PGLVVIEKVVSPEEERRMLESIDwigdedaqnAQKTLKHRKVKHFGYEF----------------RYDNNnvdK 151
Cdd:COG3145    10 NLELPdGGAVYLPGFLSPEEADALLAALR---------AEAPWRQPVIPIFGKTMsvprlnawygwvgagyRYSGT---D 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 152 DKPLPggLPEicsLFLEkcLKQ---GYIKHKPDQLTVNQYEPGQ---GIppHID--THSAFEDEIISLSLGAEIVMDFKH 223
Cdd:COG3145    78 PEPPP--WPP---ALLA--LKRrveAAAGFPFNSCLLNLYRDGQdrmGW--HQDdeEELGFNPPIASVSLGATRRFRFGH 148

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1865183900 224 PDGH--TVAVMLPRCSLLVMSGESRYLWTHGITPRK 257
Cdd:COG3145   149 KERKdpTRSLPLEHGDLLVMGGPTQLAWQHGVPKTK 184
PRK08317 PRK08317
hypothetical protein; Provisional
 369-464 2.42e-12

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 67.27  E-value: 2.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 369 EGSIVADVGCGNG---KYLG--INKDLYMIGCDRSKNLVDI-----CGEKKFQAFV-GDALSVPIRSGSCDACISIAVIH 437
Cdd:PRK08317   19 PGDRVLDVGCGPGndaRELArrVGPEGRVVGIDRSEAMLALakeraAGLGPNVEFVrGDADGLPFPDGSFDAVRSDRVLQ 98

                          90       100
                  ....*....|....*....|....*..
gi 1865183900 438 HFSTAERrlaAIRELARLLRPGGTALI 464
Cdd:PRK08317   99 HLEDPAR---ALAEIARVLRPGGRVVV 122
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 373-464 5.78e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 53.97  E-value: 5.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 373 VADVGCGNGKY---LGINKDLYMIGCDRSKNLVDICGEKKFQA-------FVGDALSVP-IRSGSCDACISIAVIHHFst 441
Cdd:cd02440     2 VLDLGCGTGALalaLASGPGARVTGVDISPVALELARKAAAALladnvevLKGDAEELPpEADESFDVIISDPPLHHL-- 79

                          90       100
                  ....*....|....*....|...
gi 1865183900 442 AERRLAAIRELARLLRPGGTALI 464
Cdd:cd02440    80 VEDLARFLEEARRLLKPGGVLVL 102
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 9-64 1.17e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.15  E-value: 1.17e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1865183900   9 GLGNGMSRQQLLKTVEEYGLVEALLMPP-----NKPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:pfam00076   5 NLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrSKGFAFVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
2-64 8.12e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.12  E-value: 8.12e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1865183900    2 NLVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPN------KPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:smart00360   1 TLFVGN--LPPDTTEEELRELFSKFGKVESVRLVRDketgksKGFAFVEFESEEDAEKALEALNGKELD 67
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-64 9.66e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 41.24  E-value: 9.66e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   1 MNLVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPN------KPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:COG0724     2 MKIYVGN--LPYSVTEEDLRELFSEYGEVTSVKLITDretgrsRGFGFVEMPDDEEAQAAIEALNGAELM 69
 
Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 1-81 1.42e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.77  E-value: 1.42e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   1 MNLVIANAGLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKELMLGDsgQNVVLYSNFVE 80
Cdd:cd12431     2 QHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKELELPQ--QNVPLYLSFVE 79


                  .
gi 1865183900  81 K 81
Cdd:cd12431    80 K 80
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
95-257 5.80e-19

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 85.06  E-value: 5.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900  95 GLVVIEKVVSPEEE----RRMLESIDWIGDED--------AQNAQKTLkhRKVKHfGYEFRYDNNNVDKDKPLPGGLPEI 162
Cdd:pfam13532   1 GLVLLPGFLSPEEAaellRELLEEGPFRQPTTqggrpmsvRMTNCGQL--GWVTD-GPGYRYSGVDPVTGEPWPPFPEAL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 163 CSLfLEKCLKQ-GYIKHKPDQLTVNQYEPGQGIPPHID-THSAFEDEIISLSLGAEIVMDFKHPDGH--TVAVMLPRCSL 238
Cdd:pfam13532  78 LQL-AERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRSdpTISLRLESGDV 156

                         170
                  ....*....|....*....
gi 1865183900 239 LVMSGESRYLWtHGITPRK 257
Cdd:pfam13532 157 LVMGGESRLAY-HGVPPIR 174
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 342-468 6.84e-19

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 83.50  E-value: 6.84e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 342 YEEIATHFSSTRhspwpRIVEFLrSLPEGSIVADVGCGNGKYLGI--NKDLYMIGCDRSKNLVDICGEK------KFQAF 413
Cdd:COG2226     1 FDRVAARYDGRE-----ALLAAL-GLRPGARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1865183900 414 VGDALSVPIRSGSCDACISIAVIHHFstaERRLAAIRELARLLRPGGTALIYVWA 468
Cdd:COG2226    75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 375-464 1.92e-18

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 80.40  E-value: 1.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 375 DVGCGNGKYLGINKDLYM--IGCDRSKNLVDICGEKKFQAF----VGDALSVPIRSGSCDACISIAVIHHFstaERRLAA 448
Cdd:pfam08241   2 DVGCGTGLLTELLARLGArvTGVDISPEMLELAREKAPREGltfvVGDAEDLPFPDNSFDLVLSSEVLHHV---EDPERA 78

                          90
                  ....*....|....*.
gi 1865183900 449 IRELARLLRPGGTALI 464
Cdd:pfam08241  79 LREIARVLKPGGILII 94
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 373-460 4.26e-18

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 79.53  E-value: 4.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 373 VADVGCGNGKYLGINKDLY---MIGCDRSKNLVDICGEK------KFQAFVGDALSVPIRSGSCDACISIAVIHHFSTAE 443
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGgarVTGVDLSPEMLERARERaaeaglNVEFVQGDAEDLPFPDGSFDLVVSSGVLHHLPDPD 80

                          90
                  ....*....|....*..
gi 1865183900 444 RRlAAIRELARLLRPGG 460
Cdd:pfam13649  81 LE-AALREIARVLKPGG 96
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 350-464 8.47e-16

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 73.90  E-value: 8.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 350 SSTRHSPW-PRIVEFLRS-LPEGSIVADVGCGNGKYL------GINkdlyMIGCDRSKNLVDICGEK----KFQAFVGDA 417
Cdd:COG2227     3 DPDARDFWdRRLAALLARlLPAGGRVLDVGCGTGRLAlalarrGAD----VTGVDISPEALEIARERaaelNVDFVQGDL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1865183900 418 LSVPIRSGSCDACISIAVIHHFSTAErrlAAIRELARLLRPGGTALI 464
Cdd:COG2227    79 EDLPLEDGSFDLVICSEVLEHLPDPA---ALLRELARLLKPGGLLLL 122
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 349-472 1.09e-13

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 70.33  E-value: 1.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 349 FSSTRHSP-WPRIVEFLRSLPEGSIVADVGCGNGKYLGINKDLY---MIGCDRSKNLVDICGEKKFQA-------FVGDA 417
Cdd:COG0500     5 YYSDELLPgLAALLALLERLPKGGRVLDLGCGTGRNLLALAARFggrVIGIDLSPEAIALARARAAKAglgnvefLVADL 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1865183900 418 L-SVPIRSGSCDACISIAVIHHFSTAERRlAAIRELARLLRPGGTALIYVWAMEQE 472
Cdd:COG0500    85 AeLDPLPAESFDLVVAFGVLHHLPPEERE-ALLRELARALKPGGVLLLSASDAAAA 139
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
89-257 2.64e-13

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 69.03  E-value: 2.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900  89 PTNLP-PGLVVIEKVVSPEEERRMLESIDwigdedaqnAQKTLKHRKVKHFGYEF----------------RYDNNnvdK 151
Cdd:COG3145    10 NLELPdGGAVYLPGFLSPEEADALLAALR---------AEAPWRQPVIPIFGKTMsvprlnawygwvgagyRYSGT---D 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 152 DKPLPggLPEicsLFLEkcLKQ---GYIKHKPDQLTVNQYEPGQ---GIppHID--THSAFEDEIISLSLGAEIVMDFKH 223
Cdd:COG3145    78 PEPPP--WPP---ALLA--LKRrveAAAGFPFNSCLLNLYRDGQdrmGW--HQDdeEELGFNPPIASVSLGATRRFRFGH 148

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1865183900 224 PDGH--TVAVMLPRCSLLVMSGESRYLWTHGITPRK 257
Cdd:COG3145   149 KERKdpTRSLPLEHGDLLVMGGPTQLAWQHGVPKTK 184
PRK08317 PRK08317
hypothetical protein; Provisional
 369-464 2.42e-12

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 67.27  E-value: 2.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 369 EGSIVADVGCGNG---KYLG--INKDLYMIGCDRSKNLVDI-----CGEKKFQAFV-GDALSVPIRSGSCDACISIAVIH 437
Cdd:PRK08317   19 PGDRVLDVGCGPGndaRELArrVGPEGRVVGIDRSEAMLALakeraAGLGPNVEFVrGDADGLPFPDGSFDAVRSDRVLQ 98

                          90       100
                  ....*....|....*....|....*..
gi 1865183900 438 HFSTAERrlaAIRELARLLRPGGTALI 464
Cdd:PRK08317   99 HLEDPAR---ALAEIARVLRPGGRVVV 122
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
335-472 1.10e-10

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 60.78  E-value: 1.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 335 QEYVHKVYEEIA----THFSSTRHSPWP-----RIVEFLRSLPEGSIVaDVGCGNGkYLGI---NKDLYMIGCDRSKNLV 402
Cdd:COG4976     4 DAYVEALFDQYAdsydAALVEDLGYEAPallaeELLARLPPGPFGRVL-DLGCGTG-LLGEalrPRGYRLTGVDLSEEML 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1865183900 403 DICGEKKFQA--FVGDALSVPIRSGSCDACISIAVIHHFstaeRRLAAI-RELARLLRPGGTALIYVWAMEQE 472
Cdd:COG4976    82 AKAREKGVYDrlLVADLADLAEPDGRFDLIVAADVLTYL----GDLAAVfAGVARALKPGGLFIFSVEDADGS 150
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 359-466 2.71e-10

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 59.17  E-value: 2.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 359 RIVEFLRsLPEGSIVADVGCGNG---KYLGINKDLYMIGCDRSKNLVDICGEK--------KFQAFVGDALSVPIRsGSC 427
Cdd:COG2230    42 LILRKLG-LKPGMRVLDIGCGWGglaLYLARRYGVRVTGVTLSPEQLEYARERaaeagladRVEVRLADYRDLPAD-GQF 119

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1865183900 428 DACISIAVIHHFSTAERRlAAIRELARLLRPGGTALIYV 466
Cdd:COG2230   120 DAIVSIGMFEHVGPENYP-AYFAKVARLLKPGGRLLLHT 157
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
373-466 3.02e-09

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 54.44  E-value: 3.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 373 VADVGCGNGKY----LGINKDLYMIGCDRSKNLVDICGEK--KFQAFVGDALSVPIRsGSCDACISIAVIHHFstaERRL 446
Cdd:COG4106     5 VLDLGCGTGRLtallAERFPGARVTGVDLSPEMLARARARlpNVRFVVADLRDLDPP-EPFDLVVSNAALHWL---PDHA 80

                          90       100
                  ....*....|....*....|
gi 1865183900 447 AAIRELARLLRPGGTALIYV 466
Cdd:COG4106    81 ALLARLAAALAPGGVLAVQV 100
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 373-464 5.78e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 53.97  E-value: 5.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 373 VADVGCGNGKY---LGINKDLYMIGCDRSKNLVDICGEKKFQA-------FVGDALSVP-IRSGSCDACISIAVIHHFst 441
Cdd:cd02440     2 VLDLGCGTGALalaLASGPGARVTGVDISPVALELARKAAAALladnvevLKGDAEELPpEADESFDVIISDPPLHHL-- 79

                          90       100
                  ....*....|....*....|...
gi 1865183900 442 AERRLAAIRELARLLRPGGTALI 464
Cdd:cd02440    80 VEDLARFLEEARRLLKPGGVLVL 102
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 335-464 5.09e-08

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 54.00  E-value: 5.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 335 QEYVHKVYEEIATHF-------SSTRHSPWPR-IVEFLRSLPeGSIVADVGCGNG-------KYLGINKdlYMIGCDRSK 399
Cdd:PRK00216   10 QEKVAEMFDSIAPKYdlmndllSFGLHRVWRRkTIKWLGVRP-GDKVLDLACGTGdlaialaKAVGKTG--EVVGLDFSE 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1865183900 400 NLVDIcGEKKFQA--------FV-GDALSVPIRSGSCDaCISIA-----VIHhfstaerRLAAIRELARLLRPGGTALI 464
Cdd:PRK00216   87 GMLAV-GREKLRDlglsgnveFVqGDAEALPFPDNSFD-AVTIAfglrnVPD-------IDKALREMYRVLKPGGRLVI 156
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 9-64 1.17e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.15  E-value: 1.17e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1865183900   9 GLGNGMSRQQLLKTVEEYGLVEALLMPP-----NKPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:pfam00076   5 NLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrSKGFAFVEFEDEEDAEKAIEALNGKELG 65
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 9-64 5.08e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 44.58  E-value: 5.08e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1865183900   9 GLGNGMSRQQLLKTVEEYGLVEALLMPPN-----KPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:cd00590     5 NLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALEALNGTELG 65
RRM smart00360
RNA recognition motif;
2-64 8.12e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.12  E-value: 8.12e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1865183900    2 NLVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPN------KPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:smart00360   1 TLFVGN--LPPDTTEEELRELFSKFGKVESVRLVRDketgksKGFAFVEFESEEDAEKALEALNGKELD 67
Methyltransf_12 pfam08242
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 375-460 1.60e-05

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 400515 [Multi-domain]  Cd Length: 98  Bit Score: 43.90  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 375 DVGCGNG----KYLGINKDLYMIGCDRSKNLVDICGEK----------KFQAFVGDALSVPIRSGscDACISIAVIHHFs 440
Cdd:pfam08242   2 EIGCGTGtllrALLEALPGLEYTGLDISPAALEAARERlaalgllnavRVELFQLDLGELDPGSF--DVVVASNVLHHL- 78

                          90       100
                  ....*....|....*....|
gi 1865183900 441 taERRLAAIRELARLLRPGG 460
Cdd:pfam08242  79 --ADPRAVLRNIRRLLKPGG 96
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 13-63 4.29e-05

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 42.05  E-value: 4.29e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1865183900  13 GMSRQQLLKTVEEYGLVEALLMPpnKPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12233    11 TTREEDIEKLFEPFGPLVRCDIR--KTFAFVEFEDSEDATKALEALHGSRI 59
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 9-72 5.32e-05

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 41.50  E-value: 5.32e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1865183900   9 GLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKELmlgdSGQNV 72
Cdd:cd12354     7 NITKGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAIVSVNGTII----NGQAV 66
RRM4_RBM19_RRM3_MRD1 cd12317
RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 13-75 8.14e-05

RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 (RRM3) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409756 [Multi-domain]  Cd Length: 72  Bit Score: 41.09  E-value: 8.14e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1865183900  13 GMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKELmlgdsgQNVVLY 75
Cdd:cd12317    11 GATEEELRELFEKFGTLGRLLLPPSRTIALVEFLEPQDARRAFKKLAYKRF------KHVPLY 67
RRM_Srp1p_like cd12467
RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and ...
 8-72 8.42e-05

RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins; This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain.


Pssm-ID: 240913 [Multi-domain]  Cd Length: 78  Bit Score: 41.33  E-value: 8.42e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   8 AGLGNGMSRQQLLKTVEEYGLVEALLMPP-----NKPYSFVKYGSMEEAKKAFDALNGKELMLGDSGQNV 72
Cdd:cd12467     5 TGFGAETRARDLAYEFERYGRLVRCDIPPprtfqSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDTLHV 74
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 363-464 9.11e-05

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 43.64  E-value: 9.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 363 FLRSLPE--GSIVADVGCGNGkYLGI-----NKDLYMIGCDRSKNLVDIC-------GEKKFQAFVGDALS--------- 419
Cdd:COG2813    41 LLEHLPEplGGRVLDLGCGYG-VIGLalakrNPEARVTLVDVNARAVELAranaaanGLENVEVLWSDGLSgvpdgsfdl 119

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1865183900 420 ----VPIRSGscdACISIAVIHHFstaerrlaaIRELARLLRPGGTALI 464
Cdd:COG2813   120 ilsnPPFHAG---RAVDKEVAHAL---------IADAARHLRPGGELWL 156
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-64 9.66e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 41.24  E-value: 9.66e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   1 MNLVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPN------KPYSFVKYGSMEEAKKAFDALNGKELM 64
Cdd:COG0724     2 MKIYVGN--LPYSVTEEDLRELFSEYGEVTSVKLITDretgrsRGFGFVEMPDDEEAQAAIEALNGAELM 69
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
 11-61 1.44e-04

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 40.38  E-value: 1.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1865183900  11 GNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGK 61
Cdd:cd12305    11 GYGITEDVLKKAFSPFGNIINISMEIEKNCAFVTFEKMESADQAIAELNGT 61
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 2-61 2.47e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 39.98  E-value: 2.47e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1865183900   2 NLVIANagLGNGMSRQQLLKTVEEYGLVEALLM-----PPNK----PYSFVKYGSMEEAKKAFDALNGK 61
Cdd:cd12355     1 RLWIGN--LDPRLTEYHLLKLLSKYGKIKKFDFlfhktGPLKgqprGYCFVTFETKEEAEKAIECLNGK 67
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
 9-63 3.13e-04

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 39.57  E-value: 3.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1865183900   9 GLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12310     5 GLGPWTSLAELEREFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPL 59
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 14-73 3.84e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 39.53  E-value: 3.84e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1865183900  14 MSRQQLLKTVEEYGLVE--ALLMPPNKPYS----FVKYGSMEEAKKAFDALNGKELMLGDSGQNVV 73
Cdd:cd12361    11 ASEEDVRPLFEQFGNIEevQILRDKQTGQSkgcaFVTFSTREEALRAIEALHNKKTMPGCSSPLQV 76
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 2-63 4.53e-04

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 39.08  E-value: 4.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1865183900   2 NLVIANagLGNGMSRQQLLKTVEEYG-LVEALLMPPN----KPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12380     3 NVYVKN--FGEDVDDDELKELFEKYGkITSAKVMKDDsgksKGFGFVNFENHEAAQKAVEELNGKEL 67
RRM3_TIA1 cd12621
RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
 8-63 7.56e-04

RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410032 [Multi-domain]  Cd Length: 72  Bit Score: 38.50  E-value: 7.56e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1865183900   8 AGLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12621     6 GGVTSGLTEQLMRQTFSPFGQIMEIRVFPDKGYSFVRFNSHESAAHAIVSVNGTTI 61
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
 10-77 1.19e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 38.16  E-value: 1.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1865183900  10 LGNGMSRQQLLKTVEEYGLVE--ALLMPPN---KPYSFVKYGSMEEAKKAFDALNGKELMLGDSGQNVVLYSN 77
Cdd:cd12635     9 LGKQQSEDDVRRLFEPFGSIEecTILRGPDgnsKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFAD 81
RRM3_TIAR cd12620
RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup ...
 8-60 1.33e-03

RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 241064 [Multi-domain]  Cd Length: 73  Bit Score: 37.69  E-value: 1.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865183900   8 AGLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNG 60
Cdd:cd12620     6 GGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 58
RRM3_MRD1 cd12568
RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 ...
 13-75 1.77e-03

RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241012 [Multi-domain]  Cd Length: 72  Bit Score: 37.37  E-value: 1.77e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1865183900  13 GMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGKElmLGDSgqnvVLY 75
Cdd:cd12568    11 GTTAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKALAYRR--FKDS----ILY 67
PLN02244 PLN02244
tocopherol O-methyltransferase
 373-467 1.91e-03

tocopherol O-methyltransferase


Pssm-ID: 215135 [Multi-domain]  Cd Length: 340  Bit Score: 40.88  E-value: 1.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 373 VADVGCGNG---KYL---------GINKDLYMIGcdRSKNLVD---ICGEKKFQafVGDALSVPIRSGSCDACISIAVIH 437
Cdd:PLN02244  122 IVDVGCGIGgssRYLarkyganvkGITLSPVQAA--RANALAAaqgLSDKVSFQ--VADALNQPFEDGQFDLVWSMESGE 197

                          90       100       110
                  ....*....|....*....|....*....|
gi 1865183900 438 HFstaERRLAAIRELARLLRPGGTALIYVW 467
Cdd:PLN02244  198 HM---PDKRKFVQELARVAAPGGRIIIVTW 224
Methyltransf_23 pfam13489
Methyltransferase domain; This family appears to be a methyltransferase domain.
 353-468 2.06e-03

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 404385 [Multi-domain]  Cd Length: 162  Bit Score: 39.33  E-value: 2.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 353 RHSPWPRIVEFL-RSLPEGSIVADVGCGNGKYLGINKDLY--MIGCDRSKNLVDICGEK-KFQAFVGDALSVPirSGSCD 428
Cdd:pfam13489   5 RERLLADLLLRLlPKLPSPGRVLDFGCGTGIFLRLLRAQGfsVTGVDPSPIAIERALLNvRFDQFDEQEAAVP--AGKFD 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1865183900 429 ACISIAVIHHFstaERRLAAIRELARLLRPGGTALIYVWA 468
Cdd:pfam13489  83 VIVAREVLEHV---PDPPALLRQIAALLKPGGLLLLSTPL 119
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 38-72 4.20e-03

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 36.82  E-value: 4.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1865183900  38 KPYSFVKYGSMEEAKKAFDALNGKELMlgdsGQNV 72
Cdd:cd12324    48 KGYALVEYETKKEAQAAIEGLNGKELL----GQTI 78
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 2-61 5.02e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 36.22  E-value: 5.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900   2 NLVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYSFVKYGSMEEAKKAFDALNGK 61
Cdd:cd12262     5 NVYVGN--LDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIK 62
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 13-63 5.28e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 36.06  E-value: 5.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1865183900  13 GMSRQQLLKTVEEYGLVEALLMPPN------KPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12284     9 NITEDMLRGIFEPFGKIEFVQLQKDpetgrsKGYGFIQFRDAEDAKKALEQLNGFEL 65
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 15-63 7.03e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 35.68  E-value: 7.03e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1865183900  15 SRQQLLKTVEEYGLVEALLMPpnKPYSFVKYGSMEEAKKAFDALNGKEL 63
Cdd:cd12251    14 TEEKLRELFSEYGKVERVKKI--KDYAFVHFEERDDAVKAMEEMNGKEL 60
PLN02233 PLN02233
ubiquinone biosynthesis methyltransferase
 341-464 8.24e-03

ubiquinone biosynthesis methyltransferase


Pssm-ID: 177877 [Multi-domain]  Cd Length: 261  Bit Score: 38.72  E-value: 8.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 341 VYEEIATHFSSTRHSPWPRIVEFLRSLPEGSIVADVGCG--------------NGKYLGIN--KDLYMIGCDRSKNLVDI 404
Cdd:PLN02233   45 VYDNLNDLLSLGQHRIWKRMAVSWSGAKMGDRVLDLCCGsgdlafllsekvgsDGKVMGLDfsSEQLAVAASRQELKAKS 124

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1865183900 405 CgEKKFQAFVGDALSVPIRSGSCDAcisIAVIHHFSTAERRLAAIRELARLLRPGGTALI 464
Cdd:PLN02233  125 C-YKNIEWIEGDATDLPFDDCYFDA---ITMGYGLRNVVDRLKAMQEMYRVLKPGSRVSI 180
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
 3-74 8.89e-03

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 35.21  E-value: 8.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1865183900   3 LVIANagLGNGMSRQQLLKTVEEYGLVEALLMPPNKPYS-FVKYGSMEEAKKAFDALNGKELmlgdSGQNVVL 74
Cdd:cd12527     4 LVILN--LLPAVSSFTLREIFQVYGDVKDVRETPLKPSQrFVEFFDVRDAARALHEMNGKEI----FGKRLVI 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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