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Conserved domains on  [gi|2098465178|gb|KAH0582542|]
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hypothetical protein H2248_010482 [Termitomyces sp. 'cryptogamus']

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 190-314 8.34e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411953  Cd Length: 123  Bit Score: 164.36  E-value: 8.34e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178 190 GQLVTVPPVLVRRLKSHFISLPCGVDLILGLNGYIWVSKHVKESEQEGEEGFdaeAVYSNLNDHIDESTRMAISRVTNII 269
Cdd:cd22525     1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSA---AIYSNNNEPVSPETREAIARVRNCI 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2098465178 270 RVFASHFVPLTDTLLLEAYEWTLDQEGAAKDLLQEDVGDALVATM 314
Cdd:cd22525    78 KALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEA 122
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 96-187 1.22e-42

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


:

Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 141.92  E-value: 1.22e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  96 RYNPEVGDLVVGRITEVQPRRWKVDANSRQDAVLMLSSVNLPggvqrrKLESDELQMRTFFEEGDLLVAEVQAFFSDGAM 175
Cdd:cd05789     1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                          90
                  ....*....|..
gi 2098465178 176 SLHTRSLKYGKL 187
Cdd:cd05789    75 SLHTRSLKYGKL 86
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 50-84 1.45e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


:

Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.45e-12
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2098465178  50 PGESLTSSQAYMRGHGTYVDNEEVIASVAGTIERV 84
Cdd:pfam14382   4 PGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 190-314 8.34e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 164.36  E-value: 8.34e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178 190 GQLVTVPPVLVRRLKSHFISLPCGVDLILGLNGYIWVSKHVKESEQEGEEGFdaeAVYSNLNDHIDESTRMAISRVTNII 269
Cdd:cd22525     1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSA---AIYSNNNEPVSPETREAIARVRNCI 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2098465178 270 RVFASHFVPLTDTLLLEAYEWTLDQEGAAKDLLQEDVGDALVATM 314
Cdd:cd22525    78 KALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEA 122
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 96-187 1.22e-42

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 141.92  E-value: 1.22e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  96 RYNPEVGDLVVGRITEVQPRRWKVDANSRQDAVLMLSSVNLPggvqrrKLESDELQMRTFFEEGDLLVAEVQAFFSDGAM 175
Cdd:cd05789     1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                          90
                  ....*....|..
gi 2098465178 176 SLHTRSLKYGKL 187
Cdd:cd05789    75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
46-256 1.13e-29

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 113.06  E-value: 1.13e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  46 KLTYPGESLtSSQAYMRGHGTYVDNEEVIASVAGTIERVNKLVTVRATRTRYNPEVGDLVVGRITEVQPRRWKVDANSRQ 125
Cdd:PRK04163    9 KIVVPGDLL-AEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178 126 DAVLMLSSVnlPGGVQrrKLESDElqMRTFFEEGDLLVAEVQAFfsDGAM----SLHTRSLkyGKLRNGQLVTVPPVLVR 201
Cdd:PRK04163   88 KAYLPVSEV--LGRPV--NVEGTD--LRKYLDIGDYIIAKVKDV--DRTRdvvlTLKGKGL--GKIEGGTIVEIKPVKVP 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2098465178 202 RL---KSHFISL---PCGVDLILGLNGYIWVSKHVKESEQEGEEGF---DAEAVYSNLNDHIDE 256
Cdd:PRK04163  158 RVigkKGSMINMlkeETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIkkiEREAHTSGLTDRIKE 221
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 46-166 1.49e-14

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 70.77  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  46 KLTYPGESLTSSQAYMRGHGTYVDNEEVIASVAGTIER--VNKLVTVRA-TRTRYNPEVGDLVVGRITEVQPRR-----W 117
Cdd:PRK09521    6 DLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIddINRKISVIPfKKTPPLLKKGDIVYGRVVDVKEQRalvriV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2098465178 118 KVDANSRQDAVLMLSSVNLPgGVQRRKLESdelqMRTFFEEGDLLVAEV 166
Cdd:PRK09521   86 SIEGSERELATSKLAYIHIS-QVSDGYVES----LTDAFKIGDIVRAKV 129
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 50-84 1.45e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.45e-12
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2098465178  50 PGESLTSSQAYMRGHGTYVDNEEVIASVAGTIERV 84
Cdd:pfam14382   4 PGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 190-232 4.14e-12

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 60.14  E-value: 4.14e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2098465178 190 GQLVTVPPVLVRRLKSHFI--SLPCGV--DLILGLNGYIWVSKHVKE 232
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHFlhELGKKGpfEIAVGLNGRIWIKSETVK 47
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 46-114 2.21e-09

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 56.06  E-value: 2.21e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2098465178  46 KLTYPGESLTSSQAYMRGHGTYVDNEEVIASVAGTIE--RVNKLVTVR-ATRTRYNPEVGDLVVGRITEVQP 114
Cdd:COG1096     7 DFVLPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVidDKNRVISVKpKKKPPPVPKKGDIVIGEVVDVRE 78
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 190-314 8.34e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 164.36  E-value: 8.34e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178 190 GQLVTVPPVLVRRLKSHFISLPCGVDLILGLNGYIWVSKHVKESEQEGEEGFdaeAVYSNLNDHIDESTRMAISRVTNII 269
Cdd:cd22525     1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTVEESGEEAGGSA---AIYSNNNEPVSPETREAIARVRNCI 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2098465178 270 RVFASHFVPLTDTLLLEAYEWTLDQEGAAKDLLQEDVGDALVATM 314
Cdd:cd22525    78 KALAALHIPITDTSILAVYEASLELGIEVKDLLKPEVMEEIVEEA 122
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 96-187 1.22e-42

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 141.92  E-value: 1.22e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  96 RYNPEVGDLVVGRITEVQPRRWKVDANSRQDAVLMLSSVNLPggvqrrKLESDELQMRTFFEEGDLLVAEVQAFFSDGAM 175
Cdd:cd05789     1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                          90
                  ....*....|..
gi 2098465178 176 SLHTRSLKYGKL 187
Cdd:cd05789    75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
46-256 1.13e-29

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 113.06  E-value: 1.13e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  46 KLTYPGESLtSSQAYMRGHGTYVDNEEVIASVAGTIERVNKLVTVRATRTRYNPEVGDLVVGRITEVQPRRWKVDANSRQ 125
Cdd:PRK04163    9 KIVVPGDLL-AEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178 126 DAVLMLSSVnlPGGVQrrKLESDElqMRTFFEEGDLLVAEVQAFfsDGAM----SLHTRSLkyGKLRNGQLVTVPPVLVR 201
Cdd:PRK04163   88 KAYLPVSEV--LGRPV--NVEGTD--LRKYLDIGDYIIAKVKDV--DRTRdvvlTLKGKGL--GKIEGGTIVEIKPVKVP 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2098465178 202 RL---KSHFISL---PCGVDLILGLNGYIWVSKHVKESEQEGEEGF---DAEAVYSNLNDHIDE 256
Cdd:PRK04163  158 RVigkKGSMINMlkeETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIkkiEREAHTSGLTDRIKE 221
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 96-187 3.72e-27

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 101.47  E-value: 3.72e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  96 RYNPEVGDLVVGRITEVQPRRWKVDANSRQDAVLMLSSVNLPggvqrrklesDELQMRTFFEEGDLLVAEVQAFFSDGAM 175
Cdd:cd04454     1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKSLQPGDLILAKVISLGDDMNV 70

                          90
                  ....*....|..
gi 2098465178 176 SLHTRSLKYGKL 187
Cdd:cd04454    71 LLTTADNELGVI 82
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 46-166 1.49e-14

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 70.77  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2098465178  46 KLTYPGESLTSSQAYMRGHGTYVDNEEVIASVAGTIER--VNKLVTVRA-TRTRYNPEVGDLVVGRITEVQPRR-----W 117
Cdd:PRK09521    6 DLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIddINRKISVIPfKKTPPLLKKGDIVYGRVVDVKEQRalvriV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2098465178 118 KVDANSRQDAVLMLSSVNLPgGVQRRKLESdelqMRTFFEEGDLLVAEV 166
Cdd:PRK09521   86 SIEGSERELATSKLAYIHIS-QVSDGYVES----LTDAFKIGDIVRAKV 129
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 50-84 1.45e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.45e-12
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2098465178  50 PGESLTSSQAYMRGHGTYVDNEEVIASVAGTIERV 84
Cdd:pfam14382   4 PGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 190-232 4.14e-12

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 60.14  E-value: 4.14e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2098465178 190 GQLVTVPPVLVRRLKSHFI--SLPCGV--DLILGLNGYIWVSKHVKE 232
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHFlhELGKKGpfEIAVGLNGRIWIKSETVK 47
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 46-114 2.21e-09

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 56.06  E-value: 2.21e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2098465178  46 KLTYPGESLTSSQAYMRGHGTYVDNEEVIASVAGTIE--RVNKLVTVR-ATRTRYNPEVGDLVVGRITEVQP 114
Cdd:COG1096     7 DFVLPGDVLAVIEEFLPGEGTYEEDGKIRAAVVGKVVidDKNRVISVKpKKKPPPVPKKGDIVIGEVVDVRE 78
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 190-226 7.41e-07

type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins; The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411873 [Multi-domain]  Cd Length: 78  Bit Score: 46.10  E-value: 7.41e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2098465178 190 GQLVTVPPVLVRRLKS------HFISLPCGVDLILGLNGYIWV 226
Cdd:cd22445     1 GLLVKVTPGLVRRLLApdceiiQEVGKLYPLEIVFGMNGRIWV 43
S1_CSL4 cd05791
S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 99-166 8.76e-04

S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240217  Cd Length: 92  Bit Score: 38.00  E-value: 8.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2098465178  99 PEVGDLVVGRITEVQPRRWKVDansrqdaVLMLSSVNLPG---GVQR----RKLESDELQMRTFFEEGDLLVAEV 166
Cdd:cd05791     4 PKVGSIVIARVTRINPRFAKVD-------ILCVGGRPLKEsfrGVIRkediRATEKDKVEMYKCFRPGDIVRAKV 71
KH-I_Rrp4_prokar cd22524
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from ...
 190-256 4.25e-03

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from archaea; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from archaea. It is a non-catalytic component of the exosome, which is a phosphorolytic 3'-5' exoribonuclease complex involved in RNA degradation and processing. Rrp4 increases the RNA binding and the efficiency of RNA degradation and confers strong poly(A) specificity to the exosome.


Pssm-ID: 411952 [Multi-domain]  Cd Length: 82  Bit Score: 35.64  E-value: 4.25e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2098465178 190 GQLVTVPPVLVRRL---KSHFISL---PCGVDLILGLNGYIWVSKHVKESEQEGEEGF---DAEAVYSNLNDHIDE 256
Cdd:cd22524     1 GILVEISPSKVPRVigkKGSMINMlkkKTNCDIFVGQNGRIWVKGPSPEDEEIAIKAIrmiEEEAHTSGLTDRVKE 76
 
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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