NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|19114154|ref|NP_593242|]
View 

putative exosome subunit Rrp40 [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 71-157 4.81e-44

S1_Rrp40: Rrp40 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: 240216  Cd Length: 86  Bit Score: 143.17  E-value: 4.81e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAFENVTRKSRPNLNVGSLVYARVSLADRDMEPELECFDAtTGK 150
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS-SGK 79


                ....*..
gi 19114154 151 AAGYGEL 157
Cdd:cd05790  80 ADGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 160-237 5.23e-36

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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 of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 122.24  E-value: 5.23e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114154 160 GYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIRNCEFMSDEEQIKYCKDLI 237
Cdd:cd22526   2 GFLFK-VSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
 
Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 71-157 4.81e-44

S1_Rrp40: Rrp40 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: 240216  Cd Length: 86  Bit Score: 143.17  E-value: 4.81e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAFENVTRKSRPNLNVGSLVYARVSLADRDMEPELECFDAtTGK 150
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS-SGK 79


                ....*..
gi 19114154 151 AAGYGEL 157
Cdd:cd05790  80 ADGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 160-237 5.23e-36

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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 of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 122.24  E-value: 5.23e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114154 160 GYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIRNCEFMSDEEQIKYCKDLI 237
Cdd:cd22526   2 GFLFK-VSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 71-219 2.17e-16

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 75.27  E-value: 2.17e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNA-LAFENVTRKSRPN----LNVGSLVYARVSLADRDMEPELecfd 145
Cdd:COG1097  57 KYIPKVGDLVIGKVTDVGPSNWEVDINSPYQALLPVsEVPGRPFNVESDDlrkyLDIGDYILAKVKNFDRTRDPLL---- 132

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114154 146 atTGKAAGYGELKNGYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIR 219
Cdd:COG1097 133 --TMKDKGLGKIEGGRIVE-ISPSKVPRVIGKKGSMINMLKKETGCEIIVGQNGRIWIKGPDEEGEELAIEAIK 203
PRK04163 PRK04163
exosome complex protein Rrp4;
69-219 1.47e-14

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 70.30  E-value: 1.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154   69 TKRYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNalAFENVTRKSRPN-------LNVGSLVYARVSLADRDMEPEL 141
Cdd:PRK04163  56 EGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLP--VSEVLGRPVNVEgtdlrkyLDIGDYIIAKVKDVDRTRDVVL 133

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114154  142 ecfdatTGKAAGYGELKNGYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIR 219
Cdd:PRK04163 134 ------TLKGKGLGKIEGGTIVE-IKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIK 204
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 160-207 2.71e-13

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: 62.45  E-value: 2.71e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 19114154   160 GYMITgLSLSHCRKLIlpKNTLLQTLGSYIPFEIAVGMNGRVWVNSEN 207
Cdd:pfam15985   1 GMLVK-VSLSLVRRLL--KSHFLHELGKKGPFEIAVGLNGRIWIKSET 45
 
Name Accession Description Interval E-value
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 71-157 4.81e-44

S1_Rrp40: Rrp40 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: 240216  Cd Length: 86  Bit Score: 143.17  E-value: 4.81e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAFENVTRKSRPNLNVGSLVYARVSLADRDMEPELECFDAtTGK 150
Cdd:cd05790   1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS-SGK 79


                ....*..
gi 19114154 151 AAGYGEL 157
Cdd:cd05790  80 ADGFGPL 86
KH-I_Rrp40 cd22526
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar ...
 160-237 5.23e-36

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins; Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, 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 of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411954 [Multi-domain]  Cd Length: 78  Bit Score: 122.24  E-value: 5.23e-36
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114154 160 GYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIRNCEFMSDEEQIKYCKDLI 237
Cdd:cd22526   2 GFLFK-VSLGLARRLLSPDCPLLKELGKHFPFEIAVGMNGRIWVKAETVQQTIAIANAIEACEFLSEAQIKAMVKKLA 78
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 71-219 2.17e-16

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 75.27  E-value: 2.17e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNA-LAFENVTRKSRPN----LNVGSLVYARVSLADRDMEPELecfd 145
Cdd:COG1097  57 KYIPKVGDLVIGKVTDVGPSNWEVDINSPYQALLPVsEVPGRPFNVESDDlrkyLDIGDYILAKVKNFDRTRDPLL---- 132

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114154 146 atTGKAAGYGELKNGYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIR 219
Cdd:COG1097 133 --TMKDKGLGKIEGGRIVE-ISPSKVPRVIGKKGSMINMLKKETGCEIIVGQNGRIWIKGPDEEGEELAIEAIK 203
PRK04163 PRK04163
exosome complex protein Rrp4;
69-219 1.47e-14

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 70.30  E-value: 1.47e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154   69 TKRYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNalAFENVTRKSRPN-------LNVGSLVYARVSLADRDMEPEL 141
Cdd:PRK04163  56 EGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLP--VSEVLGRPVNVEgtdlrkyLDIGDYIIAKVKDVDRTRDVVL 133

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114154  142 ecfdatTGKAAGYGELKNGYMITgLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIR 219
Cdd:PRK04163 134 ------TLKGKGLGKIEGGTIVE-IKPVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIK 204
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 160-207 2.71e-13

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: 62.45  E-value: 2.71e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 19114154   160 GYMITgLSLSHCRKLIlpKNTLLQTLGSYIPFEIAVGMNGRVWVNSEN 207
Cdd:pfam15985   1 GMLVK-VSLSLVRRLL--KSHFLHELGKKGPFEIAVGLNGRIWIKSET 45
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 71-150 2.28e-12

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: 61.03  E-value: 2.28e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAF-ENVTRKSRPNLNVGSLVYARVSLADRDMEPELECFDATTG 149
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSAtEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNELG 80


                .
gi 19114154 150 K 150
Cdd:cd04454  81 V 81
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 71-157 1.39e-08

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: 50.63  E-value: 1.39e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114154  71 RYIPATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAF-ENVTRKSRPN----LNVGSLVYARVSLADRDMEPELecfd 145
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnLPRTDEDELNmrsyLDEGDLIVAEVQSVDSDGSVSL---- 76

                        90
                ....*....|..
gi 19114154 146 atTGKAAGYGEL 157
Cdd:cd05789  77 --HTRSLKYGKL 86
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 162-233 1.38e-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: 47.64  E-value: 1.38e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114154 162 MITGLSLSHCRKLILPKNTLLQTLGSYIPFEIAVGMNGRVWVNSENLSTTVLICTAIRNCEFMSDE---EQIKYC 233
Cdd:cd22445   2 LLVKVTPGLVRRLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTRQQTSILANIIEACEHMHTSdqrKQIFSR 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH