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Conserved domains on  [gi|19113177|ref|NP_596385|]
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exosome subunit Rrp43 [Schizosaccharomyces pombe]

Protein Classification

exosome complex component RRP43( domain architecture ID 10183523)

exosome complex component RRP43 similar to Saccharomyces cerevisiae exosome RRP43 subunit which is involved in pre-rRNA processing and found both in the nucleus and in the cytoplasm.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 18-269 5.49e-97

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


:

Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 285.22  E-value: 5.49e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  18 KKITPEQYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLEL 97
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  98 SPLCSSKFKPGPPSDLAQVVSQELHQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKL 177
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 178 PTAVWDEDLERVICASTLTRPVQLSTEVRSFSWSVFDDK-LLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQP 256
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKhLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250
                ....*....|...
gi 19113177 257 LLLKKCIEVARSK 269
Cdd:cd11369 241 AQLQECIELAKKR 253
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 18-269 5.49e-97

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 285.22  E-value: 5.49e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  18 KKITPEQYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLEL 97
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  98 SPLCSSKFKPGPPSDLAQVVSQELHQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKL 177
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 178 PTAVWDEDLERVICASTLTRPVQLSTEVRSFSWSVFDDK-LLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQP 256
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKhLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250
                ....*....|...
gi 19113177 257 LLLKKCIEVARSK 269
Cdd:cd11369 241 AQLQECIELAKKR 253
PRK04282 PRK04282
exosome complex protein Rrp42;
19-269 1.64e-59

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 190.09  E-value: 1.64e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177   19 KITPEQYLShLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELS 98
Cdd:PRK04282  10 EIKKDYILS-LLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177   99 PLCSSKFKPGPPSD----LAQVVSqelhQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKT 174
Cdd:PRK04282  89 PLASPTFEPGPPDEnaieLARVVD----RGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLN 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  175 VKLPTAVWDEDLERVICAStlTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHI 254
Cdd:PRK04282 165 TKVPAVEEGEDGVVDKLGE--DFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSF 242

                        250
                 ....*....|....*
gi 19113177  255 QPLLLKKCIEVARSK 269
Cdd:PRK04282 243 TEEEVDKAIDIALEK 257
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 20-269 4.25e-59

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 188.47  E-value: 4.25e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  20 ITPE---QYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLE 96
Cdd:COG2123   5 IIPEikrDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAE 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  97 LSPLCSSKFKPGPPSD----LAQVVSqelhQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAAL 172
Cdd:COG2123  85 LLPLASPTFEPGPPDEnaieLARVVD----RGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAAL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 173 KTVKLPTAVWDEDLERVIcaSTLTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGT 252
Cdd:COG2123 161 LTTKVPKVEVGEDGVVVD--KGEDTPLPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSG 238

                       250
                ....*....|....*..
gi 19113177 253 HIQPLLLKKCIEVARSK 269
Cdd:COG2123 239 SFTEEEIDKAIDIALEK 255
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 43-178 7.46e-33

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 116.54  E-value: 7.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177    43 EFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELSPLCSSKFK-PGPPSDLAQVVSQEL 121
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPgEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19113177   122 HQTLQQSNLInlqslcifEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLP 178
Cdd:pfam01138  81 DRALRPSIPL--------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 18-269 5.49e-97

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 285.22  E-value: 5.49e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  18 KKITPEQYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLEL 97
Cdd:cd11369   1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  98 SPLCSSKFKPGPPSDLAQVVSQELHQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKL 177
Cdd:cd11369  81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 178 PTAVWDEDLERVICASTLTRPVQLSTEVRSFSWSVFDDK-LLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQP 256
Cdd:cd11369 161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKhLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                       250
                ....*....|...
gi 19113177 257 LLLKKCIEVARSK 269
Cdd:cd11369 241 AQLQECIELAKKR 253
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 19-269 2.80e-63

RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA.


Pssm-ID: 206770 [Multi-domain]  Cd Length: 256  Bit Score: 198.98  E-value: 2.80e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  19 KITPEQYLShLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELS 98
Cdd:cd11365   2 KIKRDYILS-LLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  99 PLCSSKFKPGPPSD----LAQVVSqelhQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKT 174
Cdd:cd11365  81 PLASPTFEPGPPDEnaieLARVVD----RGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLN 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 175 VKLPTAVWDEDleRVICASTLTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHI 254
Cdd:cd11365 157 TKVPEYEVDEN--EVIEVLGEELPLPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSF 234

                       250
                ....*....|....*
gi 19113177 255 QPLLLKKCIEVARSK 269
Cdd:cd11365 235 TEDEIDKAIDIALEK 249
PRK04282 PRK04282
exosome complex protein Rrp42;
19-269 1.64e-59

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 190.09  E-value: 1.64e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177   19 KITPEQYLShLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELS 98
Cdd:PRK04282  10 EIKKDYILS-LLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177   99 PLCSSKFKPGPPSD----LAQVVSqelhQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKT 174
Cdd:PRK04282  89 PLASPTFEPGPPDEnaieLARVVD----RGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLN 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  175 VKLPTAVWDEDLERVICAStlTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHI 254
Cdd:PRK04282 165 TKVPAVEEGEDGVVDKLGE--DFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSF 242

                        250
                 ....*....|....*
gi 19113177  255 QPLLLKKCIEVARSK 269
Cdd:PRK04282 243 TEEEVDKAIDIALEK 257
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 20-269 4.25e-59

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 188.47  E-value: 4.25e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  20 ITPE---QYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLE 96
Cdd:COG2123   5 IIPEikrDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAE 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  97 LSPLCSSKFKPGPPSD----LAQVVSqelhQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAAL 172
Cdd:COG2123  85 LLPLASPTFEPGPPDEnaieLARVVD----RGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAAL 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 173 KTVKLPTAVWDEDLERVIcaSTLTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGT 252
Cdd:COG2123 161 LTTKVPKVEVGEDGVVVD--KGEDTPLPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSG 238

                       250
                ....*....|....*..
gi 19113177 253 HIQPLLLKKCIEVARSK 269
Cdd:COG2123 239 SFTEEEIDKAIDIALEK 255
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 44-266 1.07e-45

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites.


Pssm-ID: 206766 [Multi-domain]  Cd Length: 218  Bit Score: 152.87  E-value: 1.07e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  44 FREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEP-FENSPNEGWIVPNLELSPLCSSKFKPGPPSDLAQVVSQELH 122
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPdKLERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 123 QTLQQSnlinlQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLPTAVWDED------LERVICASTlt 196
Cdd:cd11358  81 RTIEAS-----VILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERspplllMKDLIVAVS-- 153

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 197 rpvqlstevrsfSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQPLLLKKCIEVA 266
Cdd:cd11358 154 ------------VGGISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELA 211
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 24-267 1.04e-40

RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206772 [Multi-domain]  Cd Length: 272  Bit Score: 141.58  E-value: 1.04e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  24 QYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELSPLCSS 103
Cdd:cd11367   8 SYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNASP 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 104 KFKPGPPSDLAQVVSQELHQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLP--TAV 181
Cdd:cd11367  88 EFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPkvEVS 167

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 182 WDEDLERVI--------CASTLTRPVQLstevrSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTH 253
Cdd:cd11367 168 EDDEGTKEIelsddpydVKRLDVSNVPL-----IVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGS 242

                       250
                ....*....|....
gi 19113177 254 IQPLLLKKCIEVAR 267
Cdd:cd11367 243 LEPESIIEMIETAK 256
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 30-269 2.98e-39

RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206773 [Multi-domain]  Cd Length: 259  Bit Score: 137.27  E-value: 2.98e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177  30 LNQDVRSDGRSVSEFREIVINdncISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELSPLCSSKFKPGP 109
Cdd:cd11368  13 LKEGLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPMASPAFEPGR 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 110 PSDLAQVVSQELHQTLQQSNLINLQSLCIFEKKAAWVLYADIICLNYDGSAFDYA-WAALfAALKTVKLPTaVWDEDLER 188
Cdd:cd11368  90 PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAAsLAAI-AALMHFRRPD-VTVDGEEV 167

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177 189 VICASTLTRPVQLS---TEVrSFSWSVFDDK--LLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQPLLLKKCI 263
Cdd:cd11368 168 TVHSPEEREPVPLSihhIPI-CVTFAFFDDGeiVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPSQILRCV 246


                ....*.
gi 19113177 264 EVARSK 269
Cdd:cd11368 247 KIAAAK 252
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 43-178 7.46e-33

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 116.54  E-value: 7.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113177    43 EFREIVINDNCISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELSPLCSSKFK-PGPPSDLAQVVSQEL 121
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPgEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19113177   122 HQTLQQSNLInlqslcifEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLP 178
Cdd:pfam01138  81 DRALRPSIPL--------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 205-269 1.51e-15

3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 427466 [Multi-domain]  Cd Length: 67  Bit Score: 69.53  E-value: 1.51e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19113177   205 VRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKNIVKIIKLGGTHIQPLLLKKCIEVARSK 269
Cdd:pfam03725   3 VAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKEA 67
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 29-68 2.97e-03

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 38.08  E-value: 2.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 19113177   29 LLNQD-VRSDGRSVSEFREIVINDNCISTANGSAIIRAGEN 68
Cdd:PRK03983   8 LILEDgLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNN 48
 
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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