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Conserved domains on  [gi|19113410|ref|NP_596618|]
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exosome complex component mtr3 [Schizosaccharomyces pombe]

Protein Classification

exosome complex component MTR3( domain architecture ID 10183529)

exosome complex component MTR3 is a subunit of the eukaryotic exosome and a member of the RNase_PH family, named after the bacterial ribonuclease PH, a 3'-5' exoribonuclease.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 35-248 1.68e-80

MTR3 subunit of eukaryotic exosome; The MTR3 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: 206776 [Multi-domain]  Cd Length: 210  Bit Score: 240.93  E-value: 1.68e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  35 CRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKT-FAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKSYSQMIE 113
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGrTEFSDRGRLNCEVKFAPFATPGRRRHGQDSEERELSSLLH 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 114 AAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSVLFnpNTDE 181
Cdd:cd11371  81 QALEPAVRLEKYPKSQIDVFVTVLESDGsvlaaaitaaslALA--------------DAGIEMYDLVTACSAAL--IGDE 144

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19113410 182 YWIDPDYVDEraRAAKGSVVMGYMASLGHVTQVWERGTCSPSRLSFLTEKCIKNAKDTRLVINHALL 248
Cdd:cd11371 145 LLLDPTREEE--EASSGGVMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALL 209
 
Name Accession Description Interval E-value
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 35-248 1.68e-80

MTR3 subunit of eukaryotic exosome; The MTR3 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: 206776 [Multi-domain]  Cd Length: 210  Bit Score: 240.93  E-value: 1.68e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  35 CRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKT-FAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKSYSQMIE 113
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGrTEFSDRGRLNCEVKFAPFATPGRRRHGQDSEERELSSLLH 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 114 AAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSVLFnpNTDE 181
Cdd:cd11371  81 QALEPAVRLEKYPKSQIDVFVTVLESDGsvlaaaitaaslALA--------------DAGIEMYDLVTACSAAL--IGDE 144

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19113410 182 YWIDPDYVDEraRAAKGSVVMGYMASLGHVTQVWERGTCSPSRLSFLTEKCIKNAKDTRLVINHALL 248
Cdd:cd11371 145 LLLDPTREEE--EASSGGVMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALL 209
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 35-143 7.70e-28

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: 103.44  E-value: 7.70e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410    35 CRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKTFAFRSSAKLNCEFRLSPFST-SVRQGHVQTVEEKSYSQMIE 113
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASgERPGEGRPSEREIEISRLID 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 19113410   114 AAISPSILLHLYPKSSIDVYIQVIESDGAL 143
Cdd:pfam01138  82 RALRPSIPLEGYPRWTIRIDVTVLSSDGSL 111
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 30-212 7.45e-18

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 80.06  E-value: 7.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410   30 RDVDRCRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRP--SKTFAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKS 107
Cdd:PRK03983  19 RKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREmhPRHLQLPDRAVLRVRYNMAPFSVDERKRPGPDRRSIE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  108 YSQMIEAAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSV-- 173
Cdd:PRK03983  99 ISKVIREALEPAIMLELFPRTVIDVFIEVLQADAgtrvagitaaslALA--------------DAGIPMRDLVAGCAVgk 164

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 19113410  174 -----LFNPNTDEywidpDYVDEraraakGSVVMGYMASLGHVT 212
Cdd:PRK03983 165 vdgviVLDLNKEE-----DNYGE------ADMPVAIMPRLGEIT 197
 
Name Accession Description Interval E-value
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 35-248 1.68e-80

MTR3 subunit of eukaryotic exosome; The MTR3 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: 206776 [Multi-domain]  Cd Length: 210  Bit Score: 240.93  E-value: 1.68e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  35 CRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKT-FAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKSYSQMIE 113
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGrTEFSDRGRLNCEVKFAPFATPGRRRHGQDSEERELSSLLH 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 114 AAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSVLFnpNTDE 181
Cdd:cd11371  81 QALEPAVRLEKYPKSQIDVFVTVLESDGsvlaaaitaaslALA--------------DAGIEMYDLVTACSAAL--IGDE 144

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19113410 182 YWIDPDYVDEraRAAKGSVVMGYMASLGHVTQVWERGTCSPSRLSFLTEKCIKNAKDTRLVINHALL 248
Cdd:cd11371 145 LLLDPTREEE--EASSGGVMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALL 209
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 35-143 7.70e-28

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: 103.44  E-value: 7.70e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410    35 CRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKTFAFRSSAKLNCEFRLSPFST-SVRQGHVQTVEEKSYSQMIE 113
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASgERPGEGRPSEREIEISRLID 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 19113410   114 AAISPSILLHLYPKSSIDVYIQVIESDGAL 143
Cdd:pfam01138  82 RALRPSIPLEGYPRWTIRIDVTVLSSDGSL 111
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 36-212 3.89e-22

RRP41 subunit of eukaryotic exosome; The RRP41 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: 206775 [Multi-domain]  Cd Length: 226  Bit Score: 91.07  E-value: 3.89e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  36 RKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKtfafRSS------AKLNCEFRLSPFSTSVRQ----GHVQTVEe 105
Cdd:cd11370  13 RRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPR----NRSqalhdrAVVNCEYSMATFSTGERKrrgkGDRRSTE- 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 106 ksYSQMIEAAISPSILLHLYPKSSIDVYIQVIESDGAL-------ATLaaaiscassAIADANIDCIDLVTGSSVLFNPN 178
Cdd:cd11370  88 --LSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLlaacinaATL---------ALIDAGIPMKDYVCACSAGYLDS 156

                       170       180       190
                ....*....|....*....|....*....|....
gi 19113410 179 TDeyWIDPDYVDERARAAkgSVVMGYMASLGHVT 212
Cdd:cd11370 157 TP--LLDLNYLEESGDLP--DLTVAVLPKSDKVV 186
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 36-238 7.70e-19

RRP41 subunit of archaeal exosome; The RRP41 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.


Pssm-ID: 206771 [Multi-domain]  Cd Length: 214  Bit Score: 82.00  E-value: 7.70e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  36 RKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRP--SKTFAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKSYSQMIE 113
Cdd:cd11366   3 RPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREvhPRHLQLPDRAVIRVRYNMAPFSVDERKRPGPDRREIEISKVIK 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 114 AAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSVlfNPNTDE 181
Cdd:cd11366  83 EALEPAIILEEFPRTAIDVFVEVLQADAgtrvaglnaaslALA--------------DAGIPMRDLVAACAA--GKVDGK 146

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19113410 182 YWIDPDYVDERARAAkgSVVMGYMASLGHVTQVWERGTCSPSRLsfltEKCIKNAKD 238
Cdd:cd11366 147 IVLDLNKEEDNYGEA--DMPIAMMPNLGEITLLQLDGDLTPDEF----KQAIELAKK 197
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 30-212 7.45e-18

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 80.06  E-value: 7.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410   30 RDVDRCRKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRP--SKTFAFRSSAKLNCEFRLSPFSTSVRQGHVQTVEEKS 107
Cdd:PRK03983  19 RKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREmhPRHLQLPDRAVLRVRYNMAPFSVDERKRPGPDRRSIE 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  108 YSQMIEAAISPSILLHLYPKSSIDVYIQVIESDG------------ALAtlaaaiscassaiaDANIDCIDLVTGSSV-- 173
Cdd:PRK03983  99 ISKVIREALEPAIMLELFPRTVIDVFIEVLQADAgtrvagitaaslALA--------------DAGIPMRDLVAGCAVgk 164

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 19113410  174 -----LFNPNTDEywidpDYVDEraraakGSVVMGYMASLGHVT 212
Cdd:PRK03983 165 vdgviVLDLNKEE-----DNYGE------ADMPVAIMPRLGEIT 197
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 36-243 5.16e-15

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: 71.59  E-value: 5.16e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  36 RKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKTFAFRSS-AKLNCEFRLSPFSTSVRQGHVQTVEEKSYSQMIEA 114
Cdd:cd11358   2 RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDkGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLER 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410 115 AISPSILLHL---YPKSSIDVYIQVIESDG---------ALATLAA----AISCASSAIADANIDciDLVTGSSVLFNPN 178
Cdd:cd11358  82 TIEASVILDKstrKPSWVLYVDIQVLSRDGglldacwnaAIAALKDagipRVFVDERSPPLLLMK--DLIVAVSVGGISD 159

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19113410 179 TdEYWIDPDYVDERARAAKGSVVMGymaSLGHVTQVWERGTCspSRLSFLTEKCIKNAKDTRLVI 243
Cdd:cd11358 160 G-VLLLDPTGEEEELADSTLTVAVD---KSGKLCLLSKVGGG--SLDTEEIKECLELAKKRSLHL 218
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 36-187 3.21e-12

RRP46 subunit of eukaryotic exosome; The RRP46 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: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 63.74  E-value: 3.21e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19113410  36 RKIYLKLGWATKAVGSSYFESEKIKIACTVSGPRPSKtFAFRSSAKLNCEFRLSPfstsvRQGhVQTVEEKSYSQMIEAA 115
Cdd:cd11372   2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVK-LRKELPDRATLEVIVRP-----KSG-LPGVKEKLLELLLRST 74

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19113410 116 ISPSILLHLYPKSSIDVYIQVIESDGAL-------ATLaaaiscassAIADANIDCIDLVTGSSVLFNpNTDEYWIDPD 187
Cdd:cd11372  75 LEPIILLHLHPRTLISVVLQVLQDDGSLlacainaACL---------ALLDAGVPMKGLFAAVTCAIT-EDGEIILDPT 143
 
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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