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Conserved domains on  [gi|154295932|ref|XP_001548399|]
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Bcski6 [Botrytis cinerea B05.10]

Protein Classification

RRP41/SKI6 family exosome complex component( domain architecture ID 10183526)

RRP41/SKI6 family exosome complex component 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 13-253 9.56e-109

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: 313.33  E-value: 9.56e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPSklrsiggGGSNNAGEKAEVRVEISFAGFAGVD 92
Cdd:cd11370    2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPR-------NRSQALHDRAVVNCEYSMATFSTGE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  93 RKKYGRNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGST 172
Cdd:cd11370   75 RKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 173 SSYssndekadPLLDLNLGEEQ-ELPFLTVATAGEgdGDGVVALVMETRVQAGRLEGMLAVGVDGCKQVREILDGVIRTR 251
Cdd:cd11370  155 DST--------PLLDLNYLEESgDLPDLTVAVLPK--SDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREH 224


                 ..
gi 154295932 252 GK 253
Cdd:cd11370  225 TK 226
 
Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 13-253 9.56e-109

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: 313.33  E-value: 9.56e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPSklrsiggGGSNNAGEKAEVRVEISFAGFAGVD 92
Cdd:cd11370    2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPR-------NRSQALHDRAVVNCEYSMATFSTGE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  93 RKKYGRNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGST 172
Cdd:cd11370   75 RKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 173 SSYssndekadPLLDLNLGEEQ-ELPFLTVATAGEgdGDGVVALVMETRVQAGRLEGMLAVGVDGCKQVREILDGVIRTR 251
Cdd:cd11370  155 DST--------PLLDLNYLEESgDLPDLTVAVLPK--SDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREH 224


                 ..
gi 154295932 252 GK 253
Cdd:cd11370  225 TK 226
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 22-159 6.00e-35

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: 121.93  E-value: 6.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932   22 ELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPSKLRSIGGGgsnnagekaEVRVEISFAGFAGVDRKKYGRNDK 101
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPG---------RLTVEYELAPFASGERPGEGRPSE 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 154295932  102 RIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIP 159
Cdd:pfam01138  72 REIEISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 13-255 7.56e-34

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 122.44  E-value: 7.56e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCD--PSKLRSIggggsnnagEKAEVRVEISFAGFAG 90
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREmhPRHLQLP---------DRAVLRVRYNMAPFSV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  91 VDRKKYGrNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAG 170
Cdd:PRK03983  85 DERKRPG-PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVG 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 171 stssyssndeKADP--LLDLNLGEEQE----LPFLTVATAGEgdgdgVVALVMETRVQAGRLEGMLAVGVDGCKQVREIL 244
Cdd:PRK03983 164 ----------KVDGviVLDLNKEEDNYgeadMPVAIMPRLGE-----ITLLQLDGNLTREEFLEALELAKKGIKRIYQLQ 228

                        250
                 ....*....|.
gi 154295932 245 DGVIRTRGKKI 255
Cdd:PRK03983 229 REALKSKYGEI 239
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
14-54 3.55e-05

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 43.86  E-value: 3.55e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 154295932  14 RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT 54
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTAS 42
 
Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 13-253 9.56e-109

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: 313.33  E-value: 9.56e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPSklrsiggGGSNNAGEKAEVRVEISFAGFAGVD 92
Cdd:cd11370    2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPR-------NRSQALHDRAVVNCEYSMATFSTGE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  93 RKKYGRNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGST 172
Cdd:cd11370   75 RKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 173 SSYssndekadPLLDLNLGEEQ-ELPFLTVATAGEgdGDGVVALVMETRVQAGRLEGMLAVGVDGCKQVREILDGVIRTR 251
Cdd:cd11370  155 DST--------PLLDLNYLEESgDLPDLTVAVLPK--SDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREH 224


                 ..
gi 154295932 252 GK 253
Cdd:cd11370  225 TK 226
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 22-159 6.00e-35

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: 121.93  E-value: 6.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932   22 ELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPSKLRSIGGGgsnnagekaEVRVEISFAGFAGVDRKKYGRNDK 101
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPG---------RLTVEYELAPFASGERPGEGRPSE 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 154295932  102 RIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIP 159
Cdd:pfam01138  72 REIEISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 13-255 7.56e-34

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 122.44  E-value: 7.56e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCD--PSKLRSIggggsnnagEKAEVRVEISFAGFAG 90
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREmhPRHLQLP---------DRAVLRVRYNMAPFSV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  91 VDRKKYGrNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAG 170
Cdd:PRK03983  85 DERKRPG-PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVG 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 171 stssyssndeKADP--LLDLNLGEEQE----LPFLTVATAGEgdgdgVVALVMETRVQAGRLEGMLAVGVDGCKQVREIL 244
Cdd:PRK03983 164 ----------KVDGviVLDLNKEEDNYgeadMPVAIMPRLGE-----ITLLQLDGNLTREEFLEALELAKKGIKRIYQLQ 228

                        250
                 ....*....|.
gi 154295932 245 DGVIRTRGKKI 255
Cdd:PRK03983 229 REALKSKYGEI 239
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 23-240 4.14e-29

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: 108.81  E-value: 4.14e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  23 LRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCDPsKLRsiggggsNNAGEKAEVrvEISFagfagvdRKKYGRNDKR 102
Cdd:cd11372    1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEV-KLR-------KELPDRATL--EVIV-------RPKSGLPGVK 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 103 IQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGSTssyssndEKA 182
Cdd:cd11372   64 EKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAIT-------EDG 136

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 154295932 183 DPLLDLNLGEEQE-LPFLTVATAGeGDGDGVVALVMETRVQAGRLEGMLAVGVDGCKQV 240
Cdd:cd11372  137 EIILDPTAEEEKEaKAVATFAFDS-GEEKNLVLSESEGSFTEEELFACLELAQAASAAI 194
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 22-251 4.62e-29

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: 109.35  E-value: 4.62e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  22 ELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPCD--PSKLRSIggggsnnagEKAEVRVEISFAGFAGVDRKKYGRn 99
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREvhPRHLQLP---------DRAVIRVRYNMAPFSVDERKRPGP- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 100 DKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGstssyssnd 179
Cdd:cd11366   71 DRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAG--------- 141

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 154295932 180 eKADP--LLDLNLGEEQE----LPFLTVATAGEgdgdgVVALVMETRVQAGRLEGMLAVGVDGCKQVREILDGVIRTR 251
Cdd:cd11366  142 -KVDGkiVLDLNKEEDNYgeadMPIAMMPNLGE-----ITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALKRK 213
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 23-244 7.13e-23

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: 92.63  E-value: 7.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  23 LRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPcdpsklRSIGGGGSNNagEKAEVRVEISFAGFAGVDRKKYGRNDKR 102
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGP------RPIPGRTEFS--DRGRLNCEVKFAPFATPGRRRHGQDSEE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 103 iQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDAGIPMPSYICACTAGstssysSNDEKA 182
Cdd:cd11371   73 -RELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAA------LIGDEL 145

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 154295932 183 dpLLDLNLGEEQelpfltvatagEGDGDGVVA----------LVMETRVQAGRLEGMLAVGVDGCKQVREIL 244
Cdd:cd11371  146 --LLDPTREEEE-----------ASSGGVMLAympslnqvtqLWQSGEMDVDQLEEALDLCIDGCNRIHPVV 204
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 23-240 2.77e-21

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: 88.92  E-value: 2.77e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  23 LRRLTAQISTQPSSDGSSYLSMGNTQVLCTVTGPcdpsklrsIGGGGSNNAGEKAEVRVEISFAGFAGVDRKKyGRNDKR 102
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGP--------IVEPDKLERPDKGTLYVNVEISPGAVGERRQ-GPPGDE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 103 IQELSNTLSTTFTPH-LLTTLTSH--STILISLHILSLDGSLLSALINASTLALIDAGIPMPS-------------YICA 166
Cdd:cd11358   72 EMEISRLLERTIEASvILDKSTRKpsWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFvderspplllmkdLIVA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 167 CTAGSTSSYSsndekadPLLDLNLGEEQE-LPFLTVAtageGDGDGVVALVmetRVQAG------RLEGMLAVGVDGCKQ 239
Cdd:cd11358  152 VSVGGISDGV-------LLLDPTGEEEELaDSTLTVA----VDKSGKLCLL---SKVGGgsldteEIKECLELAKKRSLH 217


                 .
gi 154295932 240 V 240
Cdd:cd11358  218 L 218
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 13-55 2.26e-05

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: 44.44  E-value: 2.26e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 154295932  13 LRLDGRRWNELRRLTAQISTQpssDGSSYLSMGNTQVLCTVTG 55
Cdd:cd11368   17 LRLDGRGLDEFRPIKITFGLE---YGCVEVSLGKTRVLAQVSC 56
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
14-54 3.55e-05

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 43.86  E-value: 3.55e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 154295932  14 RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT 54
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTAS 42
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 13-159 3.67e-05

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: 44.12  E-value: 3.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTV---TGpcDPSKLRSIGGggsnnageKAEVRVEISfagfA 89
Cdd:cd11367   18 IRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVkaeVG--SPDPETPNKG--------RLEFFVDCS----P 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 154295932  90 GVDRKKYGRNDKRI-QELSNTLSTTFTPHL---LTTLT----SHSTIL-ISLHILSLDGSLLSALINASTLALIDAGIP 159
Cdd:cd11367   84 NASPEFEGRGGEELaTELSSALERALKSGSaidLSKLCivpgKQCWVLyVDVLVLESGGNLLDAISIAVKAALFNTRIP 162
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 14-53 7.82e-05

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: 42.97  E-value: 7.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 154295932  14 RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTV 53
Cdd:cd11365   17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV 56
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 14-53 1.39e-04

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: 42.10  E-value: 1.39e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 154295932  14 RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTV 53
Cdd:COG2123   23 RIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV 62
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 22-160 4.53e-04

Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase (PNPase) 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. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206769 [Multi-domain]  Cd Length: 223  Bit Score: 40.22  E-value: 4.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  22 ELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT--GPCDPSKLRSIGGGGSNNAgekaevRVEISFAGFAGVDRKKYGRN 99
Cdd:cd11364    1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTlgTLEDAQKIDSLGGEKSKRF------MLHYNFPPYSVGETGRVGGP 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 154295932 100 DKRiqELSntlsttftpH-------LLTTLTSHS----TILISLHILSLDGSLLSALINASTLALIDAGIPM 160
Cdd:cd11364   75 GRR--EIG---------HgalaeraLLPVLPSPEdfpyTIRVVSEVLESNGSSSMASVCGGSLALMDAGVPI 135
PRK04282 PRK04282
exosome complex protein Rrp42;
8-53 4.95e-04

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 40.63  E-value: 4.95e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 154295932   8 YSLALL----RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTV 53
Cdd:PRK04282  15 YILSLLkkgkRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64
rph PRK00173
ribonuclease PH; Reviewed
 14-54 2.98e-03

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 38.17  E-value: 2.98e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 154295932  14 RLDGRRWNELR--RLTAQISTQPssDGSSYLSMGNTQVLCTVT 54
Cdd:PRK00173   2 RPDGRAADQLRpvTITRNFTKHA--EGSVLVEFGDTKVLCTAS 42
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 13-54 3.34e-03

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: 37.92  E-value: 3.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 154295932  13 LRLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT 54
Cdd:cd11369   17 VRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIK 58
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 14-54 5.92e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 37.72  E-value: 5.92e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 154295932  14 RLDGRRWNELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT 54
Cdd:PRK11824 315 RIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVAT 355
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 22-248 7.71e-03

Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA.


Pssm-ID: 206767 [Multi-domain]  Cd Length: 227  Bit Score: 36.82  E-value: 7.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  22 ELRRLTAQISTQPSSDGSSYLSMGNTQVLCTVT---GPcdPSKLRSIGGGGsnnagekaeVRVEISFAGFAGVDRKK--- 95
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASveeKV--PPFLRGKGKGW---------VTAEYSMLPRSTHERTQrea 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932  96 -YGRNDKRIQELSNTLSTTFTPHLLTTLTSHSTILISLHILSLDGSLLSALINASTLALIDA-----------GIPMPSY 163
Cdd:cd11362   70 sKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAvdklvekgvleENPLKHF 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 154295932 164 ICACTAGSTssyssNDEkadPLLDLNLGEEQ--ELPFLTVATaGEGDGDGVVALVMETRVQAGRLEGMLAVGVDGCKQVR 241
Cdd:cd11362  150 VAAVSVGIV-----DGE---PLLDLDYEEDSaaDVDMNVVMT-GSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELI 220


                 ....*..
gi 154295932 242 EILDGVI 248
Cdd:cd11362  221 ELQKEAL 227
 
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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