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Conserved domains on  [gi|442627738|ref|NP_001260437|]
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Ski6, isoform B [Drosophila melanogaster]

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 ...
 12-233 2.04e-125

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: 354.93  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  12 GLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKG----NQTESVINCQYSQATFSTAERKNRPR 87
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNrsqaLHDRAVVNCEYSMATFSTGERKRRGK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  88 GDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSkSNIPL 167
Cdd:cd11370   81 GDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL-DSTPL 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627738 168 TDISQFEEVSGGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKEHL 233
Cdd:cd11370  160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHT 225
 
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 ...
 12-233 2.04e-125

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: 354.93  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  12 GLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKG----NQTESVINCQYSQATFSTAERKNRPR 87
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNrsqaLHDRAVVNCEYSMATFSTGERKRRGK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  88 GDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSkSNIPL 167
Cdd:cd11370   81 GDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL-DSTPL 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627738 168 TDISQFEEVSGGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKEHL 233
Cdd:cd11370  160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHT 225
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 7-231 2.29e-62

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 195.62  E-value: 2.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738   7 LLSEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGP------HQAKGNQteSVINCQYSQATFSTA 80
Cdd:PRK03983   8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPremhprHLQLPDR--AVLRVRYNMAPFSVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  81 ERKnRPRGDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASL 160
Cdd:PRK03983  86 ERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGK 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 442627738 161 SKSNIPLtDISQFEEVSGGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKE 231
Cdd:PRK03983 165 VDGVIVL-DLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKS 234
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 22-147 3.15e-38

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: 129.63  E-value: 3.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738   22 ELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAK--GNQTESVINCQYSQATFSTAERKNRPRGDRKSLEFKLYL 99
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKedRDFAPGRLTVEYELAPFASGERPGEGRPSEREIEISRLI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 442627738  100 QQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGI 147
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 5-53 3.58e-09

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: 55.58  E-value: 3.58e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 442627738   5 YDLLsEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:COG2123   15 LSLL-KKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV 62
 
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 ...
 12-233 2.04e-125

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: 354.93  E-value: 2.04e-125
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  12 GLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKG----NQTESVINCQYSQATFSTAERKNRPR 87
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNrsqaLHDRAVVNCEYSMATFSTGERKRRGK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  88 GDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSkSNIPL 167
Cdd:cd11370   81 GDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYL-DSTPL 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442627738 168 TDISQFEEVSGGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKEHL 233
Cdd:cd11370  160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHT 225
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 7-231 2.29e-62

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 195.62  E-value: 2.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738   7 LLSEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGP------HQAKGNQteSVINCQYSQATFSTA 80
Cdd:PRK03983   8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPremhprHLQLPDR--AVLRVRYNMAPFSVD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  81 ERKnRPRGDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASL 160
Cdd:PRK03983  86 ERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGK 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 442627738 161 SKSNIPLtDISQFEEVSGGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKE 231
Cdd:PRK03983 165 VDGVIVL-DLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKS 234
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 22-231 9.52e-55

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: 174.83  E-value: 9.52e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  22 ELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKGNQTE----SVINCQYSQATFSTAERKnRPRGDRKSLEFKL 97
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQlpdrAVIRVRYNMAPFSVDERK-RPGPDRREIEISK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  98 YLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSKSNIPLtDISQFEEVS 177
Cdd:cd11366   80 VIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVL-DLNKEEDNY 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 442627738 178 GGPKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKE 231
Cdd:cd11366  159 GEADMPIAMMPNLGEITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALKR 212
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 23-231 1.48e-52

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: 169.28  E-value: 1.48e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  23 LRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKGNQTES---VINCQYSQATFSTAERKNRPRgDRKSLEFKLYL 99
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSdrgRLNCEVKFAPFATPGRRRHGQ-DSEERELSSLL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738 100 QQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSKSNIpLTDISQFEEVSGG 179
Cdd:cd11371   80 HQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDEL-LLDPTREEEEASS 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 442627738 180 PKLTVAALPTAEKIAFLEMSERFHIDHLETVIETAMAGCREIRDILEAAVKE 231
Cdd:cd11371  159 GGVMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 23-221 1.49e-38

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: 133.61  E-value: 1.49e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  23 LRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKG---NQTESVINCQYSQATFSTAERkNRPRGDRKSLEFKLYL 99
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDkleRPDKGTLYVNVEISPGAVGER-RQGPPGDEEMEISRLL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738 100 QQALSAAI---KSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGI-------------CLNEFIVACTASLSKS 163
Cdd:cd11358   80 ERTIEASVildKSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIprvfvdersppllLMKDLIVAVSVGGISD 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738 164 NIPLTDISQFEEVSGGPKLTVAALPtAEKIAFLEMSERFH--IDHLETVIETAMAGCREI 221
Cdd:cd11358  160 GVLLLDPTGEEEELADSTLTVAVDK-SGKLCLLSKVGGGSldTEEIKECLELAKKRSLHL 218
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 22-147 3.15e-38

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: 129.63  E-value: 3.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738   22 ELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAK--GNQTESVINCQYSQATFSTAERKNRPRGDRKSLEFKLYL 99
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKedRDFAPGRLTVEYELAPFASGERPGEGRPSEREIEISRLI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 442627738  100 QQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGI 147
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 23-223 1.90e-33

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: 119.59  E-value: 1.90e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  23 LRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGP---HQAKGNQTESVINCQYSQATFSTAERKnrprgdrKSLEfkLYL 99
Cdd:cd11372    1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPievKLRKELPDRATLEVIVRPKSGLPGVKE-------KLLE--LLL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738 100 QQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSKSNIPLTDISQFEEVSGG 179
Cdd:cd11372   72 RSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAK 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 442627738 180 PKLTVAALPTAE-KIAFLEMSERFHIDHLETVIETAMAGCREIRD 223
Cdd:cd11372  152 AVATFAFDSGEEkNLVLSESEGSFTEEELFACLELAQAASAAIFD 196
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 5-53 2.66e-10

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: 58.77  E-value: 2.66e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 442627738   5 YDLLsEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:cd11365    9 LSLL-EKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV 56
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 5-53 3.58e-09

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: 55.58  E-value: 3.58e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 442627738   5 YDLLsEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:COG2123   15 LSLL-KKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV 62
PRK04282 PRK04282
exosome complex protein Rrp42;
5-53 5.61e-09

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 55.27  E-value: 5.61e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 442627738   5 YDLLsEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:PRK04282  17 LSLL-KKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 10-145 9.62e-09

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: 54.46  E-value: 9.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  10 EQGLRLDGRRPHELRRIKCKLGvfeQPDGSAYMEQGNTKVLAAVYG----PHQAKGNQTESVINCQYSqATFSTAERKNR 85
Cdd:cd11368   14 KEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCeivePKPDRPNEGILFINVELS-PMASPAFEPGR 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442627738  86 PRGDrkSLEFKLYLQQAL--SAAIKSElyprS----------QIDIYVEVLQDDGAnyavALNAATLALIDA 145
Cdd:cd11368   90 PSEE--EVELSRLLERALrdSRAVDTE----SlciiagekvwSIRVDVHVLNHDGN----LIDAASLAAIAA 151
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 22-145 4.41e-08

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: 52.23  E-value: 4.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  22 ELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVY----GPHQAKGnQTESVINCQYSQATFSTAERKNRPRGDRK----SL 93
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASveekVPPFLRG-KGKGWVTAEYSMLPRSTHERTQREASKGKqsgrTQ 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 442627738  94 EFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAVALNAATLALIDA 145
Cdd:cd11362   80 EIQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADA 131
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 10-185 2.38e-06

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 47.97  E-value: 2.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  10 EQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKGNQTESVINCQ-----YSQATF---STAE 81
Cdd:PLN00207 435 EGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADevkrfYLQYSFppsCVGE 514

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442627738  82 RKNRPRGDRKSLEFKLYLQQALSAAIKSEL-YPRSqidIYVE--VLQDDGANYAVALNAATLALIDAGICLNEFIVACTA 158
Cdd:PLN00207 515 VGRIGAPSRREIGHGMLAERALEPILPSEDdFPYT---IRVEstITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAM 591

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 442627738 159 SL---------SKSNIPLTDISQFEEVSGGPKLTVA 185
Cdd:PLN00207 592 GMvldteefggDGSPLILSDITGSEDASGDMDFKVA 627
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
14-53 9.42e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 45.41  E-value: 9.42e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 442627738  14 RLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTA 41
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 10-53 1.01e-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: 45.66  E-value: 1.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 442627738  10 EQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:cd11367   15 EQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGV 58
rph PRK00173
ribonuclease PH; Reviewed
 14-50 1.86e-04

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 41.63  E-value: 1.86e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 442627738  14 RLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVL 50
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVL 38
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 152-217 5.13e-04

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: 37.56  E-value: 5.13e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 442627738  152 FIVACTASLSKSNIpLTDISQFEEVSGGPKLTVAALPTAEKIAFLEMSER-FHIDHLETVIETAMAG 217
Cdd:pfam03725   2 PVAAVTVGKIDGQL-VVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAgLTEDELLEALELAKEA 67
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 10-53 2.27e-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: 38.31  E-value: 2.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 442627738  10 EQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:cd11369   14 AENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGI 57
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 10-53 4.06e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 38.11  E-value: 4.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 442627738  10 EQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAV 53
Cdd:PRK11824 311 EEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVA 354
 
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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