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Conserved domains on  [gi|504485878|ref|WP_014672980|]
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MULTISPECIES: ribonuclease PH [Streptomyces]

Protein Classification

ribonuclease PH( domain architecture ID 11430827)

ribonuclease PH, also called tRNA nucleotidyltransferase, is a phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates

CATH:  3.30.230.70
EC:  2.7.7.56
Gene Ontology:  GO:0003723|GO:0006396|GO:0000175|GO:0009022
SCOP:  4001767

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
3-241 1.64e-175

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 481.84  E-value: 1.64e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKG 82
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAARG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  83 KIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGTV 162
Cdd:COG0689   82 KQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLK--ENPLKDQV 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 163 SAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALAA 241
Cdd:COG0689  160 AAVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
3-241 1.64e-175

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 481.84  E-value: 1.64e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKG 82
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAARG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  83 KIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGTV 162
Cdd:COG0689   82 KQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLK--ENPLKDQV 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 163 SAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALAA 241
Cdd:COG0689  160 AAVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
rph PRK00173
ribonuclease PH; Reviewed
 2-241 1.52e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 476.91  E-value: 1.52e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   2 SRIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVK 81
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  82 GKIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGT 161
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLK--KNPLKDQ 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 162 VSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALAA 241
Cdd:PRK00173 159 VAAVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALAD 238
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 3-240 1.55e-154

ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans. [Transcription, RNA processing]


Pssm-ID: 131021  Cd Length: 236  Bit Score: 428.70  E-value: 1.55e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878    3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKG 82
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   83 KIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGTV 162
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILK--ESPIRDFV 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504485878  163 SAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALA 240
Cdd:TIGR01966 159 AAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 11-239 6.25e-139

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: 388.89  E-value: 6.25e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  11 QLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKGKIGGRTHE 90
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  91 ISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKAgrQPLTGTVSAVSVGIV 170
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEE--NPLKHFVAAVSVGIV 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 171 GGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAAL 239
Cdd:cd11362  159 DGEPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 11-141 3.76e-33

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


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 116.54  E-value: 3.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   11 QLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVtEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDResvkGKIGGRTHE 90
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTG-PIEPKEDRDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 504485878   91 ISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADA 141
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
3-241 1.64e-175

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 481.84  E-value: 1.64e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKG 82
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAARG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  83 KIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGTV 162
Cdd:COG0689   82 KQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLK--ENPLKDQV 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 163 SAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALAA 241
Cdd:COG0689  160 AAVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
rph PRK00173
ribonuclease PH; Reviewed
 2-241 1.52e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 476.91  E-value: 1.52e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   2 SRIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVK 81
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  82 GKIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGT 161
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLK--KNPLKDQ 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 162 VSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALAA 241
Cdd:PRK00173 159 VAAVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALAD 238
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 3-240 1.55e-154

ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans. [Transcription, RNA processing]


Pssm-ID: 131021  Cd Length: 236  Bit Score: 428.70  E-value: 1.55e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878    3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKG 82
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   83 KIGGRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKagRQPLTGTV 162
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILK--ESPIRDFV 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504485878  163 SAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAALA 240
Cdd:TIGR01966 159 AAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 11-239 6.25e-139

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: 388.89  E-value: 6.25e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  11 QLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESVKGKIGGRTHE 90
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  91 ISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAWAQGKKLIKAgrQPLTGTVSAVSVGIV 170
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEE--NPLKHFVAAVSVGIV 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 171 GGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFAREELDALLDLAVTGCRELAVIQQAAL 239
Cdd:cd11362  159 DGEPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 12-231 5.75e-37

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: 129.37  E-value: 5.75e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  12 LRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNtrgdrESVKGKIGGRTHEI 91
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVG-----ERRQGPPGDEEMEI 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  92 SRLIGRSLRA-VIDYKALGE--NTIVLDCDVLQADGGTRTAAITGAYVALADA---VAWAQGKKLIkagRQPLTGTVSAV 165
Cdd:cd11358   76 SRLLERTIEAsVILDKSTRKpsWVLYVDIQVLSRDGGLLDACWNAAIAALKDAgipRVFVDERSPP---LLLMKDLIVAV 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504485878 166 SVGIV-GGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEAAPFArEELDALLDLAVTGCREL 231
Cdd:cd11358  153 SVGGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDT-EEIKECLELAKKRSLHL 218
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 11-141 3.76e-33

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


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 116.54  E-value: 3.76e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   11 QLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVtEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDResvkGKIGGRTHE 90
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTG-PIEPKEDRDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 504485878   91 ISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADA 141
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 3-239 4.99e-33

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 119.74  E-value: 4.99e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFctASV---TEGVPRWRKGSGEGWVTAEYAMLPRATNTRG---- 75
Cdd:PRK03983  15 RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKII--AAVygpREMHPRHLQLPDRAVLRVRYNMAPFSVDERKrpgp 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  76 DResvkgkiggRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAwaqgkklikagr 155
Cdd:PRK03983  93 DR---------RSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGI------------ 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 156 qPLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGD-GRFVEVQGTAEaapFAREELDALLDLAVTGCRELAVI 234
Cdd:PRK03983 152 -PMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRlGEITLLQLDGN---LTREEFLEALELAKKGIKRIYQL 227


                 ....*
gi 504485878 235 QQAAL 239
Cdd:PRK03983 228 QREAL 232
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 11-239 1.79e-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: 109.73  E-value: 1.79e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  11 QLRPVTIERGWSKHAEGSVLVSFGDTKVFctASV---TEGVPRWRKGSGEGWVTAEYAMLPRATNTRG----DResvkgk 83
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKII--AAVygpREVHPRHLQLPDRAVIRVRYNMAPFSVDERKrpgpDR------ 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  84 iggRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAwaqgkklikagrqPLTGTVS 163
Cdd:cd11366   73 ---REIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGI-------------PMRDLVA 136

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504485878 164 AVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGD-GRFVEVQ--GTaeaapFAREELDALLDLAVTGCRELAVIQQAAL 239
Cdd:cd11366  137 ACAAGKVDGKIVLDLNKEEDNYGEADMPIAMMPNlGEITLLQldGD-----LTPDEFKQAIELAKKGCKRIYELQKEAL 210
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 3-239 4.59e-26

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: 101.08  E-value: 4.59e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCtaSVT---EGVPRWRKGSGEGWVTAEYAMLPRATN-----TR 74
Cdd:cd11370    3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLA--AVYgphEPRNRSQALHDRAVVNCEYSMATFSTGerkrrGK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  75 GDResvkgkiggRTHEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAvawaqGkklIkag 154
Cdd:cd11370   81 GDR---------RSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDA-----G---I--- 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 155 rqPLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNV-VCTGDGRFVEVQGTAEaapFAREELDALLDLAVTGCRELAV 233
Cdd:cd11370  141 --PMKDYVCACSAGYLDSTPLLDLNYLEESGDLPDLTVaVLPKSDKVVLLQMESR---LHLDRLEKVLELAIEGCKVIRE 215


                 ....*.
gi 504485878 234 IQQAAL 239
Cdd:cd11370  216 IMDEVV 221
PRK04282 PRK04282
exosome complex protein Rrp42;
3-231 2.44e-25

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 100.34  E-value: 2.44e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPrWRKGSGEG--WVTAEyaMLPRATNT--RG--D 76
Cdd:PRK04282  25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEP-FPDTPNEGvlIVNAE--LLPLASPTfePGppD 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  77 RESVkgkiggrthEISRLIGRSLR--AVIDYKAL----GENTIVL--DCDVLQADGGTRTAAITGAYVALADA----VAW 144
Cdd:PRK04282 102 ENAI---------ELARVVDRGIResKAIDLEKLviepGKKVWVVfiDVYVLDHDGNLLDASMLAAVAALLNTkvpaVEE 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 145 AQGKKLIKAGRQ---PLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTaEAAPFAREELDALL 221
Cdd:PRK04282 173 GEDGVVDKLGEDfplPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKS-GIGSFTEEEVDKAI 251

                        250
                 ....*....|
gi 504485878 222 DLAVTGCREL 231
Cdd:PRK04282 252 DIALEKAKEL 261
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 3-231 9.44e-25

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: 98.44  E-value: 9.44e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVP-RWRKGSGEGWVTAEYAMLPRATNTRG--DRES 79
Cdd:cd11365   17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPfPDTPNEGVLIVNAELLPLASPTFEPGppDENA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  80 VkgkiggrthEISRLIGRSLRA--VIDYKAL----GEN--TIVLDCDVLQADGGTRTAAITGAYVALADA----VAWAQG 147
Cdd:cd11365   97 I---------ELARVVDRGIREskAIDLEKLviepGKKvwVVFIDIYVLDYDGNLFDASALAAVAALLNTkvpeYEVDEN 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 148 KKLIKAGRQ---PLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTaEAAPFAREELDALLDLA 224
Cdd:cd11365  168 EVIEVLGEElplPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKG-GGGSFTEDEIDKAIDIA 246


                 ....*..
gi 504485878 225 VTGCREL 231
Cdd:cd11365  247 LEKAAEL 253
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 12-239 8.99e-17

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: 76.07  E-value: 8.99e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  12 LRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGSGEGWVTAEYAMLPRATNTRGDRESvkgkiGGRTHEI 91
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPGRRRHGQ-----DSEEREL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  92 SRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAvawaqGkklIkagrqPLTGTVSAVSVGIVG 171
Cdd:cd11371   76 SSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADA-----G---I-----EMYDLVTACSAALIG 142

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504485878 172 GVPLLDLCYEEDVRADTDM--------NVVCtgdgrFVEVQGTAEAapfarEELDALLDLAVTGCREL-AVIQQAAL 239
Cdd:cd11371  143 DELLLDPTREEEEASSGGVmlaympslNQVT-----QLWQSGEMDV-----DQLEEALDLCIDGCNRIhPVVRQALL 209
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 160-227 5.41e-12

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: 59.51  E-value: 5.41e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504485878  160 GTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGTAEaAPFAREELDALLDLAVTG 227
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGG-AGLTEDELLEALELAKEA 67
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 13-243 4.50e-11

Polyribonucleotide nucleotidyltransferase, repeat 1; 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. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206768 [Multi-domain]  Cd Length: 229  Bit Score: 60.61  E-value: 4.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  13 RPVTIERGW-SKHAEGSVLVSFGDTKVFCTAsVTEGVPRwrkgSGEGWV--TAEYAmlpratntrgDRESVKGKIGG--- 86
Cdd:cd11363   10 RTLTFETGKlAKQADGSVVVQYGDTVVLVTA-VSSKKPK----EGIDFFplTVDYR----------EKLYAAGKIPGgff 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  87 ------RTHEI--SRLIGRSLRAVIDyKALGENTIVLdCDVLQADGG--TRTAAITGAYVALAdavawaqgkklikAGRQ 156
Cdd:cd11363   75 kregrpSEKEIltSRLIDRPIRPLFP-KGFRNEVQVI-ATVLSVDGVndPDVLAINGASAALS-------------LSDI 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 157 PLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDgRFVEVQGTAEAAPfaREELDALLDLAVTGCRELAVIQQ 236
Cdd:cd11363  140 PFNGPVGAVRVGRIDGEFVVNPTREELEESDLDLVVAGTKD-AVLMVEAGAKEVS--EEDMLEAIKFGHEAIQQLIAAQE 216


                 ....*..
gi 504485878 237 AALAATR 243
Cdd:cd11363  217 ELAAEVG 223
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 3-139 1.23e-08

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: 54.07  E-value: 1.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGwskHAEGSVLVSFGDTKVFC--TASVTEgvPRWRKGSgEGWVTAEYAMLPRA-TNTRGDRES 79
Cdd:cd11368   18 RLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAqvSCEIVE--PKPDRPN-EGILFINVELSPMAsPAFEPGRPS 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504485878  80 VKGKiggrthEISRLIGRSLR--AVIDYKAL----GEN--TIVLDCDVLQADGGTRTAAITGAYVALA 139
Cdd:cd11368   92 EEEV------ELSRLLERALRdsRAVDTESLciiaGEKvwSIRVDVHVLNHDGNLIDAASLAAIAALM 153
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 3-198 1.25e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 54.90  E-value: 1.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFctASVTEGvprwrkgsgegwvtaEYAMLPRATNTRGDRESVK- 81
Cdd:PLN00207 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQAL--AVVTLG---------------DKQMAQRIDNLVDADEVKRf 501

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  82 --------------GKIGGRT-HEI--SRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADAVAw 144
Cdd:PLN00207 502 ylqysfppscvgevGRIGAPSrREIghGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGV- 580

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504485878 145 aqgkklikagrqPLTGTVSAVSVGIV--------GGVPLL--DLCYEEDVRADTDMNVVCTGDG 198
Cdd:PLN00207 581 ------------PVKCPIAGIAMGMVldteefggDGSPLIlsDITGSEDASGDMDFKVAGNEDG 632
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 12-232 1.44e-08

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: 52.95  E-value: 1.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  12 LRPVTIERGWSKHAEGSVLVSFGDTKVfcTASVTegvprwrkGSGEgwVTAEYAMLPRAT---NTRgdreSVKGKIGGRT 88
Cdd:cd11372    1 LRPLSCELGLLSRADGSARFSQGDTSV--LAAVY--------GPIE--VKLRKELPDRATlevIVR----PKSGLPGVKE 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  89 HEISRLIGRSLRAVIDYKALGENTIVLDCDVLQADGGTRTAAITGAYVALADA-VawaqgkklikagrqPLTGTVSAVSV 167
Cdd:cd11372   65 KLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAgV--------------PMKGLFAAVTC 130

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504485878 168 GIV-GGVPLLDLCYEE--DVRAdtdmNVVCTGDGR------FVEVQGTaeaapFAREELDALLDLAVTGCRELA 232
Cdd:cd11372  131 AITeDGEIILDPTAEEekEAKA----VATFAFDSGeeknlvLSESEGS-----FTEEELFACLELAQAASAAIF 195
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 13-198 9.20e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 46.20  E-value: 9.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  13 RPVTIERG-WSKHAEGSVLVSFGDTKVFCTA----SVTEGV---PrwrkgsgegwVTAEYamlpratntrgdREsvK--- 81
Cdd:PRK11824  14 RTLTLETGkLARQANGAVLVRYGDTVVLVTVvaskEPKEGQdffP----------LTVDY------------EE--Ktya 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  82 -GKI-GG---R-----THEI--SRLIGRSLRA--VIDYKalgeNTIVLDCDVLQADGGTR--TAAITGAYVALA--DAva 143
Cdd:PRK11824  70 aGKIpGGffkRegrpsEKETltSRLIDRPIRPlfPKGFR----NEVQVVATVLSVDPENDpdILAMIGASAALSisGI-- 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504485878 144 waqgkklikagrqPLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDG 198
Cdd:PRK11824 144 -------------PFNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVAGTKDA 185
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 3-232 2.59e-04

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: 41.00  E-value: 2.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFC-----TASVTEGVPRwrkgsgEGWVTAEYAMLPR-ATNTRGD 76
Cdd:cd11369   18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCgikaeVATPAADTPD------EGYLVPNVDLPPLcSSKFRPG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  77 RESVKGKIGgrTHEISRLIGRSlrAVIDYKAL----GENTIVLDCDV--LQADGGTRTAAITGAYVAL------------ 138
Cdd:cd11369   92 PPSEEAQVL--SSFLADILLNS--NVLDLEQLcivpGKLAWVLYCDVycLDYDGNLLDAALLALVAALknlrlpavtide 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878 139 ADAVAWAQGKK--LIKAGRQPLTGTVSAVSVGIVggvpLLDLCYEEDVRADTDMNVVCTGDGRFVEVQGtAEAAPFAREE 216
Cdd:cd11369  168 ETELVVVNPEErrPLNLKNLPVSTTFAVFDDKHL----LADPTAEEELLASGLVTVVVDENGELCSVHK-PGGSPLSQAQ 242

                        250
                 ....*....|....*.
gi 504485878 217 LDALLDLAVTGCRELA 232
Cdd:cd11369  243 LQECIELAKKRAKELQ 258
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 3-141 7.43e-04

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: 39.89  E-value: 7.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   3 RIDGRTPEQLRPVTIERGWSKHAEGSVLVSFGDTKVFCTASVTEGVPRWRKGsGEGWVTAEYAMLPRAT---NTRGDREs 79
Cdd:cd11367   19 RNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETP-NKGRLEFFVDCSPNASpefEGRGGEE- 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  80 vkgkiggRTHEISRLIGRSL--RAVIDYKAL----GENTIVL--DCDVLQADGGTRTAAITGAYVALADA 141
Cdd:cd11367   97 -------LATELSSALERALksGSAIDLSKLcivpGKQCWVLyvDVLVLESGGNLLDAISIAVKAALFNT 159
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 7-198 9.78e-04

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 40.26  E-value: 9.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878   7 RTPEQLRPVTIERG-WSKHAEGSVLVSFGDTKVFCTASVTEgvprwrkgsgegwVTAEYA-MLPRATNTRgDRESVKGKI 84
Cdd:PLN00207  83 KIPVGDRHILVETGhIGRQASGSVTVTDGETIVYTSVCLAD-------------VPSEPSdFFPLSVHYQ-ERFSAAGRT 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504485878  85 GG---------RTHE--ISRLIGRSLRAVIdYKALGENTIVLDCdVLQADG--GTRTAAITGAYVALAdavawaqgkkli 151
Cdd:PLN00207 149 SGgffkregrtKDHEvlICRLIDRPLRPTM-PKGFYHETQILSW-VLSYDGlhSPDSLAVTAAGIAVA------------ 214

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 504485878 152 kAGRQPLTGTVSAVSVGIVGGVPLLDLCYEEDVRADTDMNVVCTGDG 198
Cdd:PLN00207 215 -LSEVPNLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDSA 260
 
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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