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Conserved domains on  [gi|515600329|ref|WP_017032929|]
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MULTISPECIES: ribonuclease PH [Vibrio]

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];
1-238 0e+00

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 498.79  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAAS 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVS 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515600329 161 AVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-238 0e+00

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 498.79  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAAS 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVS 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515600329 161 AVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
rph PRK00173
ribonuclease PH; Reviewed
 1-238 5.15e-177

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 485.38  E-value: 5.15e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAAS 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVS 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515600329 161 AVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALAD 238
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 3.71e-146

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: 407.00  E-value: 3.71e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAASGKQGGRTME 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  90 IQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVSAVSVGIVDG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515600329 170 KGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-237 2.19e-144

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: 402.90  E-value: 2.19e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329    2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAASG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   82 KQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVSA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515600329  162 VSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALA 237
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 7.53e-32

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: 113.07  E-value: 7.53e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEEnVPRWLKGKGKGWVTAEYGMLPRATHTRNRReaasGKQGGRTME 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPI-EPKEDRDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 515600329   90 IQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-238 0e+00

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 498.79  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAAS 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVS 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515600329 161 AVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALGE 238
rph PRK00173
ribonuclease PH; Reviewed
 1-238 5.15e-177

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 485.38  E-value: 5.15e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAAS 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVS 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515600329 161 AVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALAD 238
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 3.71e-146

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: 407.00  E-value: 3.71e-146
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAASGKQGGRTME 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  90 IQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVSAVSVGIVDG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515600329 170 KGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-237 2.19e-144

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: 402.90  E-value: 2.19e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329    2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRREAASG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   82 KQGGRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAFQKLVAQGKLKANPMKGHVSA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515600329  162 VSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFSHEELMELLALAQKGIADIIEVQKAALA 237
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 12-228 9.22e-43

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: 144.01  E-value: 9.22e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  12 RPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRreaasGKQGGRTMEIQ 91
Cdd:cd11358    2 RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVGERRQ-----GPPGDEEMEIS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  92 RLIARSLRAVVDLEAMGEIMVT---VDCDVIQADGGTRTASISGASVAMADAfqKL----VAQGKLKANPMKGHVSAVSV 164
Cdd:cd11358   77 RLLERTIEASVILDKSTRKPSWvlyVDIQVLSRDGGLLDACWNAAIAALKDA--GIprvfVDERSPPLLLMKDLIVAVSV 154

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515600329 165 GIV-DGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGEPFShEELMELLALAQKGIADI 228
Cdd:cd11358  155 GGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDT-EEIKECLELAKKRSLHL 218
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 10-238 8.51e-38

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: 131.30  E-value: 8.51e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLcnASV---EENVPRWLKGKGKGWVTAEYGMLPRATHTRnRREAASGkqggR 86
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKII--AAVygpREVHPRHLQLPDRAVIRVRYNMAPFSVDER-KRPGPDR----R 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  87 TMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKGHVSAVSVGI 166
Cdd:cd11366   74 EIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADA-----------GIPMRDLVAACAAGK 142

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515600329 167 VDGKGLCDLEYVEDSAADTDMNVVM---TEEGKMIEVQGTaegepFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:cd11366  143 VDGKIVLDLNKEEDNYGEADMPIAMmpnLGEITLLQLDGD-----LTPDEFKQAIELAKKGCKRIYELQKEALKR 212
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 1-236 1.06e-37

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 131.68  E-value: 1.06e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   1 MRPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLcnASV---EENVPRWLKGKGKGWVTAEYGMLPRATHTRnRRE 77
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKII--AAVygpREMHPRHLQLPDRAVLRVRYNMAPFSVDER-KRP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  78 AASGkqggRTMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKG 157
Cdd:PRK03983  91 GPDR----RSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADA-----------GIPMRD 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 158 HVSAVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMI---EVQGTaegepFSHEELMELLALAQKGIADIIEVQKA 234
Cdd:PRK03983 156 LVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEItllQLDGN-----LTREEFLEALELAKKGIKRIYQLQRE 230


                 ..
gi 515600329 235 AL 236
Cdd:PRK03983 231 AL 232
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 7.53e-32

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: 113.07  E-value: 7.53e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEEnVPRWLKGKGKGWVTAEYGMLPRATHTRNRReaasGKQGGRTME 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPI-EPKEDRDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 515600329   90 IQRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 24-238 1.62e-25

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: 99.54  E-value: 1.62e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  24 AEGSVLVEFGNTKVLCnaSVeeNVPRWLKGKG-----KGWVTAEYGMLPRATHTRNRReaasGKQGGRTMEIQRLIARSL 98
Cdd:cd11370   25 ADGSAYLEQGNTKVLA--AV--YGPHEPRNRSqalhdRAVVNCEYSMATFSTGERKRR----GKGDRRSTELSLAIRQTF 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  99 RAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKGHVSAVSVGIVDGKGLCDLEYV 178
Cdd:cd11370   97 EAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDA-----------GIPMKDYVCACSAGYLDSTPLLDLNYL 165

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515600329 179 EDSAADTDMNV-VMTEEGKMIEVQGTAEgepFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:cd11370  166 EESGDLPDLTVaVLPKSDKVVLLQMESR---LHLDRLEKVLELAIEGCKVIREIMDEVVRE 223
PRK04282 PRK04282
exosome complex protein Rrp42;
2-238 1.06e-20

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 87.62  E-value: 1.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEENVP-RWLKGKGKGWVTAEygMLPRATHTrnrREAas 80
Cdd:PRK04282  25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPfPDTPNEGVLIVNAE--LLPLASPT---FEP-- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  81 GKQGGRTMEIQRLIARSLR--AVVDLEAM----GEI--MVTVDCDVIQADGGTRTASISGASVAMADAF---------QK 143
Cdd:PRK04282  98 GPPDENAIELARVVDRGIResKAIDLEKLviepGKKvwVVFIDVYVLDHDGNLLDASMLAAVAALLNTKvpaveegedGV 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 144 LVAQGKLKANPMKGHVSAVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGePFSHEELMELLALAQK 223
Cdd:PRK04282 178 VDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG-SFTEEEVDKAIDIALE 256

                        250
                 ....*....|....*
gi 515600329 224 GIADIIEVQKAALAE 238
Cdd:PRK04282 257 KAKELREKLKEALGI 271
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 2-230 2.76e-18

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: 81.11  E-value: 2.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVE-----ENVPrwlkGKGKGWVTAEYgmLPRAThtrnrR 76
Cdd:cd11365   17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEvgepfPDTP----NEGVLIVNAEL--LPLAS-----P 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  77 EAASGKQGGRTMEIQRLIARSLRA--VVDLEAM----GE--IMVTVDCDVIQADGGTRTASISGASVAMADA------FQ 142
Cdd:cd11365   86 TFEPGPPDENAIELARVVDRGIREskAIDLEKLviepGKkvWVVFIDIYVLDYDGNLFDASALAAVAALLNTkvpeyeVD 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 143 KLVAQGKLKAN---PMKGHVSAVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGePFSHEELMELLA 219
Cdd:cd11365  166 ENEVIEVLGEElplPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG-SFTEDEIDKAID 244

                        250
                 ....*....|.
gi 515600329 220 LAQKGIADIIE 230
Cdd:cd11365  245 IALEKAAELRE 255
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 24-238 2.25e-16

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: 74.91  E-value: 2.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  24 AEGSVLVEFGNTKVLCNASVEENVPRWLKGKGKGWVTAEYGMLPRATHTRNRReaasgKQGGRTMEIQRLIARSLRAVVD 103
Cdd:cd11371   14 AKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPGRRRH-----GQDSEERELSSLLHQALEPAVR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 104 LEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKGHVSAVSVGIVDGKGLCDLEYVEDSAA 183
Cdd:cd11371   89 LEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADA-----------GIEMYDLVTACSAALIGDELLLDPTREEEEAS 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515600329 184 DTDMNV-VMTEEGKMieVQGTAEGEpFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:cd11371  158 SGGVMLaYMPSLNQV--TQLWQSGE-MDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 159-224 7.25e-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: 59.13  E-value: 7.25e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515600329  159 VSAVSVGIVDGKGLCDLEYVEDSAADTDMNVVMTEEGKMIEVQGTAEGePFSHEELMELLALAQKG 224
Cdd:pfam03725   3 VAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGA-GLTEDELLEALELAKEA 67
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 12-228 7.17e-10

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: 56.80  E-value: 7.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  12 RPIKMTRNYTAYAEGSVLVEFGNTKVLCNASveenvprwlkgkGKGWVTAEYGMLPRATHTRNRReAASGKQGGRTMEIQ 91
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVY------------GPIEVKLRKELPDRATLEVIVR-PKSGLPGVKEKLLE 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  92 RLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKGHVSAVSVGIVDGKG 171
Cdd:cd11372   69 LLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDA-----------GVPMKGLFAAVTCAITEDGE 137

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515600329 172 L----CDLEyvEDSAADTDMNVVMTEEGKMI---EVQGTaegepFSHEELMELLALAQKGIADI 228
Cdd:cd11372  138 IildpTAEE--EKEAKAVATFAFDSGEEKNLvlsESEGS-----FTEEELFACLELAQAASAAI 194
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 10-238 2.19e-09

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: 55.63  E-value: 2.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  10 QVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASV----EENVPRWLKGKGKGWVTAEYGMLPRAT-HTR-----NRREAA 79
Cdd:cd11364    1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLgtleDAQKIDSLGGEKSKRFMLHYNFPPYSVgETGrvggpGRREIG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  80 SGkqggrtmeiqRLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkANPMKGHV 159
Cdd:cd11364   81 HG----------ALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMASVCGGSLALMDA-----------GVPIKAPV 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 160 SAVSVGIVDGKG-----LCDLEYVEDSAADTDMNVVMTEEG----KM-IEVQGtaegepFSHEELMELLALAQKGIADII 229
Cdd:cd11364  140 AGIAMGLITEGIddyrvLTDILGLEDHLGDMDFKVAGTRDGitalQMdIKIPG------ITLEIMREALQQAKEGRLHIL 213


                 ....*....
gi 515600329 230 EVQKAALAE 238
Cdd:cd11364  214 DIMEKAISE 222
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 24-238 1.42e-08

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: 53.29  E-value: 1.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  24 AEGSVLVEFGNTKVLCNASVEENvprwlKGKGKGWV--TAEY-------GMLPratHTRNRREaasGKQGGRTMEIQRLI 94
Cdd:cd11363   23 ADGSVVVQYGDTVVLVTAVSSKK-----PKEGIDFFplTVDYreklyaaGKIP---GGFFKRE---GRPSEKEILTSRLI 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  95 ARSLRAvvdLEAMG---EIMVTvdCDVIQADGG--TRTASISGASVAMAdafqklvaqgkLKANPMKGHVSAVSVGIVDG 169
Cdd:cd11363   92 DRPIRP---LFPKGfrnEVQVI--ATVLSVDGVndPDVLAINGASAALS-----------LSDIPFNGPVGAVRVGRIDG 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 170 KGLCDLEYVEDSAADTDMNVVMTEEG-KMIEvqgtAEGEPFSHEELMELLALAQKGIADIIEVQKAALAE 238
Cdd:cd11363  156 EFVVNPTREELEESDLDLVVAGTKDAvLMVE----AGAKEVSEEDMLEAIKFGHEAIQQLIAAQEELAAE 221
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 2-231 1.35e-07

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: 50.99  E-value: 1.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   2 RPNDRAVDQVRPIKMT--RNYtayaeGSVLVEFGNTKVLCNASVEENVPRWLKGK-GKGWVTAEYGMLPRATHtrnrrea 78
Cdd:cd11368   18 RLDGRGLDEFRPIKITfgLEY-----GCVEVSLGKTRVLAQVSCEIVEPKPDRPNeGILFINVELSPMASPAF------- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  79 ASGKQGGRTMEIQRLIARSLR--AVVDLEAM----GEI--MVTVDCDVIQADGG-TRTASIsgASVAMADAFQK---LVA 146
Cdd:cd11368   86 EPGRPSEEEVELSRLLERALRdsRAVDTESLciiaGEKvwSIRVDVHVLNHDGNlIDAASL--AAIAALMHFRRpdvTVD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 147 QGKLKANPMKGHVS----------AVSVGIVDGKGLC--DLEYVEDSAADTDMNVVMTEEGKMIEVQgTAEGEPFSHEEL 214
Cdd:cd11368  164 GEEVTVHSPEEREPvplsihhipiCVTFAFFDDGEIVvvDPTLLEEAVADGSLTVALNKHREICALS-KSGGAPLSPSQI 242

                        250
                 ....*....|....*..
gi 515600329 215 MELLALAQKGIADIIEV 231
Cdd:cd11368  243 LRCVKIAAAKAKELTEL 259
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 2-202 7.23e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 49.51  E-value: 7.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVEEnvpRWLKGKGKGWVTAE--------YGMLPRATHTR 73
Cdd:PLN00207 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGD---KQMAQRIDNLVDADevkrfylqYSFPPSCVGEV 515

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  74 NRREAASGKQGGRTMeiqrLIARSLRAVVDLEAMGEIMVTVDCDVIQADGGTRTASISGASVAMADAfqklvaqgklkAN 153
Cdd:PLN00207 516 GRIGAPSRREIGHGM----LAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDA-----------GV 580

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515600329 154 PMKGHVSAVSVGIV--------DGKG--LCDLEYVEDSAADTDMNVVMTEEG----KM-IEVQG 202
Cdd:PLN00207 581 PVKCPIAGIAMGMVldteefggDGSPliLSDITGSEDASGDMDFKVAGNEDGitafQMdIKVGG 644
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 2-229 1.40e-06

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: 47.94  E-value: 1.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329   2 RPNDRAVDQVRPIKMTRNYTAYAEGSVLVEFGNTKVLCNASVE-----ENVPRwlkgkgKGWVTAEYGMLPR-ATHTRnr 75
Cdd:cd11369   18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEvatpaADTPD------EGYLVPNVDLPPLcSSKFR-- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329  76 reaaSGKQGGRTMEIQRLIARSLR--AVVDLEAM----GEIMVTVDCDV--IQADGGTRTASIsgasVAMADAFQKL--- 144
Cdd:cd11369   90 ----PGPPSEEAQVLSSFLADILLnsNVLDLEQLcivpGKLAWVLYCDVycLDYDGNLLDAAL----LALVAALKNLrlp 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515600329 145 -----VAQGKLKANP-------MKGHVSAVSVGIVDGKG-LCDLEYVEDSAADTDMNVVMTEEGKMIEVQGtAEGEPFSH 211
Cdd:cd11369  162 avtidEETELVVVNPeerrplnLKNLPVSTTFAVFDDKHlLADPTAEEELLASGLVTVVVDENGELCSVHK-PGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 515600329 212 EELMELLALAQ---KGIADII 229
Cdd:cd11369  241 AQLQECIELAKkraKELQKLI 261
ASKHA_NBD_ROK_EcNanK-like cd24069
nucleotide-binding domain (NBD) of Escherichia coli N-acetylmannosamine kinase and similar ...
 87-163 8.73e-03

nucleotide-binding domain (NBD) of Escherichia coli N-acetylmannosamine kinase and similar proteins; N-acetylmannosamine kinase (NanK; EC 2.7.1.60), also called ManNAc kinase, or N-acetyl-D-mannosamine kinase, catalyzes the phosphorylation of N-acetylmannosamine (ManNAc) to ManNAc-6-P. It has also low level glucokinase activity in vitro. This subfamily also contains Brucella melitensis bifunctional enzyme NanE/NanK (EC 5.1.3.9/EC 2.7.1.60), which also converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities.


Pssm-ID: 466919 [Multi-domain]  Cd Length: 283  Bit Score: 36.49  E-value: 8.73e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515600329  87 TMEIQRLIARSLRAVVDLEAMGEIMVTVDCDVIqadggtrtasisGASVAMADAFQKLVAQgKLKANPMKGHVSAVS 163
Cdd:cd24069  205 DEEAARLIDRAARALADLIADLKATLDLDCVVI------------GGSVGLAEGFLERVEQ-YLADEPAIFRVSLEP 268
 
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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