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Conserved domains on  [gi|498112275|ref|WP_010426431|]
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MULTISPECIES: ribonuclease PH [Enterobacter]

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];
1-237 5.63e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 485.30  E-value: 5.63e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAALE 237
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALG 237
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-237 5.63e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 485.30  E-value: 5.63e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAALE 237
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALG 237
rph PRK00173
ribonuclease PH; Reviewed
 1-237 4.16e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 475.37  E-value: 4.16e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVA 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAALE 237
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 3.51e-140

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: 391.98  E-value: 3.51e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAKGKQGGRTME 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  90 IQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVAAVSVGIVNG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 170 EALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-236 3.03e-139

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: 389.80  E-value: 3.03e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275    2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAKG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   82 KQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVAA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498112275  162 VSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAAL 236
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 5.37e-34

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: 118.85  E-value: 5.37e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFlKGQGQGWITAEYGMLPRATHTRNAReaakGKQGGRTME 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKED-RDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 498112275   90 IQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-237 5.63e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 485.30  E-value: 5.63e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAALE 237
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEALG 237
rph PRK00173
ribonuclease PH; Reviewed
 1-237 4.16e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 475.37  E-value: 4.16e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVA 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAALE 237
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 3.51e-140

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: 391.98  E-value: 3.51e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAKGKQGGRTME 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  90 IQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVAAVSVGIVNG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 170 EALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-236 3.03e-139

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: 389.80  E-value: 3.03e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275    2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAREAAKG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   82 KQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADALNKLVAAGKLKTNPMKGMVAA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498112275  162 VSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFTHEELLSLLALARGGIESIVTTQKAAL 236
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 12-210 1.49e-40

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: 138.61  E-value: 1.49e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  12 RPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAreaakGKQGGRTMEIQ 91
Cdd:cd11358    2 RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVGERRQ-----GPPGDEEMEIS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  92 RLIARALRAAVDLKILGE---FTITLDCDVIQADGGTRTASITGACVALADAlnKL----VAAGKLKTNPMKGMVAAVSV 164
Cdd:cd11358   77 RLLERTIEASVILDKSTRkpsWVLYVDIQVLSRDGGLLDACWNAAIAALKDA--GIprvfVDERSPPLLLMKDLIVAVSV 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 498112275 165 GIV-NGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGEPFT 210
Cdd:cd11358  155 GGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDT 201
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 1-238 2.09e-34

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 123.21  E-value: 2.09e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLctASI---EEGVPRFLKGQGQGWITAEYGMLPRATHTRnare 77
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKII--AAVygpREMHPRHLQLPDRAVLRVRYNMAPFSVDER---- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  78 aakgKQGG---RTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADAlnklvaagklkTNP 154
Cdd:PRK03983  88 ----KRPGpdrRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADA-----------GIP 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275 155 MKGMVAAVSVGIVNGEALCDLEYVEDSAAETDMNVVMTED-GRIIEVQ--GTAEGEPFtheelLSLLALARGGIESIVTT 231
Cdd:PRK03983 153 MRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRlGEITLLQldGNLTREEF-----LEALELAKKGIKRIYQL 227


                 ....*..
gi 498112275 232 QKAALEN 238
Cdd:PRK03983 228 QREALKS 234
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 5.37e-34

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: 118.85  E-value: 5.37e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFlKGQGQGWITAEYGMLPRATHTRNAReaakGKQGGRTME 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKED-RDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 498112275   90 IQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 10-238 3.08e-32

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: 116.66  E-value: 3.08e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLctASI---EEGVPRFLKGQGQGWITAEYGMLPRATHTRnareaakgKQGG- 85
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKII--AAVygpREVHPRHLQLPDRAVIRVRYNMAPFSVDER--------KRPGp 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  86 --RTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADAlnklvaagklkTNPMKGMVAAVS 163
Cdd:cd11366   71 drREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADA-----------GIPMRDLVAACA 139

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 498112275 164 VGIVNGEALCDLEYVEDSAAETDMNVVMTEDGR---IIEVQGTAEGEPFtheelLSLLALARGGIESIVTTQKAALEN 238
Cdd:cd11366  140 AGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGeitLLQLDGDLTPDEF-----KQAIELAKKGCKRIYELQKEALKR 212
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 2-202 1.26e-23

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: 94.53  E-value: 1.26e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTAS-IEEGVPRFLKGQGQGWITAEYGMLPRATHTRNAReaak 80
Cdd:cd11370    3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYgPHEPRNRSQALHDRAVVNCEYSMATFSTGERKRR---- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  81 GKQGGRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADalnklvaAGKlktnPMKGMVA 160
Cdd:cd11370   79 GKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALID-------AGI----PMKDYVC 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 498112275 161 AVSVGIVNGEALCDLEYVEDSAAETDMNV-VMTEDGRIIEVQG 202
Cdd:cd11370  148 ACSAGYLDSTPLLDLNYLEESGDLPDLTVaVLPKSDKVVLLQM 190
PRK04282 PRK04282
exosome complex protein Rrp42;
2-211 1.16e-22

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 93.02  E-value: 1.16e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPrFLKGQGQGWITAEYGMLPRATHTRNAreaakG 81
Cdd:PRK04282  25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEP-FPDTPNEGVLIVNAELLPLASPTFEP-----G 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  82 KQGGRTMEIQRLIARALR--AAVDLKIL----GE--FTITLDCDVIQADGGTRTASITGACVALADA---------LNKL 144
Cdd:PRK04282  99 PPDENAIELARVVDRGIResKAIDLEKLviepGKkvWVVFIDVYVLDHDGNLLDASMLAAVAALLNTkvpaveegeDGVV 178

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 145 VAAGKLKTNPMKGMVAAVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGePFTH 211
Cdd:PRK04282 179 DKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG-SFTE 244
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 2-211 1.89e-19

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: 84.19  E-value: 1.89e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPrFLKGQGQGWITAEYGMLPRAthtrnAREAAKG 81
Cdd:cd11365   17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEP-FPDTPNEGVLIVNAELLPLA-----SPTFEPG 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  82 KQGGRTMEIQRLIARALRA--AVDLKIL----GE--FTITLDCDVIQADGGTRTASITGACVALADA---------LNKL 144
Cdd:cd11365   91 PPDENAIELARVVDRGIREskAIDLEKLviepGKkvWVVFIDIYVLDYDGNLFDASALAAVAALLNTkvpeyevdeNEVI 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498112275 145 VAAGKLKTNPMKGMVAAVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEGePFTH 211
Cdd:cd11365  171 EVLGEELPLPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG-SFTE 236
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 23-211 1.76e-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: 75.29  E-value: 1.76e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  23 HAEGSVLVEFGDTKVLCTASIEEGVPRFLKGQGQGWITAEYGMLPRATHTRnareaAKGKQGGRTMEIQRLIARALRAAV 102
Cdd:cd11371   13 QAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPGR-----RRHGQDSEERELSSLLHQALEPAV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275 103 DLKILGEFTITLDCDVIQADGGTRTASITGACVALADalnklvaAGKlktnPMKGMVAAVSVGIVNGEALCDLEYVEDSA 182
Cdd:cd11371   88 RLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALAD-------AGI----EMYDLVTACSAALIGDELLLDPTREEEEA 156

                        170       180       190
                 ....*....|....*....|....*....|..
gi 498112275 183 AETDMNV-VMTEDGRI--IEVQGTAEGEPFTH 211
Cdd:cd11371  157 SSGGVMLaYMPSLNQVtqLWQSGEMDVDQLEE 188
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 157-206 3.97e-10

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: 54.12  E-value: 3.97e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 498112275  157 GMVAAVSVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRIIEVQGTAEG 206
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGA 50
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 12-172 1.54e-09

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: 55.65  E-value: 1.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  12 RPVTLTRNYTKHAEGSVLVEFGDTKVLCTASieegvprflkgqGQGWITAEYGMLPRATHTRNAReAAKGKQGGRTMEIQ 91
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVY------------GPIEVKLRKELPDRATLEVIVR-PKSGLPGVKEKLLE 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  92 RLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADalnklvaAGKlktnPMKGMVAAVSVGIVNGEA 171
Cdd:cd11372   69 LLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLD-------AGV----PMKGLFAAVTCAITEDGE 137


                 .
gi 498112275 172 L 172
Cdd:cd11372  138 I 138
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 2-195 3.14e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 53.74  E-value: 3.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASI--------------EEGVPRFLkgqgqgwitAEYGMLP 67
Cdd:PLN00207 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLgdkqmaqridnlvdADEVKRFY---------LQYSFPP 509

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  68 RATHTRNAREAAKGKQGGRTMeiqrLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADAlnklvaa 147
Cdd:PLN00207 510 SCVGEVGRIGAPSRREIGHGM----LAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDA------- 578

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 498112275 148 gklkTNPMKGMVAAVSVGIV------NGEA----LCDLEYVEDSAAETDMNVVMTEDG 195
Cdd:PLN00207 579 ----GVPVKCPIAGIAMGMVldteefGGDGspliLSDITGSEDASGDMDFKVAGNEDG 632
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 2-138 6.10e-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: 51.76  E-value: 6.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLT--RNYtkhaeGSVLVEFGDTKVLCTASIEEGVPR-------FLKgqgqgwITAEYG-MLPRATH 71
Cdd:cd11368   18 RLDGRGLDEFRPIKITfgLEY-----GCVEVSLGKTRVLAQVSCEIVEPKpdrpnegILF------INVELSpMASPAFE 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 498112275  72 TRNAREAAkgkqggrtMEIQRLIARALR--AAVDLKIL----GE--FTITLDCDVIQADGGTRTASITGACVALA 138
Cdd:cd11368   87 PGRPSEEE--------VELSRLLERALRdsRAVDTESLciiaGEkvWSIRVDVHVLNHDGNLIDAASLAAIAALM 153
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 2-200 1.03e-07

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: 51.40  E-value: 1.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   2 RPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRfLKGQGQGWITAEYGMLPR-ATHTRNAR--EA 78
Cdd:cd11369   18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPA-ADTPDEGYLVPNVDLPPLcSSKFRPGPpsEE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  79 AkgkqggrtMEIQRLIARALRAA--VDLKIL----GEFTITLDCDV--IQADGGTRTASITGACVALADAlnKL------ 144
Cdd:cd11369   97 A--------QVLSSFLADILLNSnvLDLEQLcivpGKLAWVLYCDVycLDYDGNLLDAALLALVAALKNL--RLpavtid 166

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 498112275 145 VAAGKLKTNP-------MKGMVAAVSVGIVNGEA-LCDLEYVEDSAAETDMNVVMTEDGRIIEV 200
Cdd:cd11369  167 EETELVVVNPeerrplnLKNLPVSTTFAVFDDKHlLADPTAEEELLASGLVTVVVDENGELCSV 230
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 10-195 1.12e-05

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: 44.84  E-value: 1.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  10 QVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASI----EEGVPRFLKGQGQGWITAEYGMLPRATHtrnarEAAK-GKQG 84
Cdd:cd11364    1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLgtleDAQKIDSLGGEKSKRFMLHYNFPPYSVG-----ETGRvGGPG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  85 GRTMEIQRLIARALRAAVDLKILGEFTITLDCDVIQADGGTRTASITGACVALADalnklvaAGKlktnPMKGMVAAVSV 164
Cdd:cd11364   76 RREIGHGALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMASVCGGSLALMD-------AGV----PIKAPVAGIAM 144

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 498112275 165 GIVNGEA-----LCDLEYVEDSAAETDMNVVMTEDG 195
Cdd:cd11364  145 GLITEGIddyrvLTDILGLEDHLGDMDFKVAGTRDG 180
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 22-205 3.30e-05

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: 43.66  E-value: 3.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  22 KHAEGSVLVEFGDTKVLCTASIEEGVPR---FLKgqgqgwITAEY-------GMLPrATHTRnaREaakGKQGGRTMEIQ 91
Cdd:cd11363   21 KQADGSVVVQYGDTVVLVTAVSSKKPKEgidFFP------LTVDYreklyaaGKIP-GGFFK--RE---GRPSEKEILTS 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275  92 RLIARALRA------AVDLKILgeftitldCDVIQADGG--TRTASITGACVALAdaLNKLvaagklktnPMKGMVAAVS 163
Cdd:cd11363   89 RLIDRPIRPlfpkgfRNEVQVI--------ATVLSVDGVndPDVLAINGASAALS--LSDI---------PFNGPVGAVR 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 498112275 164 VGIVNGEALCDLEYVEDSAAETDMNVVMTEDgRIIEVQGTAE 205
Cdd:cd11363  150 VGRIDGEFVVNPTREELEESDLDLVVAGTKD-AVLMVEAGAK 190
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 1-123 3.50e-03

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: 37.58  E-value: 3.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498112275   1 MRPSGRSANQVRPVTLTRNYTKHAEGSVLVEFGDTKVLCTASIEEGVPRFLKGqGQGWITAEYGMLPRATHTRNAREAAK 80
Cdd:cd11367   18 IRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETP-NKGRLEFFVDCSPNASPEFEGRGGEE 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 498112275  81 gkqggRTMEIQRLIARAL--RAAVDLKIL----GE--FTITLDCDVIQADG 123
Cdd:cd11367   97 -----LATELSSALERALksGSAIDLSKLcivpGKqcWVLYVDVLVLESGG 142
 
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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