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Conserved domains on  [gi|490257560|ref|WP_004154791|]
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ribonuclease PH [Erwinia amylovora]

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];
1-236 8.08e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 484.92  E-value: 8.08e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560 161 AISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEAL 236
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-236 8.08e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 484.92  E-value: 8.08e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560 161 AISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEAL 236
rph PRK00173
ribonuclease PH; Reviewed
 1-236 1.30e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 476.52  E-value: 1.30e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAK 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVA 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560 161 AISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAAL 236
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 2.17e-141

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: 395.06  E-value: 2.17e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAKGKQGGRTLE 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  90 IQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVAAISVGIVNG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490257560 170 EALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-237 8.88e-140

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: 391.34  E-value: 8.88e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560    2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAKG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   82 KQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVAA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560  162 ISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAALT 237
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 8.72e-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: 118.08  E-value: 8.72e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFlKGQGQGWVTAEYGMLPRATHSRNAReaakGKQGGRTLE 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKED-RDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 490257560   90 IQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
 
Name Accession Description Interval E-value
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
1-236 8.08e-177

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 484.92  E-value: 8.08e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAK 80
Cdd:COG0689    1 MRPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTASVEEGVPPFLKGSGQGWVTAEYGMLPRATHTRNRREAAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVA 160
Cdd:COG0689   81 GKQSGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVLQADGGTRTASITGAFVALADALNKLVEKGLLKENPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560 161 AISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:COG0689  161 AVSVGIVDGEPVLDLDYEEDSAAEVDMNVVMTGSGEFVEVQGTAEGAPFSREELDALLDLAEKGIAELIALQKEAL 236
rph PRK00173
ribonuclease PH; Reviewed
 1-236 1.30e-173

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 476.52  E-value: 1.30e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAK 80
Cdd:PRK00173   1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVA 160
Cdd:PRK00173  81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560 161 AISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAAL 236
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 10-236 2.17e-141

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: 395.06  E-value: 2.17e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAKGKQGGRTLE 89
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGKGKGWVTAEYSMLPRSTHERTQREASKGKQSGRTQE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  90 IQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVAAISVGIVNG 169
Cdd:cd11362   81 IQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490257560 170 EALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAAL 236
Cdd:cd11362  161 EPLLDLDYEEDSAADVDMNVVMTGSGRFVEVQGTGEEAPFSRDELNELLDLAEKGIQELIELQKEAL 227
RNasePH TIGR01966
ribonuclease PH; This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and ...
 2-237 8.88e-140

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: 391.34  E-value: 8.88e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560    2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAREAAKG 81
Cdd:TIGR01966   1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   82 KQGGRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANPMKGMVAA 161
Cdd:TIGR01966  81 KQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490257560  162 ISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFSHEELLKLLELARGGIDTLVAAQKAALT 237
Cdd:TIGR01966 161 VSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 12-210 2.16e-38

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites.


Pssm-ID: 206766 [Multi-domain]  Cd Length: 218  Bit Score: 132.84  E-value: 2.16e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  12 RPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAreaakGKQGGRTLEIQ 91
Cdd:cd11358    2 RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVGERRQ-----GPPGDEEMEIS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  92 RLIARSLRAAIDLKALGE---FTITLDCDVLQADGGTRTASITGACVALADALNHLVFIGKLKANP--MKGMVAAISVGI 166
Cdd:cd11358   77 RLLERTIEASVILDKSTRkpsWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERSPPLllMKDLIVAVSVGG 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490257560 167 V-NGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGEPFS 210
Cdd:cd11358  157 IsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDT 201
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 10-140 8.72e-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: 118.08  E-value: 8.72e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFlKGQGQGWVTAEYGMLPRATHSRNAReaakGKQGGRTLE 89
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKED-RDFAPGRLTVEYELAPFASGERPGE----GRPSEREIE 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 490257560   90 IQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADA 140
Cdd:pfam01138  76 ISRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADA 126
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 1-198 1.28e-31

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 115.89  E-value: 1.28e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLctATI---EEGVPRFLKGQGQGWVTAEYGMLPRATHSRnare 77
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKII--AAVygpREMHPRHLQLPDRAVLRVRYNMAPFSVDER---- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  78 aakgKQGG---RTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANP 154
Cdd:PRK03983  88 ----KRPGpdrRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADA-----------GIP 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 490257560 155 MKGMVAAISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMI 198
Cdd:PRK03983 153 MRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEI 196
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 10-237 1.11e-30

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: 112.81  E-value: 1.11e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLctATI---EEGVPRFLKGQGQGWVTAEYGMLPRATHSRnareaakgKQGG- 85
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKII--AAVygpREVHPRHLQLPDRAVIRVRYNMAPFSVDER--------KRPGp 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  86 --RTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANPMKGMVAAIS 163
Cdd:cd11366   71 drREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADA-----------GIPMRDLVAACA 139

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490257560 164 VGIVNGEALCDLEYVEDSAAETDMNVVMTEDGR---MIEVQGTAEGEPFSheellKLLELARGGIDTLVAAQKAALT 237
Cdd:cd11366  140 AGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGeitLLQLDGDLTPDEFK-----QAIELAKKGCKRIYELQKEALK 211
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 24-183 3.67e-22

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: 90.68  E-value: 3.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  24 AEGSVLVEFGDTKVLCTAT-IEEGVPRFLKGQGQGWVTAEYGMLPRATHSRNAReaakGKQGGRTLEIQRLIARSLRAAI 102
Cdd:cd11370   25 ADGSAYLEQGNTKVLAAVYgPHEPRNRSQALHDRAVVNCEYSMATFSTGERKRR----GKGDRRSTELSLAIRQTFEAVI 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560 103 DLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANPMKGMVAAISVGIVNGEALCDLEYVEDSA 182
Cdd:cd11370  101 LTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDA-----------GIPMKDYVCACSAGYLDSTPLLDLNYLEESG 169


                 .
gi 490257560 183 A 183
Cdd:cd11370  170 D 170
PRK04282 PRK04282
exosome complex protein Rrp42;
2-211 1.70e-19

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 84.54  E-value: 1.70e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPrFLKGQGQG--WVTAEygMLPRAthsrnAREAA 79
Cdd:PRK04282  25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEP-FPDTPNEGvlIVNAE--LLPLA-----SPTFE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  80 KGKQGGRTLEIQRLIARSLR--AAIDLKAL----GE--FTITLDCDVLQADGGTRTASITGACVALADA---------LN 142
Cdd:PRK04282  97 PGPPDENAIELARVVDRGIResKAIDLEKLviepGKkvWVVFIDVYVLDHDGNLLDASMLAAVAALLNTkvpaveegeDG 176

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490257560 143 HLVFIGKLKANPMKGMVAAISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEGePFSH 211
Cdd:PRK04282 177 VVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG-SFTE 244
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 2-206 8.14e-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: 79.57  E-value: 8.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPrFLKGQGQG--WVTAEYgmLPRAthsrnAREAA 79
Cdd:cd11365   17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEP-FPDTPNEGvlIVNAEL--LPLA-----SPTFE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  80 KGKQGGRTLEIQRLIARSLRA--AIDLKAL----GE--FTITLDCDVLQADGGTRTASITGACVALADA------LNHLV 145
Cdd:cd11365   89 PGPPDENAIELARVVDRGIREskAIDLEKLviepGKkvWVVFIDIYVLDYDGNLFDASALAAVAALLNTkvpeyeVDENE 168

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490257560 146 FIGKLKAN---PMKGMVAAISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEG 206
Cdd:cd11365  169 VIEVLGEElplPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG 232
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 11-187 3.39e-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: 74.52  E-value: 3.39e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  11 VRPVTLTRHYTKHAEGSVLVEFGDTKVLCTatieegV--PRFLKGQ----GQGWVTAEYGMLPRATHSRnareaAKGKQG 84
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICS------VygPRPIPGRtefsDRGRLNCEVKFAPFATPGR-----RRHGQD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  85 GRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANPMKGMVAAISV 164
Cdd:cd11371   70 SEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADA-----------GIEMYDLVTACSA 138

                        170       180
                 ....*....|....*....|...
gi 490257560 165 GIVNGEALCDLEYVEDSAAETDM 187
Cdd:cd11371  139 ALIGDELLLDPTREEEEASSGGV 161
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 12-172 1.63e-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: 58.34  E-value: 1.63e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  12 RPVTLTRHYTKHAEGSVLVEFGDTKVLCTATieegvprflkgqGQGWVTAEYGMLPRATHSRNAReAAKGKQGGRTLEIQ 91
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVY------------GPIEVKLRKELPDRATLEVIVR-PKSGLPGVKEKLLE 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  92 RLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANPMKGMVAAISVGIVNGEA 171
Cdd:cd11372   69 LLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDA-----------GVPMKGLFAAVTCAITEDGE 137


                 .
gi 490257560 172 L 172
Cdd:cd11372  138 I 138
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 157-206 3.65e-09

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: 51.81  E-value: 3.65e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 490257560  157 GMVAAISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDGRMIEVQGTAEG 206
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGA 50
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 2-202 6.79e-09

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 55.67  E-value: 6.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATI--------------EEGVPRF-LKGQGQGWVTAEYGML 66
Cdd:PLN00207 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLgdkqmaqridnlvdADEVKRFyLQYSFPPSCVGEVGRI 518

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  67 PRAthSRnaREAAKGkqggrtleiqRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvf 146
Cdd:PLN00207 519 GAP--SR--REIGHG----------MLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDA------ 578

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490257560 147 igklkANPMKGMVAAISVGIV------NGEA----LCDLEYVEDSAAETDMNVVMTEDG----RM-IEVQG 202
Cdd:PLN00207 579 -----GVPVKCPIAGIAMGMVldteefGGDGspliLSDITGSEDASGDMDFKVAGNEDGitafQMdIKVGG 644
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 2-138 1.46e-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: 53.69  E-value: 1.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   2 RPSGRSAQQVRPVTLT--RHYtkhaeGSVLVEFGDTKVLC--TATIEEGVPRFLKgQGQGWVTAEYG-MLPRATHSRNAR 76
Cdd:cd11368   18 RLDGRGLDEFRPIKITfgLEY-----GCVEVSLGKTRVLAqvSCEIVEPKPDRPN-EGILFINVELSpMASPAFEPGRPS 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  77 EAAKgkqggrtlEIQRLIARSLR--AAIDLKAL----GE--FTITLDCDVLQADGGTRTASITGACVALA 138
Cdd:cd11368   92 EEEV--------ELSRLLERALRdsRAVDTESLciiaGEkvWSIRVDVHVLNHDGNLIDAASLAAIAALM 153
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 10-195 2.35e-08

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: 52.93  E-value: 2.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  10 QVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATI----EEGVPRFLKGQGQGWVTAEYGMLPRATHsrnarEAAK-GKQG 84
Cdd:cd11364    1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLgtleDAQKIDSLGGEKSKRFMLHYNFPPYSVG-----ETGRvGGPG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  85 GRTLEIQRLIARSLRAAIDLKALGEFTITLDCDVLQADGGTRTASITGACVALADAlnhlvfigklkANPMKGMVAAISV 164
Cdd:cd11364   76 RREIGHGALAERALLPVLPSPEDFPYTIRVVSEVLESNGSSSMASVCGGSLALMDA-----------GVPIKAPVAGIAM 144

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 490257560 165 GIVNGEA-----LCDLEYVEDSAAETDMNVVMTEDG 195
Cdd:cd11364  145 GLITEGIddyrvLTDILGLEDHLGDMDFKVAGTRDG 180
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 12-202 7.86e-07

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: 48.28  E-value: 7.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  12 RPVTL-TRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPR---FLKgqgqgwVTAEY-------GMLPrATHSRnaREaak 80
Cdd:cd11363   10 RTLTFeTGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEgidFFP------LTVDYreklyaaGKIP-GGFFK--RE--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  81 GKQGGRTLEIQRLIARSLRAaidLKALGEFTIT-LDCDVLQADGG--TRTASITGACVALAdalnhlvfIGKLkanPMKG 157
Cdd:cd11363   78 GRPSEKEILTSRLIDRPIRP---LFPKGFRNEVqVIATVLSVDGVndPDVLAINGASAALS--------LSDI---PFNG 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 490257560 158 MVAAISVGIVNGEALCDLEYVEDSAAETDMNVVMTEDG-RMIEVQG 202
Cdd:cd11363  144 PVGAVRVGRIDGEFVVNPTREELEESDLDLVVAGTKDAvLMVEAGA 189
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 2-200 1.47e-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: 1.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   2 RPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRfLKGQGQGWVTAEYGMLP----RATHSRNARE 77
Cdd:cd11369   18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPA-ADTPDEGYLVPNVDLPPlcssKFRPGPPSEE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  78 AAKGKQggrtlEIQRLIARSlrAAIDLKAL----GEFTITLDCDV--LQADGGTRTASITGACVALADALNHLVFI---- 147
Cdd:cd11369   97 AQVLSS-----FLADILLNS--NVLDLEQLcivpGKLAWVLYCDVycLDYDGNLLDAALLALVAALKNLRLPAVTIdeet 169

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490257560 148 GKLKANP-------MKGMVAAISVGIVNGEA-LCDLEYVEDSAAETDMNVVMTEDGRMIEV 200
Cdd:cd11369  170 ELVVVNPeerrplnLKNLPVSTTFAVFDDKHlLADPTAEEELLASGLVTVVVDENGELCSV 230
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 1-123 8.95e-04

RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206772 [Multi-domain]  Cd Length: 272  Bit Score: 39.50  E-value: 8.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560   1 MRPSGRSAQQVRPVTLTRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPRFLKGqgqgwvtaEYGML-------PRATHSR 73
Cdd:cd11367   18 IRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETP--------NKGRLeffvdcsPNASPEF 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 490257560  74 NAREAAKgkqggRTLEIQRLIARSL--RAAIDLKAL----GE--FTITLDCDVLQADG 123
Cdd:cd11367   90 EGRGGEE-----LATELSSALERALksGSAIDLSKLcivpGKqcWVLYVDVLVLESGG 142
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 12-199 1.46e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 39.26  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  12 RPVTL-TRHYTKHAEGSVLVEFGDTKVLCTATIEEGVPrflkgQGQGWV--TAEYgmlprathsrNAREAAKGK-QGG-- 85
Cdd:PRK11824  14 RTLTLeTGKLARQANGAVLVRYGDTVVLVTVVASKEPK-----EGQDFFplTVDY----------EEKTYAAGKiPGGff 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  86 -R--------TLeIQRLIARSLRAAI--DLKAlgEFTITldCDVLQADGGTR--TASITGACVALAdalnhlvfIGKLka 152
Cdd:PRK11824  79 kRegrpsekeTL-TSRLIDRPIRPLFpkGFRN--EVQVV--ATVLSVDPENDpdILAMIGASAALS--------ISGI-- 143

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490257560 153 nPMKGMVAAISVGIVNGealcdlEYV----EDSAAETDMNVVM--TEDG-RMIE 199
Cdd:PRK11824 144 -PFNGPIAAVRVGYIDG------EFVlnptVEELEESDLDLVVagTKDAvLMVE 190
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 17-199 2.68e-03

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 38.72  E-value: 2.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  17 TRHYTKHAEGSVLVEFGDTKVLCTATIEEgVPrflkgqgqgwvTAEYGMLPRATHSRNaREAAKG-------KQGGRTLE 89
Cdd:PLN00207  95 TGHIGRQASGSVTVTDGETIVYTSVCLAD-VP-----------SEPSDFFPLSVHYQE-RFSAAGrtsggffKREGRTKD 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490257560  90 ----IQRLIARSLRAAIdLKALGEFTITLDCdVLQADG--GTRTASITGACVALAdalnhlvfigkLKANPMKGMVAAIS 163
Cdd:PLN00207 162 hevlICRLIDRPLRPTM-PKGFYHETQILSW-VLSYDGlhSPDSLAVTAAGIAVA-----------LSEVPNLKAIAGVR 228

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490257560 164 VGIVNGEALCDLEYVEDSAAETDMNVVMTEDG-RMIE 199
Cdd:PLN00207 229 VGLIGGKFIVNPTTKEMEESELDLIMAGTDSAiLMIE 265
 
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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