254780636
ribonuclease D
GeneID in NCBI database: | 8209637 | Locus tag: | CLIBASIA_02615 |
Protein GI in NCBI database: | 254780636 | Protein Accession: | YP_003065049.1 |
Gene range: | +(633342, 633965) | Protein Length: | 207aa |
Gene description: | ribonuclease D | ||
COG prediction: | [J] Ribonuclease D | ||
KEGG prediction: | ribonuclease D; K03684 ribonuclease D [EC:3.1.13.5] | ||
SEED prediction: | Ribonuclease D related protein | ||
Pathway involved in KEGG: | not defined | ||
Subsystem involved in SEED: | - none - | ||
sequence | sequence profile |
Prediction of Local Sequence Properties
Source | Summary | Result |
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Close Homologs Detected by BLAST or PSI-BLAST
Homolog within the Genome Detected by BLAST
Original result of BLAST against C. L. asiaticus genome
No hits with e-value below 0.05
Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations
Original result of PSI-BLAST first 2 iterations
Identity | Alignment graph | Length | Definition | Round | E-value |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | |||
315122172 | 209 | ribonuclease D [Candidatus Liberibacter solanacearum CL | 1 | 6e-96 | |
332716830 | 208 | Ribonuclease D [Agrobacterium sp. H13-3] Length = 208 | 1 | 1e-83 | |
222147114 | 208 | ribonuclease D [Agrobacterium vitis S4] Length = 208 | 1 | 2e-83 | |
209551599 | 208 | 3'-5' exonuclease [Rhizobium leguminosarum bv. trifolii | 1 | 4e-83 | |
222084303 | 208 | RNAse D protein [Agrobacterium radiobacter K84] Length | 1 | 1e-82 | |
86355756 | 208 | RNAse D protein [Rhizobium etli CFN 42] Length = 208 | 1 | 2e-82 | |
195970213 | 208 | hypothetical protein SMc00342 [Sinorhizobium meliloti 1 | 1 | 2e-82 | |
218508865 | 208 | ribonuclease III protein [Rhizobium etli Brasil 5] Leng | 1 | 2e-82 | |
218661189 | 208 | ribonuclease III protein [Rhizobium etli IE4771] Length | 1 | 2e-82 | |
116249870 | 208 | ribonuclease [Rhizobium leguminosarum bv. viciae 3841] | 1 | 3e-82 |
>gi|315122172|ref|YP_004062661.1| ribonuclease D [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 209 | Back alignment and organism information |
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Score = 353 bits (907), Expect = 6e-96, Method: Compositional matrix adjust. Identities = 166/206 (80%), Positives = 183/206 (88%) Query: 1 MTTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQ 60 MTTIRVH GDIP EC ARY IAVDTETLGL+PRRDRLC+VQLSPGDGT DIIRIAA Q Sbjct: 1 MTTIRVHNGDIPTECIARYTGPIAVDTETLGLIPRRDRLCVVQLSPGDGTADIIRIAAEQ 60 Query: 61 KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLK 120 KNAPNLV ML +E +EKIFHY RFDIAVLFYTFGVRV+P+FCTKIASRLTRTY ++HGLK Sbjct: 61 KNAPNLVTMLANETQEKIFHYARFDIAVLFYTFGVRVKPIFCTKIASRLTRTYIDRHGLK 120 Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 DNL+ELLG++ISK QQ SDWS DDLS EQLQYAASDVVHLHALR +F KLQ LGRSD+A Sbjct: 121 DNLRELLGVDISKKQQLSDWSEDDLSHEQLQYAASDVVHLHALREKFIAKLQSLGRSDVA 180 Query: 181 TSCCNFLMDRAELDLLGWENVDIFSH 206 ++C NFLM RAELDLLGW+N+DIFSH Sbjct: 181 SACFNFLMSRAELDLLGWDNIDIFSH 206 |
Species: Candidatus Liberibacter solanacearum Genus: Candidatus Liberibacter Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|332716830|ref|YP_004444296.1| Ribonuclease D [Agrobacterium sp. H13-3] Length = 208 | Back alignment and organism information |
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Score = 313 bits (801), Expect = 1e-83, Method: Compositional matrix adjust. Identities = 150/205 (73%), Positives = 172/205 (83%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY+ AIA+DTETLGL+PRRDRLC+VQLSPGDGT D+IRIAAGQK Sbjct: 4 TIRYHEGDISAADAARYLGAIAIDTETLGLVPRRDRLCVVQLSPGDGTADVIRIAAGQKE 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNL ML D R+KIFHYGRFDIAVLF+TFGV PVFCTKIASRLTRTYT++HGLKDN Sbjct: 64 APNLTHMLADPARQKIFHYGRFDIAVLFHTFGVTTTPVFCTKIASRLTRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L ++ISKAQQSSDW+A+ LS QL+YAASDV+HLHALR + T +L R GR D A + Sbjct: 124 LKEMLEVDISKAQQSSDWAAEKLSPAQLEYAASDVLHLHALRDKLTHRLVRDGRLDHADA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGW+ DIF+HS Sbjct: 184 CFAFLPTRAKLDLLGWDETDIFAHS 208 |
Species: Agrobacterium sp. H13-3 Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|222147114|ref|YP_002548071.1| ribonuclease D [Agrobacterium vitis S4] Length = 208 | Back alignment and organism information |
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Score = 312 bits (799), Expect = 2e-83, Method: Compositional matrix adjust. Identities = 147/206 (71%), Positives = 173/206 (83%) Query: 2 TTIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQK 61 +TIR HEGDI +E AARY AIA+DTETLGL+PRRDRLC+VQLSPGDGT D+IRIA GQ+ Sbjct: 3 STIRYHEGDISSEDAARYTRAIAIDTETLGLIPRRDRLCVVQLSPGDGTADVIRIAPGQR 62 Query: 62 NAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKD 121 APNL +L D REKIFHYGRFDIAVLF+TFGV PVFCTKIASRL+RTYT++HGLKD Sbjct: 63 QAPNLTALLEDPTREKIFHYGRFDIAVLFHTFGVTTTPVFCTKIASRLSRTYTDRHGLKD 122 Query: 122 NLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLAT 181 NLKE+L +++SKAQQSSDW+A+ LS QL+YAASDV++LHALR + T +L R GR D AT Sbjct: 123 NLKEMLDVDVSKAQQSSDWAAETLSPAQLEYAASDVLYLHALRDKLTARLVRDGRMDHAT 182 Query: 182 SCCNFLMDRAELDLLGWENVDIFSHS 207 +C FL RA+LDLLGWE DIF+HS Sbjct: 183 ACFEFLPTRAKLDLLGWEETDIFAHS 208 |
Species: Agrobacterium vitis Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|209551599|ref|YP_002283516.1| 3'-5' exonuclease [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 208 | Back alignment and organism information |
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Score = 311 bits (796), Expect = 4e-83, Method: Compositional matrix adjust. Identities = 149/205 (72%), Positives = 172/205 (83%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY AIA+DTETLGL+PRRDRLC+VQLSPGDGT D+IRIA+GQK Sbjct: 4 TIRYHEGDISAADAARYTGAIAIDTETLGLVPRRDRLCVVQLSPGDGTADVIRIASGQKE 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV +L D +KIFHYGRFDIAVLF+TFGV PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVALLEDPTHQKIFHYGRFDIAVLFHTFGVTTNPVFCTKIASRLIRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L ++ISKAQQSSDW+A+ LS QL+YAASDV++LHALR + TE+L R GR D AT+ Sbjct: 124 LKEMLDVDISKAQQSSDWAAETLSPAQLEYAASDVLYLHALRDKLTERLLRDGRFDHATA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFAFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|222084303|ref|YP_002542832.1| RNAse D protein [Agrobacterium radiobacter K84] Length = 208 | Back alignment and organism information |
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Score = 310 bits (793), Expect = 1e-82, Method: Compositional matrix adjust. Identities = 149/205 (72%), Positives = 170/205 (82%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY AIA+DTETLGL+PRRDRLC+VQLSPGDGT DIIRIA+GQ Sbjct: 4 TIRYHEGDISAADAARYTGAIAIDTETLGLIPRRDRLCVVQLSPGDGTADIIRIASGQSQ 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV ML D R+KIFHYGRFDIAVLF+TFGV PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVAMLADTTRQKIFHYGRFDIAVLFHTFGVTTTPVFCTKIASRLCRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKELL ++ISKAQQSSDW+A+ LS QL+YAASDV++LHALR + T +L R GR + A + Sbjct: 124 LKELLEVDISKAQQSSDWAAEKLSPAQLEYAASDVLYLHALRDKLTARLVRDGRMEHAEA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFAFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Agrobacterium tumefaciens Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|86355756|ref|YP_467648.1| RNAse D protein [Rhizobium etli CFN 42] Length = 208 | Back alignment and organism information |
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Score = 309 bits (791), Expect = 2e-82, Method: Compositional matrix adjust. Identities = 149/205 (72%), Positives = 171/205 (83%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY AIA+DTETLGL+PRRDRLC+VQLSPGDGT DIIRIAAGQK Sbjct: 4 TIRYHEGDISAADAARYTGAIAIDTETLGLVPRRDRLCVVQLSPGDGTADIIRIAAGQKA 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV +L D +KIFHYGRFDIAVLF+TFGV PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVALLEDPTHQKIFHYGRFDIAVLFHTFGVTTNPVFCTKIASRLCRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L +++SKAQQSSDW+A+ LS QL+YAASDV++LHALR + T +L R GR D AT+ Sbjct: 124 LKEMLDVDVSKAQQSSDWAAETLSPAQLEYAASDVLYLHALRDKLTARLIRDGRFDHATA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFAFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|195970213|ref|NP_384368.2| hypothetical protein SMc00342 [Sinorhizobium meliloti 1021] Length = 208 | Back alignment and organism information |
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Score = 309 bits (791), Expect = 2e-82, Method: Compositional matrix adjust. Identities = 149/205 (72%), Positives = 170/205 (82%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI AARY AIA+DTETLGL+PRRDRLC+VQLS GDGT D+IRI+AGQK Sbjct: 4 TIRFHEGDISETDAARYTGAIAIDTETLGLVPRRDRLCVVQLSSGDGTADVIRISAGQKQ 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV ML D R+KIFH+GRFDIAVLF+TFGV PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVSMLADPTRQKIFHFGRFDIAVLFHTFGVTASPVFCTKIASRLARTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKELL I+ISK QQSSDW+AD LS QL+YAASDV+HLHALR + T +L R GR +LA + Sbjct: 124 LKELLDIDISKQQQSSDWAADILSPAQLEYAASDVLHLHALRDKLTARLLRDGRMELAEA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C +FL RA+LDLLGWE DIF+HS Sbjct: 184 CFSFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Sinorhizobium meliloti Genus: Sinorhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|218508865|ref|ZP_03506743.1| ribonuclease III protein [Rhizobium etli Brasil 5] Length = 208 | Back alignment and organism information |
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Score = 309 bits (791), Expect = 2e-82, Method: Compositional matrix adjust. Identities = 147/205 (71%), Positives = 171/205 (83%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY A+A+DTETLGL+PRRDRLC+VQLSPGDGT D+IRIAAGQK Sbjct: 4 TIRYHEGDISAADAARYTGAVAIDTETLGLVPRRDRLCVVQLSPGDGTADVIRIAAGQKE 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV +L D +KIFHYGRFDIAVLF+TFGV PVFCTKIASRL+RTYT++HGLKDN Sbjct: 64 APNLVALLEDPTHQKIFHYGRFDIAVLFHTFGVTTTPVFCTKIASRLSRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L ++ISK QQSSDW+A+ LS QL+YAASDV++LHALR + T +L R GR D AT+ Sbjct: 124 LKEMLDVDISKTQQSSDWAAETLSQAQLEYAASDVLYLHALRDKLTARLIRDGRFDHATA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFAFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|218661189|ref|ZP_03517119.1| ribonuclease III protein [Rhizobium etli IE4771] Length = 208 | Back alignment and organism information |
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Score = 308 bits (790), Expect = 2e-82, Method: Compositional matrix adjust. Identities = 148/205 (72%), Positives = 170/205 (82%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A AARY A+A+DTETLGL+PRRDRLC+VQLSPGDGT D+IRIAAGQK Sbjct: 4 TIRYHEGDISAADAARYTGAVAIDTETLGLVPRRDRLCVVQLSPGDGTADVIRIAAGQKE 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV +L D +KIFHYGRFDIAVLF+TFGV PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVALLEDPTHQKIFHYGRFDIAVLFHTFGVTTTPVFCTKIASRLIRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L I+ISK QQSSDW+A+ LS QL+YAASDV++LHALR + T +L R GR D AT+ Sbjct: 124 LKEMLDIDISKTQQSSDWAAETLSPAQLEYAASDVLYLHALRDKLTARLIRDGRFDHATA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFEFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|116249870|ref|YP_765708.1| ribonuclease [Rhizobium leguminosarum bv. viciae 3841] Length = 208 | Back alignment and organism information |
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Score = 308 bits (789), Expect = 3e-82, Method: Compositional matrix adjust. Identities = 148/205 (72%), Positives = 170/205 (82%) Query: 3 TIRVHEGDIPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN 62 TIR HEGDI A ARY AIA+DTETLGL+PRRDRLC+VQLSPGDGT DIIRIAAGQK Sbjct: 4 TIRYHEGDISAADVARYTGAIAIDTETLGLVPRRDRLCVVQLSPGDGTADIIRIAAGQKE 63 Query: 63 APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDN 122 APNLV +L D +KIFHYGRFDIAVLF+TF V PVFCTKIASRL RTYT++HGLKDN Sbjct: 64 APNLVALLEDPTHQKIFHYGRFDIAVLFHTFSVTTTPVFCTKIASRLIRTYTDRHGLKDN 123 Query: 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 LKE+L +++SKAQQSSDW+A+ LS QL+YAASDV++LHALR + TE+L R GR D AT+ Sbjct: 124 LKEMLDVDVSKAQQSSDWAAERLSPAQLEYAASDVLYLHALRDKLTERLIRDGRYDHATA 183 Query: 183 CCNFLMDRAELDLLGWENVDIFSHS 207 C FL RA+LDLLGWE DIF+HS Sbjct: 184 CFEFLPTRAKLDLLGWEEADIFAHS 208 |
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | ||
cd06142 | 178 | cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of | 2e-46 | |
pfam01612 | 172 | pfam01612, 3_5_exonuc, 3'-5' exonuclease | 1e-29 | |
smart00474 | 172 | smart00474, 35EXOc, 3'-5' exonuclease | 6e-26 | |
cd00007 | 155 | cd00007, 35EXOc, 3'-5' exonuclease | 1e-23 | |
TIGR01388 | 367 | TIGR01388, rnd, ribonuclease D | 7e-20 | |
PRK10829 | 373 | PRK10829, PRK10829, ribonuclease D; Provisional | 3e-09 | |
cd09018 | 150 | cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuc | 6e-09 | |
cd06148 | 197 | cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain o | 2e-08 | |
PRK05755 | 880 | PRK05755, PRK05755, DNA polymerase I; Provisional | 5e-08 | |
COG0749 | 593 | COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and | 2e-07 | |
KOG2206 | 687 | KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonucleas | 2e-05 | |
cd06140 | 178 | cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3 | 4e-04 | |
COG0349 | 361 | COG0349, Rnd, Ribonuclease D [Translation, ribosomal st | 7e-58 | |
cd06129 | 161 | cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of | 2e-12 | |
cd06141 | 170 | cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN | 9e-11 | |
cd06139 | 193 | cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonucl | 9e-07 | |
cd06147 | 192 | cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain | 1e-05 | |
PRK14975 | 553 | PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA | 1e-07 | |
cd06146 | 193 | cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain | 2e-05 |
>gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins | Back alignment and domain information |
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Score = 180 bits (459), Expect = 2e-46 Identities = 64/171 (37%), Positives = 94/171 (54%), Gaps = 7/171 (4%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGT--VDIIRIAAGQKNAPNLVGMLVDEKREKI 78 IAVDTE + L RLC++Q+S G +D + I + L +L D K+ Sbjct: 13 GVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI----GDLSPLKELLADPNIVKV 68 Query: 79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 FH R D+ +L FG+ + +F T+IA+RL + GL ++ELLG+ + K +Q S Sbjct: 69 FHAAREDLELLKRDFGILPQNLFDTQIAARLLGLG-DSVGLAALVEELLGVELDKGEQRS 127 Query: 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMD 189 DWS L+DEQL+YAA DV +L L + E+L+ GR + A C L+D Sbjct: 128 DWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECELLLD 178 |
Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein. Length = 178 |
>gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease | Back alignment and domain information |
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Score = 125 bits (315), Expect = 1e-29 Identities = 53/155 (34%), Positives = 83/155 (53%), Gaps = 4/155 (2%) Query: 20 VDAIAVDTET--LGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREK 77 +AVDTET L C++Q+S G+G II A + L +L D K Sbjct: 20 AKVVAVDTETTSLDTYSYTLVGCLIQISTGEGAY-IIDPLALGDDLEGLKRLLEDPNITK 78 Query: 78 IFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137 + H +FD+ VL FG+++ +F T +A+ L Y H L D ++ LG+ + K++Q Sbjct: 79 VGHNAKFDLEVLARDFGIKLENLFDTMLAAYL-LGYPRSHSLDDLAEKYLGVELDKSEQC 137 Query: 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172 +DW A LS+EQL+YAA D +L L + ++L+ Sbjct: 138 ADWRARPLSEEQLRYAAEDADYLLRLYDKLRKELE 172 |
This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. Length = 172 |
>gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease | Back alignment and domain information |
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Score = 112 bits (283), Expect = 6e-26 Identities = 56/152 (36%), Positives = 81/152 (53%), Gaps = 1/152 (0%) Query: 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIF 79 +A+DTET GL +L ++Q+S II A + L +L DE K+ Sbjct: 21 GGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVG 80 Query: 80 HYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139 H +FD+ VL FG+ + +F T +A+ L ++HGL LKE LG+ + K +Q SD Sbjct: 81 HNAKFDLHVL-ARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSD 139 Query: 140 WSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 W A LS+EQLQYAA D L L + ++L Sbjct: 140 WGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 |
3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes. Length = 172 |
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease | Back alignment and domain information |
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Score = 105 bits (262), Expect = 1e-23 Identities = 48/155 (30%), Positives = 69/155 (44%), Gaps = 4/155 (2%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 +A DTET GL R +L +Q++ I +++ L +L DE K+ H Sbjct: 1 KEVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGH 60 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 +FD+ VL +F T +A+ L H L D KE LGI + K +Q Sbjct: 61 DAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGK 120 Query: 141 S----ADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 A LS+E L+YAA D L L + E+L Sbjct: 121 GAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155 |
The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).. Length = 155 |
>gnl|CDD|130455 TIGR01388, rnd, ribonuclease D | Back alignment and domain information |
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Score = 92.5 bits (230), Expect = 7e-20 Identities = 55/194 (28%), Positives = 92/194 (47%), Gaps = 14/194 (7%) Query: 7 HEGDIPAEC-AARYVDAIAVDTETLGLMPRRDR-----LCIVQLSPGDGTVDIIRIAAGQ 60 + ++ C A R +A+DTE + R+R L ++Q++ G+ I + Sbjct: 4 TDDELATVCEAVRTFPFVALDTEFV-----RERTFWPQLGLIQVADGEQLALIDPLVIID 58 Query: 61 KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLK 120 + L +L DE K+ H D+ V FG +P+F T+IA+ + G Sbjct: 59 WSP--LKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFC-GFGMSMGYA 115 Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 ++E+LG+ + K++ +DW A L+D QL+YAA+DV +L L + E+L+ GR Sbjct: 116 KLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWL 175 Query: 181 TSCCNFLMDRAELD 194 C L DR Sbjct: 176 EEECTLLTDRRTYV 189 |
This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. Length = 367 |
>gnl|CDD|182762 PRK10829, PRK10829, ribonuclease D; Provisional | Back alignment and domain information |
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Score = 57.3 bits (139), Expect = 3e-09 Identities = 50/176 (28%), Positives = 82/176 (46%), Gaps = 5/176 (2%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKR 75 AAR AIA+DTE + +L ++QL G+ + +I +P +L D + Sbjct: 18 AARAFPAIALDTEFVRTRTYYPQLGLIQLYDGE-QLSLIDPLGITDWSP-FKALLRDPQV 75 Query: 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKI-ASRLTRTYTNQHGLKDNLKELLGINISKA 134 K H G D+ V FG +P+ T+I A+ R + G ++E G+ + K+ Sbjct: 76 TKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLS--CGFASMVEEYTGVTLDKS 133 Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 + +DW A LS+ Q +YAA+DV +L + + + + G A C L R Sbjct: 134 ESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQR 189 |
Length = 373 |
>gnl|CDD|176656 cd09018, DEDDy_polA_RNaseD_like_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins | Back alignment and domain information |
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Score = 56.1 bits (135), Expect = 6e-09 Identities = 38/153 (24%), Positives = 63/153 (41%), Gaps = 8/153 (5%) Query: 22 AIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLV-DEKREKIFH 80 A DTET L L ++QL+ G +I + A A L+ L+ DEK K+ Sbjct: 1 VFAFDTETDSLDNISANLVLIQLAIEPGVAALIPV-AHDYLALELLKPLLEDEKALKVGQ 59 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINI--SKAQQSS 138 ++D +L F F T + + + + + + ++ LG + ++ Sbjct: 60 NLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGK 119 Query: 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 W L++EQ +YAA D LQ KL Sbjct: 120 LWFNQPLTEEQGRYAAEDADVT----LQIHLKL 148 |
DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity. Length = 150 |
>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins | Back alignment and domain information |
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Score = 54.6 bits (132), Expect = 2e-08 Identities = 41/183 (22%), Positives = 78/183 (42%), Gaps = 26/183 (14%) Query: 11 IPAECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGM- 69 A + I +D E + + R+ +LC+VQ++ G + + I ++V + Sbjct: 1 KEAIIHLKKQKVIGLDCEGVN-LGRKGKLCLVQIATRTGQIYLFDILKL----GSIVFIN 55 Query: 70 -----LVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIA-----SRLTRTYT--NQH 117 L +K K+ H R D L++ +G+++ VF T++A + T + Sbjct: 56 GLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVI 115 Query: 118 GLKDNLKELLGINISK--------AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 L L + L I+IS + W+ L+++ ++YAA DV+ L L + Sbjct: 116 SLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLD 175 Query: 170 KLQ 172 L Sbjct: 176 ALI 178 |
The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif. Length = 197 |
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional | Back alignment and domain information |
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Score = 53.2 bits (129), Expect = 5e-08 Identities = 37/161 (22%), Positives = 62/161 (38%), Gaps = 7/161 (4%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA-PNLVGMLVDEK 74 + A DTET L P + L + + G I + + L +L D Sbjct: 311 KLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370 Query: 75 REKIFHYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 +K+ ++D+ VL +G+ +R + F T +AS L +HGL + LG Sbjct: 371 IKKVGQNLKYDLHVL-ARYGIELRGIAFDTMLASYLLDP-GRRHGLDSLAERYLGHKTIS 428 Query: 134 AQQS--SDWSADDLSDEQL-QYAASDVVHLHALRLQFTEKL 171 ++ + + E+ +YAA D L KL Sbjct: 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKL 469 |
Length = 880 |
>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] | Back alignment and domain information |
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Score = 51.0 bits (122), Expect = 2e-07 Identities = 41/167 (24%), Positives = 63/167 (37%), Gaps = 11/167 (6%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN---LVGMLVD 72 IA DTET GL P L + ++ + I + G + L +L D Sbjct: 18 KLNAAANIAFDTETDGLDPHGADLVGLSVASEEEAA-YIPLLHGPEQLNVLAALKPLLED 76 Query: 73 EKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGI--- 129 E +K+ ++D VL G+ F T +AS L H L D K LG+ Sbjct: 77 EGIKKVGQNLKYDYKVL-ANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETI 135 Query: 130 ---NISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 +I+ + AD ++ +YAA D L +L + Sbjct: 136 TFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182 |
Length = 593 |
>gnl|CDD|37417 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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Score = 44.6 bits (105), Expect = 2e-05 Identities = 45/171 (26%), Positives = 73/171 (42%), Gaps = 7/171 (4%) Query: 20 VDAIAVDTETLGLMPRRDRLCIVQLS--PGDGTVDIIRIAAGQKNAPNLVGMLVDEKREK 77 V AVD E C++Q+S D +D ++ + + L + D K Sbjct: 212 VIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKL---RDHIGILNEVFSDPGIVK 268 Query: 78 IFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137 +FH DI L FG+ V +F T ASRL + L L+ + G+ +K Q Sbjct: 269 VFHGADTDIIWLQRDFGIYVVNLFDTIQASRLLGL--PRPSLAYLLECVCGVLTNKKYQL 326 Query: 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLM 188 +DW L +E ++YA D +L + ++L+RL + T + M Sbjct: 327 ADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDM 377 |
Length = 687 |
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases | Back alignment and domain information |
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Score = 40.3 bits (95), Expect = 4e-04 Identities = 34/165 (20%), Positives = 62/165 (37%), Gaps = 10/165 (6%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 D +A+ E LG + + L+ G G I + + L L DEK K+ H Sbjct: 4 DEVALYVELLGENYHTADIIGLALANGGGAY-YIPLELALLDLAALKEWLEDEKIPKVGH 62 Query: 81 YGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKA----- 134 + V G+ + V F T +A+ L + + L D K LG + Sbjct: 63 DAKRAY-VALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYG 121 Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 + + D+ + ++ A + L + E+L+ + +L Sbjct: 122 KGAKFAVPDE--EVLAEHLARKAAAIARLAPKLEEELEENEQLEL 164 |
Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases. Length = 178 |
>gnl|CDD|30697 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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Score = 218 bits (557), Expect = 7e-58 Identities = 81/203 (39%), Positives = 112/203 (55%), Gaps = 7/203 (3%) Query: 6 VHEGDIPAECAARY--VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA 63 + GD+ A A AIA+DTE + L RLC++Q+S G+G +I AG + Sbjct: 1 ITTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEGA-SLIDPLAGILDL 59 Query: 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNL 123 P LV +L D KIFH RFD+ VL FG+ P+F T+IA++L T HGL D + Sbjct: 60 PPLVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLV 118 Query: 124 KELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSC 183 +ELLG+ + K++Q SDW A LS+ QL+YAA+DV +L L + TE+L R GR + A Sbjct: 119 EELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDE 178 Query: 184 CNFLMDRA---ELDLLGWENVDI 203 L R L W + I Sbjct: 179 FRLLPTRRTYKVLPEDAWREIKI 201 |
Length = 361 |
>gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins | Back alignment and domain information |
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Score = 67.9 bits (166), Expect = 2e-12 Identities = 35/141 (24%), Positives = 61/141 (43%), Gaps = 9/141 (6%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLS---PGDGTVDIIRIAAGQKNAPNLVGMLVDEKR-E 76 D IA D E + ++QL D + ++ + ML++ Sbjct: 14 DVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVD----WQGLKMLLENPSIV 69 Query: 77 KIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ 136 K H D+ L FG +++ +F T IA+ L + + L ++ LG + K+ Sbjct: 70 KALHGIEGDLWKLLRDFGEKLQRLFDTTIAANL-KGLPERWSLASLVEHFLGKTLDKSIS 128 Query: 137 SSDWSADDLSDEQLQYAASDV 157 +DWS L+++Q YAA+DV Sbjct: 129 CADWSYRPLTEDQKLYAAADV 149 |
The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif. Length = 161 |
>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar proteins | Back alignment and domain information |
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Score = 62.2 bits (152), Expect = 9e-11 Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 3/123 (2%) Query: 36 RDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95 R+++ ++QL+ + + ++A K P+L +L D K+ + D L FG+ Sbjct: 36 RNKVALLQLA-TESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGI 94 Query: 96 RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLG--INISKAQQSSDWSADDLSDEQLQYA 153 VR V ++ L ++E+LG ++ K + S+W A LS EQ+ YA Sbjct: 95 EVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYA 154 Query: 154 ASD 156 A+D Sbjct: 155 ATD 157 |
WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability. Length = 170 |
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases | Back alignment and domain information |
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Score = 49.1 bits (118), Expect = 9e-07 Identities = 38/154 (24%), Positives = 59/154 (38%), Gaps = 20/154 (12%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA--GQKNAPN------LVGMLVD 72 A DTET L P + L + + G I + G + P L +L D Sbjct: 6 KVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLED 65 Query: 73 EKREKIFHYGRFDIAVLFYTFGVRVRPVFC-TKIASRLTRTYTNQHGLKDNLKELLG--- 128 +K+ +FD+ VL G+ +R T +AS L +HGL D + LG Sbjct: 66 PSIKKVGQNLKFDLHVL-ANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKT 124 Query: 129 INISK-----AQQSSDWSADDLSDEQLQYAASDV 157 I+ +Q + ++ +YAA D Sbjct: 125 ISFEDLVGKGKKQITF--DQVPLEKAAEYAAEDA 156 |
Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. Length = 193 |
>gnl|CDD|99850 cd06147, Rrp6p_like_exo, DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins | Back alignment and domain information |
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Score = 45.3 bits (108), Expect = 1e-05 Identities = 40/142 (28%), Positives = 63/142 (44%), Gaps = 19/142 (13%) Query: 23 IAVDTET------LGLMPRRDRLCIVQLSP--GDGTVDIIRIAAGQKNAPNLVGMLVDEK 74 IAVD E LG C++Q+S D VD +++ + + L + D Sbjct: 27 IAVDLEHHSYRSYLGFT------CLMQISTREEDYIVDTLKL---RDDMHILNEVFTDPN 77 Query: 75 REKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134 K+FH DI L FG+ V +F T A+R+ +H L L++ ++ K Sbjct: 78 ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNL--PRHSLAYLLQKYCNVDADKK 135 Query: 135 QQSSDWSADDLSDEQLQYAASD 156 Q +DW L +E ++YA D Sbjct: 136 YQLADWRIRPLPEEMIKYARED 157 |
Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome. Length = 192 |
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional | Back alignment and domain information |
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Score = 52.3 bits (126), Expect = 1e-07 Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 3/86 (3%) Query: 91 YTFGVRVRPVFCTKIASRLTRTYTN--QHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148 GVRV +AS+L L LG + K Q+S S D +E Sbjct: 63 LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEE 121 Query: 149 QLQYAASDVVHLHALRLQFTEKLQRL 174 QL YAA+D L L ++L R+ Sbjct: 122 QLLYAAADADVLLELYAVLADQLNRI 147 |
Length = 553 |
>gnl|CDD|176655 cd06146, mut-7_like_exo, DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins | Back alignment and domain information |
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Score = 44.6 bits (106), Expect = 2e-05 Identities = 17/40 (42%), Positives = 26/40 (65%) Query: 117 HGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASD 156 GL D ++E+LG + K++Q S+W L +EQ+ YAA D Sbjct: 141 KGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALD 180 |
The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Length = 193 |
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | ||
COG0349 | 361 | Rnd Ribonuclease D [Translation, ribosomal structure an | 100.0 | |
TIGR01388 | 374 | rnd ribonuclease D; InterPro: IPR006292 These proteins | 100.0 | |
PRK10829 | 373 | ribonuclease D; Provisional | 100.0 | |
cd06142 | 178 | RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme | 100.0 | |
cd06147 | 192 | Rrp6p_like_exo Yeast Rrp6p and its human homolog, the P | 100.0 | |
cd06148 | 197 | Egl_like_exo The Egalitarian (Egl) protein subfamily is | 100.0 | |
cd06139 | 193 | DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain | 100.0 | |
PRK07556 | 977 | consensus | 100.0 | |
PRK06887 | 954 | consensus | 100.0 | |
PRK05755 | 889 | DNA polymerase I; Provisional | 100.0 | |
PRK07997 | 928 | consensus | 100.0 | |
PRK07456 | 975 | consensus | 100.0 | |
PRK07625 | 922 | consensus | 100.0 | |
PRK08786 | 927 | consensus | 100.0 | |
PRK08835 | 931 | consensus | 99.98 | |
cd06140 | 178 | DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilu | 99.97 | |
PRK07898 | 902 | consensus | 99.97 | |
PRK05797 | 869 | consensus | 99.97 | |
PRK08434 | 887 | consensus | 99.96 | |
PRK08076 | 877 | consensus | 99.96 | |
PRK05929 | 870 | consensus | 99.95 | |
PRK08928 | 861 | consensus | 99.93 | |
COG0749 | 593 | PolA DNA polymerase I - 3'-5' exonuclease and polymeras | 99.92 | |
PRK07300 | 880 | consensus | 99.86 | |
PRK06309 | 232 | DNA polymerase III subunit epsilon; Validated | 99.41 | |
TIGR01405 | 1264 | polC_Gram_pos DNA polymerase III, alpha subunit, Gram-p | 99.19 | |
COG2176 | 1444 | PolC DNA polymerase III, alpha subunit (gram-positive t | 98.97 | |
cd06129 | 159 | RNaseD_like The RNase D-like group is composed of RNase | 100.0 | |
pfam01612 | 172 | 3_5_exonuc 3'-5' exonuclease. This domain is responsibl | 100.0 | |
smart00474 | 172 | 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofread | 100.0 | |
cd06146 | 191 | mut-7_like_exo The mut-7 subfamily is composed of Caeno | 100.0 | |
cd06141 | 168 | WRN_exo WRN is a unique RecQ DNA helicase exhibiting an | 100.0 | |
cd00007 | 155 | 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsi | 100.0 | |
cd06128 | 166 | DNA_polA_exo The 3'-5' exonuclease domain of family-A D | 99.98 | |
KOG2206 | 687 | consensus | 99.94 | |
cd06126 | 181 | DEDDy DEDDy exonucleases, part of the DnaQ-like (or DED | 99.78 | |
KOG2207 | 617 | consensus | 99.77 | |
KOG4373 | 319 | consensus | 99.38 | |
PRK07740 | 240 | hypothetical protein; Provisional | 99.31 | |
PRK06310 | 250 | DNA polymerase III subunit epsilon; Validated | 99.28 | |
PRK06631 | 229 | consensus | 99.28 | |
PRK07942 | 234 | DNA polymerase III subunit epsilon; Provisional | 99.22 | |
PRK08074 | 932 | bifunctional ATP-dependent DNA helicase/DNA polymerase | 99.16 | |
PRK06022 | 234 | consensus | 99.14 | |
PRK08517 | 259 | DNA polymerase III subunit epsilon; Provisional | 99.14 | |
PRK08858 | 246 | consensus | 99.13 | |
PRK07246 | 820 | bifunctional ATP-dependent DNA helicase/DNA polymerase | 99.13 | |
PRK07009 | 241 | consensus | 99.12 | |
PRK05711 | 240 | DNA polymerase III subunit epsilon; Provisional | 99.09 | |
PRK08816 | 244 | consensus | 99.08 | |
cd06131 | 167 | DNA_pol_III_epsilon_Ecoli_like This subfamily is compos | 99.07 | |
PRK06807 | 313 | DNA polymerase III subunit epsilon; Validated | 99.07 | |
PRK07982 | 243 | consensus | 99.02 | |
TIGR01406 | 246 | dnaQ_proteo DNA polymerase III, epsilon subunit; InterP | 99.01 | |
cd06134 | 189 | RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribon | 99.01 | |
PRK00448 | 1436 | polC DNA polymerase III PolC; Validated | 99.01 | |
PRK07883 | 575 | hypothetical protein; Validated | 98.99 | |
PRK06859 | 253 | consensus | 98.99 | |
PRK05168 | 213 | ribonuclease T; Provisional | 98.98 | |
PRK09145 | 203 | DNA polymerase III subunit epsilon; Validated | 98.97 | |
cd06127 | 159 | DEDDh DEDDh exonucleases, part of the DnaQ-like (or DED | 98.9 | |
TIGR01407 | 944 | dinG_rel DnaQ family exonuclease/DinG family helicase, | 98.85 | |
cd06144 | 152 | REX4_like This subfamily is composed of RNA exonuclease | 98.84 | |
PRK09146 | 239 | DNA polymerase III subunit epsilon; Validated | 98.83 | |
PRK06063 | 313 | DNA polymerase III subunit epsilon; Provisional | 98.8 | |
pfam00929 | 162 | Exonuc_X-T Exonuclease. This family includes a variety | 98.79 | |
smart00479 | 169 | EXOIII exonuclease domain in DNA-polymerase alpha and e | 98.77 | |
PRK07247 | 195 | DNA polymerase III subunit epsilon; Validated | 98.67 | |
PRK06195 | 309 | DNA polymerase III subunit epsilon; Validated | 98.6 | |
cd06137 | 161 | DEDDh_RNase This group is composed of eukaryotic exorib | 98.58 | |
KOG2249 | 280 | consensus | 98.5 | |
cd06130 | 156 | DNA_pol_III_epsilon_like This subfamily is composed of | 98.4 | |
cd06138 | 183 | ExoI_N This subfamily is composed of the N-terminal dom | 98.35 | |
cd06149 | 157 | ISG20 Interferon (IFN) Stimulated Gene product of 20 kD | 98.34 | |
cd06145 | 150 | REX1_like This subfamily is composed of RNA exonuclease | 98.29 | |
KOG2405 | 458 | consensus | 98.24 | |
PRK07983 | 219 | exodeoxyribonuclease X; Provisional | 98.21 | |
cd06133 | 176 | ERI-1_3'hExo_like This subfamily is composed of Caenorh | 98.19 | |
cd05781 | 188 | DNA_polB_B3_exo The 3'-5' exonuclease domain of archaea | 98.15 | |
COG0847 | 243 | DnaQ DNA polymerase III, epsilon subunit and related 3' | 98.1 | |
COG3359 | 278 | Predicted exonuclease [DNA replication, recombination, | 97.88 | |
TIGR00573 | 228 | dnaq exonuclease, DNA polymerase III, epsilon subunit f | 97.8 | |
cd05780 | 195 | DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of | 97.76 | |
cd05160 | 200 | DNA_polB_exo The 3'-5' exonuclease domain of family-B D | 97.74 | |
cd05785 | 207 | DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease | 97.42 | |
PRK05762 | 785 | DNA polymerase II; Reviewed | 97.37 | |
cd05784 | 193 | DNA_polB_II_exo The 3'-5' exonuclease domain of Escheri | 97.08 | |
PRK11779 | 477 | sbcB exonuclease I; Provisional | 96.51 | |
PTZ00166 | 1081 | DNA polymerase delta catalytic subunit; Provisional | 96.46 | |
TIGR01298 | 201 | RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease | 94.58 | |
cd05783 | 204 | DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolo | 92.7 | |
TIGR00593 | 1005 | pola DNA polymerase I; InterPro: IPR002298 DNA carries | 99.52 | |
KOG1275 | 1118 | consensus | 97.24 | |
cd06125 | 130 | DnaQ_like_exo The DnaQ-like exonuclease superfamily is | 99.05 | |
PRK09182 | 293 | DNA polymerase III subunit epsilon; Validated | 97.57 | |
pfam04857 | 235 | CAF1 CAF1 family ribonuclease. The major pathways of mR | 97.48 | |
KOG2405 | 458 | consensus | 96.66 | |
cd06136 | 177 | TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 a | 98.55 | |
cd06143 | 174 | PAN2_exo PAN2 is the catalytic subunit of poly(A) nucle | 98.28 | |
KOG3657 | 1075 | consensus | 97.69 | |
cd05779 | 204 | DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eu | 97.55 | |
cd05782 | 208 | DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease | 97.01 | |
KOG2248 | 380 | consensus | 96.74 | |
cd05777 | 230 | DNA_polB_delta_exo The 3'-5' exonuclease domain of euka | 96.7 | |
cd05776 | 234 | DNA_polB_alpha_exo The 3'-5' exonuclease domain of euka | 95.21 | |
smart00486 | 471 | POLBc DNA polymerase type-B family. DNA polymerase alph | 94.25 | |
PRK06722 | 242 | exonuclease; Provisional | 94.77 | |
cd06135 | 173 | Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3 | 92.78 |
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
---|
Probab=100.00 E-value=0 Score=349.01 Aligned_cols=198 Identities=42% Similarity=0.644 Sum_probs=180.1 Q ss_pred CCCCCCHH-H-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCH Q ss_conf 25788857-8-424898279971777898544507999984189428997465778570677677732364023010000 Q gi|254780636|r 7 HEGDIPAE-C-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRF 84 (207) Q Consensus 7 ~~~dl~~~-~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~ 84 (207) T Consensus 2 ~~~~~l~~~~~~~~~~~~iAIDTEf~r~~t~~p~LcLIQi~~~e~-~~lIdp~~~~~d~~~l~~Ll~d~~v~KIfHaa~~ 80 (361) T COG0349 2 TTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEG-ASLIDPLAGILDLPPLVALLADPNVVKIFHAARF 80 (361) T ss_pred CCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCEEEEEEECCCC-CEEECCCCCCCCCCHHHHHHCCCCEEEEECCCCC T ss_conf 742679999997428980798322246643688337999844888-6686226554666369998628760255025635 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 16888654200000004578988652110000008877765420024675200365654432368999986459999999 Q gi|254780636|r 85 DIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 85 D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 81 DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~ 159 (361) T COG0349 81 DLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLY 159 (361) T ss_pred CHHHHHHHCCCCCCCHHHHHHHHHHCCCCC-CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 199999861888773468999999809863-2329999999968853644454655557999999999999999999999 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHH--HH-HHHCCCCCCCCCCCC Q ss_conf 99999999749189999999640068--99-986679888844359 Q gi|254780636|r 165 LQFTEKLQRLGRSDLATSCCNFLMDR--AE-LDLLGWENVDIFSHS 207 (207) Q Consensus 165 ~~l~~~L~~~~~~~~~~~e~~~l~~~--~~-me~~g~~~~~~~~~~ 207 (207) T Consensus 160 ~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~~~~~~w~~i~~-a~~ 204 (361) T COG0349 160 DKLTEELAREGRLEWAEDEFRLLPTRRTYKVLPEDAWREIKI-AHS 204 (361) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH-HHC T ss_conf 999999987485499999999731023455681767888666-504 |
|
>TIGR01388 rnd ribonuclease D; InterPro: IPR006292 These proteins represent ribonuclease D, a 3-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo | Back alignment and domain information |
---|
Probab=100.00 E-value=0 Score=328.40 Aligned_cols=186 Identities=30% Similarity=0.479 Sum_probs=168.8 Q ss_pred CCCCCCHHHH-CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHH Q ss_conf 2578885784-248982799717778985445079999841894289974657785706776777323640230100001 Q gi|254780636|r 7 HEGDIPAECA-ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFD 85 (207) Q Consensus 7 ~~~dl~~~~~-l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D 85 (207) T Consensus 4 ~~~~La~~c~~~~~~p~valDTEF~R~~TFwP~LgLiQ~a~g~~~~LIDPL~~~~-~~~Pl~~lL~d~~v~KvlHAaseD 82 (374) T TIGR01388 4 TDDELATVCEALRTEPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIDI-DLSPLLELLADESVVKVLHAASED 82 (374) T ss_pred CHHHHHHHHHHHCCCCEEECCCCEECCCCCCHHHCCEECCCCCEEEEECCCCCCC-CHHHHHHHHHCCCCEEEECCCCHH T ss_conf 6688999998614788374155411265320204003113787568765888752-347999997389815853045047 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 68886542000000045789886521100000088777654200246752003656544323689999864599999999 Q gi|254780636|r 86 IAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRL 165 (207) Q Consensus 86 ~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~ 165 (207) T Consensus 83 lEvF~~l~g~lP~PLfDTQi~Aa~~-G~g~s~gY~~LV~~~~~v~LdKse~rtDW~~RPLtd~Ql~YAaaDV~yL~~~y~ 161 (374) T TIGR01388 83 LEVFLNLFGVLPKPLFDTQIAAAFL-GFGESMGYDKLVQEVLGVELDKSETRTDWLARPLTDKQLEYAAADVTYLLPLYE 161 (374) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCHHHHHHHHHHHCEECCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 9999987057988830588999983-678521089999997370317888722210478987789999999999999999 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999997491899999996400689998 Q gi|254780636|r 166 QFTEKLQRLGRSDLATSCCNFLMDRAELD 194 (207) Q Consensus 166 ~l~~~L~~~~~~~~~~~e~~~l~~~~~me 194 (207) T Consensus 162 ~L~~~l~~~~R~~~l~ee~~~~~~~~~~~ 190 (374) T TIGR01388 162 KLTERLAEEGRLAWLEEECELLTDRRTYD 190 (374) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99999988645999972059873024207 |
Members of this family are restricted to the Proteobacteria; Aquifex, Mycobacteria and eukaryotes. Ribonuclease D is not essential in Escherichia coli but is deleterious when overexpressed. The precise biological role of ribonuclease D is still unknown. ; GO: 0004540 ribonuclease activity, 0008033 tRNA processing, 0005737 cytoplasm. |
>PRK10829 ribonuclease D; Provisional | Back alignment and domain information |
---|
Probab=100.00 E-value=0 Score=323.69 Aligned_cols=185 Identities=24% Similarity=0.344 Sum_probs=166.7 Q ss_pred CCEEECCC--CCCHHHH-CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEE Q ss_conf 72153257--8885784-24898279971777898544507999984189428997465778570677677732364023 Q gi|254780636|r 2 TTIRVHEG--DIPAECA-ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKI 78 (207) Q Consensus 2 ~~~~~~~~--dl~~~~~-l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV 78 (207) T Consensus 1 m~y~~I~t~~~L~~~~~~l~~~~~iavDTEf~r~~ty~p~l~LiQi~~~~~~~lIDpl~-~-~dl~~l~~ll~~~~i~kv 78 (373) T PRK10829 1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEQLALIDPLG-I-TDWSPFKALLRDPSITKF 78 (373) T ss_pred CEEEEECCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCEEEEECCC-C-CCHHHHHHHHCCCCCEEE T ss_conf 91599798999999999970799189857745677789845899985189679994787-7-776999999709884165 Q ss_pred ECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHH Q ss_conf 01000016888654200000004578988652110000008877765420024675200365654432368999986459 Q gi|254780636|r 79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV 158 (207) Q Consensus 79 ~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~ 158 (207) T Consensus 79 ~Haa~qDle~l~~~~g~~p~~iFDTQiAa~~l-g~~~~~gy~~Lv~~~l~v~l~K~~~~sDW~~RPLs~~ql~YA~~DV~ 157 (373) T PRK10829 79 LHAGSEDLEVFLNAFGELPQPLIDTQILAAFC-GRPLSWGFASMVEEYSGVALDKSESRTDWLARPLSERQCEYAAADVW 157 (373) T ss_pred EECCCCHHHHHHHHCCCCCCHHHHHHHHHHHC-CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 20642159999998198874077648899865-78655589999999939665666462757889999899999999999 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9999999999999974918999999964006 Q gi|254780636|r 159 HLHALRLQFTEKLQRLGRSDLATSCCNFLMD 189 (207) Q Consensus 159 ~l~~L~~~l~~~L~~~~~~~~~~~e~~~l~~ 189 (207) T Consensus 158 yL~~l~~~L~~~l~~~~r~~w~~eE~~~l~~ 188 (373) T PRK10829 158 YLLPIAAKLMVETEAAGWLPAALDECRLMQQ 188 (373) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 9999999999999835755899999999972 |
|
>cd06142 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA | Back alignment and domain information |
---|
Probab=100.00 E-value=0 Score=313.18 Aligned_cols=175 Identities=36% Similarity=0.526 Sum_probs=160.5 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHH Q ss_conf 88578-42489827997177789854450799998418942899746577857067767773236402301000016888 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVL 89 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L 89 (207) T Consensus 2 l~~~~~~l~~~~~i~~DtE~~~~~~~~~~l~LiQia~~~-~~ylid~~~~~-~~~~L~~lL~d~~i~KVgh~~~~Dl~~L 79 (178) T cd06142 2 LADLCERLAGAGVIAVDTEFMRLRTYYPRLCLIQISTGG-QAYLIDPLAIG-DLSPLKELLADPNIVKVFHAAREDLELL 79 (178) T ss_pred HHHHHHHHCCCCEEEEECCCCCCCCCCCEEEEEEEEECC-CEEEEECCCCC-CHHHHHHHHCCCCCEEEEEEHHHHHHHH T ss_conf 899999970799489989867885588728999998689-06999531234-4699999975999439996279999999 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 65420000000457898865211000000887776542002467520036565443236899998645999999999999 Q gi|254780636|r 90 FYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 90 ~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) T Consensus 80 ~~~~~~~~~~v~Dt~ia~~~l~-~~~~~~L~~L~~~~lg~~l~K~~q~s~W~~rPLs~~qi~YAa~Da~~l~~l~~~l~~ 158 (178) T cd06142 80 KRDFGILPVNLFDTQIAARLLG-LGDSVGLAALVEELLGVELDKGEQRSDWLKRPLTDEQLEYAANDVRYLLPLYEKLKE 158 (178) T ss_pred HHHHCCCCCCEEEHHHHHHHCC-CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9973967654530899999828-867378999999992987777736466433678289999999979999999999999 Q ss_pred HHHHCCCHHHHHHHHHHHH Q ss_conf 9997491899999996400 Q gi|254780636|r 170 KLQRLGRSDLATSCCNFLM 188 (207) Q Consensus 170 ~L~~~~~~~~~~~e~~~l~ 188 (207) T Consensus 159 ~L~~~~~~~~~~~e~~~~~ 177 (178) T cd06142 159 ELEEEGRLEWAEEECELLL 177 (178) T ss_pred HHHHCCHHHHHHHHHHHCC T ss_conf 9998683999999998626 |
It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100 and the Drosophila melanogaster egalitarian protein. |
>cd06147 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs | Back alignment and domain information |
---|
Probab=100.00 E-value=0 Score=297.09 Aligned_cols=178 Identities=22% Similarity=0.237 Sum_probs=153.9 Q ss_pred CCCCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHH Q ss_conf 57888578-42489827997177789854450799998418942899746577857067767773236402301000016 Q gi|254780636|r 8 EGDIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDI 86 (207) Q Consensus 8 ~~dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~ 86 (207) T Consensus 11 ~~~L~~~~~~L~~~~~ialDtE~~~~~~~~~~l~LiQiat~~~~-yliD~l~l~~~~~~L~~ll~~~~I~KV~H~~~~Dl 89 (192) T cd06147 11 EEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREED-YIVDTLKLRDDMHILNEVFTDPNILKVFHGADSDI 89 (192) T ss_pred HHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEECCCCC-EEEEECCCCCCHHHHHHHHCCCCEEEEEECHHHHH T ss_conf 99999999998269969997973788569982799999509988-79874343003799999975988379985578779 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 88865420000000457898865211000000887776542002467520036565443236899998645999999999 Q gi|254780636|r 87 AVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQ 166 (207) Q Consensus 87 ~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~ 166 (207) T Consensus 90 ~~L~~~~gi~~~n~fDT~iaa~~l~~--~~~sL~~Lv~~~lg~~l~K~~q~SdW~~RPLs~~Ql~YAA~Dv~~Ll~ly~~ 167 (192) T cd06147 90 IWLQRDFGLYVVNLFDTGQAARVLNL--PRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDR 167 (192) T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 99999858987660428999998488--8111999999993958873231143799989999999999999999999999 Q ss_pred HHHHHHHCC-CHHHHHHHHHHHH Q ss_conf 999999749-1899999996400 Q gi|254780636|r 167 FTEKLQRLG-RSDLATSCCNFLM 188 (207) Q Consensus 167 l~~~L~~~~-~~~~~~~e~~~l~ 188 (207) T Consensus 168 L~~~L~e~~~~~~~~~~~~~~~~ 190 (192) T cd06147 168 LRNELLERANALAPNLLESVLNC 190 (192) T ss_pred HHHHHHHHHCCCHHHHHHHHHHH T ss_conf 99999984286416788999972 |
Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome. |
>cd06148 Egl_like_exo The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins | Back alignment and domain information |
---|
Probab=100.00 E-value=3.1e-43 Score=270.53 Aligned_cols=169 Identities=24% Similarity=0.319 Sum_probs=147.3 Q ss_pred HHHCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC--CHHHHHHHHCCCCCEEECCCCHHHHHHHH Q ss_conf 7842489827997177789854450799998418942899746577857--06776777323640230100001688865 Q gi|254780636|r 14 ECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN--APNLVGMLVDEKREKIFHYGRFDIAVLFY 91 (207) Q Consensus 14 ~~~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~--~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~ 91 (207) T Consensus 4 i~~L~~~~vi~iD~E~~~~~~~-g~l~LiQiat~~~~vyl~D~~~~~~~~~~~~Lk~iLe~~~I~KV~H~~r~D~~~L~~ 82 (197) T cd06148 4 IIHLKKQKVIGLDCEGVNLGRK-GKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYH 82 (197) T ss_pred HHHHHHCCEEEEECCCCCCCCC-CCEEEEEEEECCCCEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHH T ss_conf 9998759999998886788989-988799996489988999616676344568999995699823999610999999999 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHC-------CCHHHHHHHHHHHCCCCCCC--------CEECCCCCCCCCHHHHHHHHHH Q ss_conf 42000000045789886521100-------00008877765420024675--------2003656544323689999864 Q gi|254780636|r 92 TFGVRVRPVFCTKIASRLTRTYT-------NQHGLKDNLKELLGINISKA--------QQSSDWSADDLSDEQLQYAASD 156 (207) Q Consensus 92 ~~gi~~~~i~DT~ias~l~~~~~-------~~~~L~~L~~~~lg~~ldK~--------~q~SdW~~rpLs~~Qi~YAA~D 156 (207) T Consensus 83 ~~gi~~~nvfDTqiA~~ll~~~~~~~~~~~~~~sl~~l~~~~l~~~~~~~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~D 162 (197) T cd06148 83 QYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALD 162 (197) T ss_pred HHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH T ss_conf 70997067031999999975313147677564159999999957640177877888750655446799999999999998 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 599999999999999974918999999 Q gi|254780636|r 157 VVHLHALRLQFTEKLQRLGRSDLATSC 183 (207) Q Consensus 157 v~~l~~L~~~l~~~L~~~~~~~~~~~e 183 (207) T Consensus 163 V~yL~~L~~~L~~~Li~~~~~~~~~~~ 189 (197) T cd06148 163 VLCLLPLYYAMLDALISKFLKAVFKYL 189 (197) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999999998 |
Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. |
>cd06139 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity | Back alignment and domain information |
---|
Probab=100.00 E-value=3.1e-38 Score=241.43 Aligned_cols=174 Identities=25% Similarity=0.275 Sum_probs=150.3 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC--------CHHHHHHHHCCCCCEEECCCCHHHHH Q ss_conf 2489827997177789854450799998418942899746577857--------06776777323640230100001688 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN--------APNLVGMLVDEKREKIFHYGRFDIAV 88 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~--------~~~L~~ll~d~~i~KV~Hn~~~D~~~ 88 (207) T Consensus 2 l~~~~~ia~DtETtgl~~~~~~ivGisls~~~~~~~YiP~~h~~~~~~l~~~~v~~~lk~~led~~i~Kv~hn~k~D~~~ 81 (193) T cd06139 2 LEKAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHV 81 (193) T ss_pred CCCCCEEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCHHHHHH T ss_conf 75598789978369998688849999998079968998723656544679999999999997399986887547978999 Q ss_pred HHHHHHCCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC-------CCCCEECCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 86542000000-04578988652110000008877765420024-------67520036565443236899998645999 Q gi|254780636|r 89 LFYTFGVRVRP-VFCTKIASRLTRTYTNQHGLKDNLKELLGINI-------SKAQQSSDWSADDLSDEQLQYAASDVVHL 160 (207) Q Consensus 89 L~~~~gi~~~~-i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~l-------dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l 160 (207) T Consensus 82 L~~~-gi~~~~~~~DTmiaa~ll~~~~~~~~L~~La~~~l~~~~~~~~~l~gkg~~~~~~~~~~~-~~~~~YAa~Da~~t 159 (193) T cd06139 82 LANH-GIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADIT 159 (193) T ss_pred HHHC-CCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCCCCHHHCCH-HHHHHHHHHHHHHH T ss_conf 9983-986678302189999872799888899999999818876638998377855378313329-99999999999999 Q ss_pred HHHHHHHHHHHHHC-CCHHHHHH-HHHHHHHHHH Q ss_conf 99999999999974-91899999-9964006899 Q gi|254780636|r 161 HALRLQFTEKLQRL-GRSDLATS-CCNFLMDRAE 192 (207) Q Consensus 161 ~~L~~~l~~~L~~~-~~~~~~~~-e~~~l~~~~~ 192 (207) T Consensus 160 ~~L~~~l~~~L~~~~~l~~ly~~iE~PL~~VLa~ 193 (193) T cd06139 160 LRLYELLKPKLKEEPGLLELYEEIEMPLIPVLAE 193 (193) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCC T ss_conf 9999999999984220999999984569998279 |
E.coli-like Polymerase I (pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. E. coli DNA pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. |
>PRK07556 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=4.1e-35 Score=223.29 Aligned_cols=190 Identities=23% Similarity=0.203 Sum_probs=160.7 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC------------------CHHHHHHHH Q ss_conf 88578-42489827997177789854450799998418942899746577857------------------067767773 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN------------------APNLVGMLV 71 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~------------------~~~L~~ll~ 71 (207) T Consensus 377 L~~li~~l~~~~~~a~DtETtsld~~~a~lVGisls~~~~~a~YIPl~h~~~~~~~~~~~~~~~ql~~~~vL~~LkplLe 456 (977) T PRK07556 377 LKAWIARARETGIVAFDTETTSLDPMQAELVGFSLALAPGRACYIPLGHKSGDGDLFGGGLAEGQIPLRDALAALKPVLE 456 (977) T ss_pred HHHHHHHHHHCCEEEEEEECCCCCHHHCCEEEEEEEECCCCEEEEECCCCCCCCCHHCCCCCHHHCCHHHHHHHHHHHHC T ss_conf 99999998767958999731887830155357999806897899961444564201102222323059999999898853 Q ss_pred CCCCCEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC-------CCCEECCCCCCC Q ss_conf 2364023010000168886542000000045789886521100000088777654200246-------752003656544 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINIS-------KAQQSSDWSADD 144 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ld-------K~~q~SdW~~rp 144 (207) T Consensus 457 d~~i~KighnlK~d~~vL~~~-gi~l~~i~DtmLaaYLLdp~~~~~~Ld~La~~yL~~~~~~~~dl~g~gk~~~~f~~v~ 535 (977) T PRK07556 457 DPSVLKIGQNMKYDALVLARH-GITVAPFDDTMLISYALDAGRGGHGMDALSERWLGHTPIAYKDLTGSGKSAITFDQVD 535 (977) T ss_pred CCCHHHHHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCHHCCCCCCCCCCHHHHH T ss_conf 873114441256889999976-9602685318888888348866478799999964887621000034550104765520 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 32368999986459999999999999997491899999-996400689998667988884 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 536 ~-~~~~~YaaedA~~t~~L~~~L~~~L~~~~l~~Ly~~IE~PLi~VLa~ME~~GI~-vD~ 593 (977) T PRK07556 536 I-DRATAYAAEDADVTLRLWQVLKPRLAAEGLTTVYERLERPLVPVLARMEERGIS-VDR 593 (977) T ss_pred H-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 6-899999999999999999999999984235789999997899999999856969-869 |
|
>PRK06887 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=2e-33 Score=213.52 Aligned_cols=189 Identities=21% Similarity=0.196 Sum_probs=155.1 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCC---------------------------- Q ss_conf 88578-4248982799717778985445079999841894289974657785---------------------------- Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQK---------------------------- 61 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~---------------------------- 61 (207) T Consensus 346 l~~~~~~l~~~~~va~DtEt~~ld~~~a~lVGis~s~~~g~a~YiPl~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~ql~ 425 (954) T PRK06887 346 LTSWIEKLNQAKLIAVDTETDSLDYMSANLVGISFALENGEACYIPLAHKQQVAEQPQSDLFAEEAETQTDYLLAPKQLN 425 (954) T ss_pred HHHHHHHHHHCCEEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCCCHHHHHHCCCCHHHHHCCHHHCC T ss_conf 99999987637927999635998713266578999835897899864442100013200233200100122210232127 Q ss_pred ---CCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEE Q ss_conf ---706776777323640230100001688865420000000-4578988652110000008877765420024675200 Q gi|254780636|r 62 ---NAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137 (207) Q Consensus 62 ---~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~ 137 (207) T Consensus 426 ~~~vl~~Lkplled~~i~KIghNlK~dl~vL~~~-Gi~l~g~~fDTmLAaYLLdp-~~r~~Ld~LA~~yL~~~~i~~edl 503 (954) T PRK06887 426 KSTCLAALKPLLENPDIHKIGQNIKYDLTIFANH-GIELQGVAFDTMLESYTLNS-TGRHNMDDLAERYLGHETIAFESI 503 (954) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHCC-CCCCCHHHHHHHHCCCCCCCHHHH T ss_conf 9999999899852975022211478899999977-96247765169899875187-555788999999638865334642 Q ss_pred -------CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf -------3656544323689999864599999999999999974-91899999-996400689998667988884 Q gi|254780636|r 138 -------SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL-GRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 138 -------SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 504 ~gkGk~ql~f~~v~l-~~~~~YAaedA~itl~L~~~L~~~L~~~~~L~~Ly~~IE~PLi~VLa~ME~~GI~-vD~ 576 (954) T PRK06887 504 AGKGKNQLTFDQIPL-EQATEYAAEDADVTMKLHQVLWLELQKEPTLVKLYKTMELPLVHVLSRIERNGVL-IDS 576 (954) T ss_pred CCCCCCCCCHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEE-ECH T ss_conf 254433378443446-7999999999999999999999999854547899999997999999999973858-879 |
|
>PRK05755 DNA polymerase I; Provisional | Back alignment and domain information |
---|
Probab=100.00 E-value=2.4e-33 Score=213.04 Aligned_cols=189 Identities=23% Similarity=0.247 Sum_probs=159.1 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC-----CHHHHHHHHCCCCCEEECCCCH Q ss_conf 88578-42489827997177789854450799998418942899746577857-----0677677732364023010000 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN-----APNLVGMLVDEKREKIFHYGRF 84 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~-----~~~L~~ll~d~~i~KV~Hn~~~ 84 (207) T Consensus 309 l~~ll~~l~~~~~va~dtEttsld~~~a~lVGis~s~~~g~a~YIPl~~~~~~~~~~vl~~Lk~lLed~~i~KIghNlK~ 388 (889) T PRK05755 309 LEAWLAKLKKAGLVAFDTETTSLDPMSANLVGLSFAVEEGEAAYIPLAHDDQLDRDDALAALKPLLEDPAIPKVGQNLKY 388 (889) T ss_pred HHHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEEECCCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEECHHH T ss_conf 99999986528849999841788756576259999827996899844431336889999999999709887243203189 Q ss_pred HHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE------ECCCCCCCCCHHHHHHHHHHH Q ss_conf 1688865420000000-457898865211000000887776542002467520------036565443236899998645 Q gi|254780636|r 85 DIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ------SSDWSADDLSDEQLQYAASDV 157 (207) Q Consensus 85 D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q------~SdW~~rpLs~~Qi~YAA~Dv 157 (207) T Consensus 389 dl~vL~~~-GI~l~g~~fDTmLAaYLLdP~~~~~~Ld~La~~yL~~~~~~~eel~gkg~~~~~~~v~~-e~~~~YaaedA 466 (889) T PRK05755 389 DRHILANY-GIELRGIAFDTMLASYLLDPGAGRHDLDSLAERYLGHKTISFEEVAGKGNQLTFAQVAL-EEAAEYAAEDA 466 (889) T ss_pred HHHHHHHC-CEECCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCH-HHHHHHHHHHH T ss_conf 99999977-92357763019999987478877677899999863234420343136565566100787-89999999988 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHH-HHHHHHHHHHHHHCCCCCCC Q ss_conf 9999999999999997491899999-99640068999866798888 Q gi|254780636|r 158 VHLHALRLQFTEKLQRLGRSDLATS-CCNFLMDRAELDLLGWENVD 202 (207) Q Consensus 158 ~~l~~L~~~l~~~L~~~~~~~~~~~-e~~~l~~~~~me~~g~~~~~ 202 (207) T Consensus 467 ~~~~~L~~~L~~~L~~~~l~~Ly~~IE~PLi~VLa~ME~~GI~-VD 511 (889) T PRK05755 467 DVTLRLHQVLKPELEEEGLLELYEEIELPLVPVLARMERNGIK-VD 511 (889) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCEE-EC T ss_conf 6899999999999986047889999875199999999960868-66 |
|
>PRK07997 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=2.1e-33 Score=213.34 Aligned_cols=190 Identities=22% Similarity=0.219 Sum_probs=156.3 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC----------HHHHHHHHCCCCCEEE Q ss_conf 88578-424898279971777898544507999984189428997465778570----------6776777323640230 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA----------PNLVGMLVDEKREKIF 79 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~----------~~L~~ll~d~~i~KV~ 79 (207) T Consensus 339 l~~~~~~l~~~~~~a~DtEt~sld~~~a~lvGiS~s~~~g~a~YiPl~h~~l~~~~ql~~~~vl~~LkplLed~~i~KIg 418 (928) T PRK07997 339 LKAWIEKLKKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYLPVAHDYLDAPDQISRERVLELLKPLLEDEKALKVG 418 (928) T ss_pred HHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCEEEEECCCCEEEEECCCCCCCCHHHCCHHHHHHHHHHHHCCCCCCHHC T ss_conf 99999986429869999512786600024443389862774687402212347600124999999989875286530321 Q ss_pred CCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------CCEECCCCCCCCCHHHHH Q ss_conf 100001688865420000000-457898865211000000887776542002467-------520036565443236899 Q gi|254780636|r 80 HYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK-------AQQSSDWSADDLSDEQLQ 151 (207) Q Consensus 80 Hn~~~D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-------~~q~SdW~~rpLs~~Qi~ 151 (207) T Consensus 419 hnlK~d~~vL~~~-GI~l~gi~fDTmLAaYLLnp~~~~~~Ld~La~~yL~~~~i~~~el~gkgk~q~~f~~v~~-~~~~~ 496 (928) T PRK07997 419 QNLKFDRGILANY-GIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIAL-EEAGR 496 (928) T ss_pred CHHHHHHHHHHHC-CCEECCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHCCCCCCCCCHHHHHH-HHHHH T ss_conf 2168899999977-941056430345532222443344788999999713466433543244645477435359-99999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-CCCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 9986459999999999999997-491899999-996400689998667988884 Q gi|254780636|r 152 YAASDVVHLHALRLQFTEKLQR-LGRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 152 YAA~Dv~~l~~L~~~l~~~L~~-~~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 497 Ya~edA~~t~~L~~~L~~~L~~~~~l~~Ly~~IE~PLi~VLa~ME~~GI~-vD~ 549 (928) T PRK07997 497 YAAEDADVTLQLHLKMWPKLQQHKGPLNVFENIEMPLVPVLSRIERNGVK-IDP 549 (928) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 99999999999999999998621449999999998999999999853959-989 |
|
>PRK07456 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=3.1e-32 Score=206.56 Aligned_cols=177 Identities=25% Similarity=0.280 Sum_probs=148.3 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEE--CCCCEEEECCCCCCC--------CCHHHHHHHHCCCCCEEECCCCHHHHHH Q ss_conf 982799717778985445079999841--894289974657785--------7067767773236402301000016888 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSP--GDGTVDIIRIAAGQK--------NAPNLVGMLVDEKREKIFHYGRFDIAVL 89 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~--~~~~~~l~~~~~~~~--------~~~~L~~ll~d~~i~KV~Hn~~~D~~~L 89 (207) T Consensus 382 ~~~vA~DtETtsLdp~~A~lVGis~s~~~~~~~a~YIPl~h~~~~~~l~~~~vl~~LkpiLed~~i~KighNlKyD~~vL 461 (975) T PRK07456 382 EAPVAWDTETTSLNPRDAELVGIGCCWGEELDDLAYIPLGHQQAGEQLPLETVLEALRPWLESPEHPKALQNAKFDRLIL 461 (975) T ss_pred CCEEEEECCCCCCCHHHCCEEEEEEECCCCCCCEEEEECCCCCCHHHCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 76589980468877423210266641155787269977345561310579999999999862887531021114679999 Q ss_pred HHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC-------CCCCEECCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 65420000000-4578988652110000008877765420024-------675200365654432368999986459999 Q gi|254780636|r 90 FYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINI-------SKAQQSSDWSADDLSDEQLQYAASDVVHLH 161 (207) Q Consensus 90 ~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~l-------dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~ 161 (207) T Consensus 462 ~~~-GI~l~g~~fDTmLAsYLLnP-~~~h~Ld~La~~yL~~~~i~~edl~gkgk~---~~~v~~-~~~~~ya~~dA~~~~ 535 (975) T PRK07456 462 LRH-GIALKGVVFDTLLADYLLNP-EAKHNLDDLAQRELGFTPTSYKDLVGKGQT---FADVDI-ATASQYCGMDVYLTY 535 (975) T ss_pred HHC-CCCCCCCCCCHHHHHHHHCC-CCCCCHHHHHHHHHCCCCCCHHHHCCCCCC---CCCCCH-HHHHHHHHHHHHHHH T ss_conf 976-95106755139999987687-655898999999718887749986288876---020897-899999999999999 Q ss_pred HHHHHHHHHHHHCC--CHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 99999999999749--1899999-996400689998667988884 Q gi|254780636|r 162 ALRLQFTEKLQRLG--RSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 162 ~L~~~l~~~L~~~~--~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 536 ~L~~~l~~~L~~~~~~L~~l~~~iE~PLi~VLa~ME~~GI~-vD~ 579 (975) T PRK07456 536 RLAPILREQLAKTGPELIKLLEEVELPLEPVLAEMEATGIR-IDI 579 (975) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCH T ss_conf 99999999998623699999999873699999999971850-169 |
|
>PRK07625 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=9.4e-32 Score=203.80 Aligned_cols=189 Identities=20% Similarity=0.195 Sum_probs=155.1 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC----------CHHHHHHHHCCCCCEEE Q ss_conf 88578-42489827997177789854450799998418942899746577857----------06776777323640230 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN----------APNLVGMLVDEKREKIF 79 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~----------~~~L~~ll~d~~i~KV~ 79 (207) T Consensus 334 l~~~~~~l~~~~~~a~dtEttsld~~~a~lvGis~s~~~g~a~YiPl~h~~~d~~~~l~~~~vl~~Lk~~Led~~i~KIg 413 (922) T PRK07625 334 FDAWLAKISAAELTAFDTETTSLDPMLAQLVGLSFSVEPGHAAYIPVAHRGPDMPAQLPRDEVLARLRPWLEDAGRKKLG 413 (922) T ss_pred HHHHHHHHHCCCEEEEEEECCCCCHHHCEEEEEEEEECCCCEEEEEECCCCCCHHHHCCHHHHHHHHHHHHHCCCCHHHH T ss_conf 99999986408848999522776500130565797743886799970215865232158999999879987434403554 Q ss_pred CCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------CCEECCCCCCCCCHHHHH Q ss_conf 100001688865420000000-457898865211000000887776542002467-------520036565443236899 Q gi|254780636|r 80 HYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK-------AQQSSDWSADDLSDEQLQ 151 (207) Q Consensus 80 Hn~~~D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-------~~q~SdW~~rpLs~~Qi~ 151 (207) T Consensus 414 hNlK~d~~vL~~~-GI~l~g~~fDTmLAaYLL~~-~r~~~Ld~La~~yL~~~~i~~edl~Gkg~~q~~~~~v~~-~~~~~ 490 (922) T PRK07625 414 QHLKYDAQVLANY-GIALNGIEHDTLLESYVLES-HRTHDMDSLALRHLGVKTIKYEDVAGKGAKQIGFDEVAL-AQASE 490 (922) T ss_pred HHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHCC-CCCCCHHHHHHHHHCCCCCCHHHHCCCCCCCCCHHHCCH-HHHHH T ss_conf 2577899999977-96458754039999887546-767887999998725565541321233333378322467-99999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 99864599999999999999974-91899999-996400689998667988884 Q gi|254780636|r 152 YAASDVVHLHALRLQFTEKLQRL-GRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 152 YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 491 Ya~eda~~t~~L~~~L~~~L~~e~~L~~ly~~iE~PLi~VLa~ME~~GI~-vD~ 543 (922) T PRK07625 491 YAAEDADITLQLHHALYPQVAREPGLERVYRDIELPVSLVLRKMERTGVL-IDA 543 (922) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCH T ss_conf 99999999999999999998340547999999995899999999982840-269 |
|
>PRK08786 consensus | Back alignment and domain information |
---|
Probab=100.00 E-value=2.9e-32 Score=206.77 Aligned_cols=190 Identities=20% Similarity=0.211 Sum_probs=156.5 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC----------HHHHHHHHCCCCCEEE Q ss_conf 88578-424898279971777898544507999984189428997465778570----------6776777323640230 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA----------PNLVGMLVDEKREKIF 79 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~----------~~L~~ll~d~~i~KV~ 79 (207) T Consensus 338 L~~~i~~l~~~~~~afdtET~sld~~~a~lVGiS~s~~~g~a~YiP~~h~~~g~~~qld~~~~l~~LkplLed~~I~KIg 417 (927) T PRK08786 338 LDSWIARLRAAGQFAFDTETDSLDPLQADLIGLSVAAEPGQAAYLPFGHDFPGAPVQLDRTQALAQLAPLLTDPAVRKVG 417 (927) T ss_pred HHHHHHHHHHCCEEEEEEECCCCCHHHHHHHCEEEECCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHH T ss_conf 99999998736838999723886655531212245426786677532445678603413999999989986086511232 Q ss_pred CCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------CCEECCCCCCCCCHHHHH Q ss_conf 100001688865420000000-457898865211000000887776542002467-------520036565443236899 Q gi|254780636|r 80 HYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK-------AQQSSDWSADDLSDEQLQ 151 (207) Q Consensus 80 Hn~~~D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-------~~q~SdW~~rpLs~~Qi~ 151 (207) T Consensus 418 hnlK~Dl~vL~~~-GI~l~g~~~DTmLAaYLL~p~~~~~~Ld~La~~yLg~~~~~~~~l~gkg~k~~~~~~v~~-~~~~~ 495 (927) T PRK08786 418 QHGKYDLHVMRRH-GIALAGYADDTLLESFVLNSGSARHDMDSLAKRYLGYDTVKYEDVCGKGAKQIPFAQVSL-EDATR 495 (927) T ss_pred HHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCCHHHCCH-HHHHH T ss_conf 1178889999967-971167664258888623776454788999999669775426754244322288333259-99999 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HCCCHHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 998645999999999999999-749189999-9996400689998667988884 Q gi|254780636|r 152 YAASDVVHLHALRLQFTEKLQ-RLGRSDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 152 YAA~Dv~~l~~L~~~l~~~L~-~~~~~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 496 Ya~eda~~tl~L~~~l~~kL~~e~~l~~ly~~iE~PLi~VLa~ME~~GI~-vD~ 548 (927) T PRK08786 496 YAAEDADITLRLHCVLGPKLAAEPGLERVYRDIEMPLVDVLERIEANGVC-VDA 548 (927) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 99999999999999999999850529999999997999999998856879-889 |
|
>PRK08835 consensus | Back alignment and domain information |
---|
Probab=99.98 E-value=5.7e-32 Score=205.04 Aligned_cols=190 Identities=17% Similarity=0.170 Sum_probs=155.2 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC----------CHHHHHHHHCCCCCEEE Q ss_conf 88578-42489827997177789854450799998418942899746577857----------06776777323640230 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN----------APNLVGMLVDEKREKIF 79 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~----------~~~L~~ll~d~~i~KV~ 79 (207) T Consensus 341 l~~~l~~l~~~~~~a~dtEt~~ld~~~a~lvGis~~~~~g~a~YiPl~h~~l~~~~ql~~d~vl~~LkplLed~~i~KIg 420 (931) T PRK08835 341 FQLWLDKLKAAELFAFDTETDSLDYMVANLVGLSFAVAEGEAAYVPVAHDYLDAPEQLDRDWVLAQLKPLLEDDAKAKVG 420 (931) T ss_pred HHHHHHHHHCCCEEEEEEECCCCCHHHCCCCCEEEEECCCCEEEEEECCCCCCCHHHCCHHHHHHHHHHHHCCCCHHHHH T ss_conf 99999985338859999504874322213354268764785799971233345510136999999979984284243662 Q ss_pred CCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-------CCEECCCCCCCCCHHHHH Q ss_conf 100001688865420000000-457898865211000000887776542002467-------520036565443236899 Q gi|254780636|r 80 HYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK-------AQQSSDWSADDLSDEQLQ 151 (207) Q Consensus 80 Hn~~~D~~~L~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-------~~q~SdW~~rpLs~~Qi~ 151 (207) T Consensus 421 hNlK~d~~vL~~~-gI~l~gi~fDTmLAaYLLnp~~~~~~Ld~La~~~L~~~~i~~e~l~gkgk~q~~f~~v~~-~~~~~ 498 (931) T PRK08835 421 QNLKYDASVLARY-GIEMKGIKHDTMLASYVYNSVGGKHDMDSLALRFLQHSCISFEQVAGKGKNQLTFNQIDL-EEAAP 498 (931) T ss_pred CCHHHHHHHHHHC-CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCCHHHHHH-HHHHH T ss_conf 2115789999977-977678661243575300477787898999998648776347765144534478334328-89999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-CCCHHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 9986459999999999999997-49189999-9996400689998667988884 Q gi|254780636|r 152 YAASDVVHLHALRLQFTEKLQR-LGRSDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 152 YAA~Dv~~l~~L~~~l~~~L~~-~~~~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 499 YaaedA~~t~~L~~~L~~~L~~~~~L~~Ly~~IE~PLi~VLa~ME~~GI~-vD~ 551 (931) T PRK08835 499 YAAEDADVTLRLHNRLFANIEQDEKLKSVYEEIEMPLVPVLSRIERTGVL-IDD 551 (931) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEE-ECH T ss_conf 99999999999999999999854778899999986899999999972848-789 |
|
>cd06140 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilus-like Polymerase I (pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region | Back alignment and domain information |
---|
Probab=99.97 E-value=1.2e-30 Score=197.34 Aligned_cols=170 Identities=21% Similarity=0.189 Sum_probs=145.9 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCC Q ss_conf 98279971777898544507999984189428997465778570677677732364023010000168886542000000 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRP 99 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~ 99 (207) T Consensus 3 ~~~~av~~e~~~~~~~~~~i~gi~l~~~-~~~~yi~~~~~~~~~~~lk~~l~d~~i~Ki~hn~K~~~~~L~~~-Gi~l~g 80 (178) T cd06140 3 ADEVALYVELLGENYHTADIIGLALANG-GGAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRH-GIELAG 80 (178) T ss_pred CCCEEEEEECCCCCCCCCEEEEEEEEEC-CEEEEEECCCCHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHC-CCCCCC T ss_conf 8866999737999845354999999889-97999956673646999999972999988986579999999988-980688 Q ss_pred H-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE----ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 0-457898865211000000887776542002467520----03656544323689999864599999999999999974 Q gi|254780636|r 100 V-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ----SSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 100 i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q----~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) T Consensus 81 ~~fDtmiaayLl~p~~~~~~L~~L~~~yl~~~~~~~~~~~gk~~~~~~-~~~~~~~~ya~~~a~~~~~L~~~l~~~L~e~ 159 (178) T cd06140 81 VAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAV-PDEEVLAEHLARKAAAILRLAPKLEEELEEN 159 (178) T ss_pred CHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 303688898875489777999999999828666547886176656243-9979999999999999999999999999982 Q ss_pred CCHHHHHH-HHHHHHHHHH Q ss_conf 91899999-9964006899 Q gi|254780636|r 175 GRSDLATS-CCNFLMDRAE 192 (207) Q Consensus 175 ~~~~~~~~-e~~~l~~~~~ 192 (207) T Consensus 160 ~l~~Ly~~iE~PL~~VLa~ 178 (178) T cd06140 160 EQLELYYEVELPLAEVLAE 178 (178) T ss_pred HHHHHHHHHHHHHHHHHCC T ss_conf 4899999987129998189 |
The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases. |
>PRK07898 consensus | Back alignment and domain information |
---|
Probab=99.97 E-value=2.2e-30 Score=195.81 Aligned_cols=183 Identities=19% Similarity=0.136 Sum_probs=154.0 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCC-CCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHC Q ss_conf 24898279971777898544507999984189428997465778-57067767773236402301000016888654200 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQ-KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~-~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi 95 (207) T Consensus 334 ~~~~~~~a~~~~~t~~-~~~a~lvgisl~~~~g~a~yip~~~~~~~~~~~L~~~Led~~i~KIghNlK~d~~vL~~~-Gi 411 (902) T PRK07898 334 AGDGRRLGLAVVGTHL-PGDGDATALAIAAADGHAAYIDTADLTPDDEAALAAWLADPARPKALHEAKGAMHALAGR-GW 411 (902) T ss_pred HCCCCEEEEEEECCCC-CCCCCEEEEEEEEECCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHC-CC T ss_conf 4359869999853678-665738999999538808997220179789999999860877654554048999999966-98 Q ss_pred CCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCC---EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00000-45789886521100000088777654200246752---003656544323689999864599999999999999 Q gi|254780636|r 96 RVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQ---QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 96 ~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~---q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) T Consensus 412 ~l~g~~fDTmLAaYLLdp~~~~~~Ld~La~~yL~~~~~~~~~~~~~~~~~~~~~-~~~~~yaa~dA~~~~~L~~~l~~~L 490 (902) T PRK07898 412 TLAGVTSDTALAAYLVRPGQRSFTLDDLSLRYLRRELRAEAPAQQQLSLDDAVD-AAAAQTLILRARAVLDLADALDAEL 490 (902) T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 657753228999987568878787999999974976651565354347132676-8999999999999999999999986 Q ss_pred HHCCCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 97491899999-996400689998667988884 Q gi|254780636|r 172 QRLGRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 172 ~~~~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 491 ~~~~l~~L~~~IE~PLi~VLa~ME~~GI~-vD~ 522 (902) T PRK07898 491 ARIDSAALLRDMELPLQRVLAEMERAGIA-VDL 522 (902) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 16558999999760589999999850819-819 |
|
>PRK05797 consensus | Back alignment and domain information |
---|
Probab=99.97 E-value=9.1e-30 Score=192.25 Aligned_cols=169 Identities=17% Similarity=0.133 Sum_probs=145.9 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCC---CCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHC Q ss_conf 8982799717778985445079999841894289974657785---7067767773236402301000016888654200 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQK---NAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~---~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi 95 (207) T Consensus 318 ~~~~~~~~~ett~~~~~~~~~vg~s~~~~~~~a~yip~~~~~~~~~~L~~Lk~lLed~~i~KIGhNlK~dl~vL~~~-GI 396 (869) T PRK05797 318 KNNQVYINFTLEDENLYSKIEIKKIFINFGEKTYYIDFKELIDEEEFIEDLKEIFENEEIKKIGHDIKNFLTILKKL-GI 396 (869) T ss_pred HCCCEEEEEECCCCCHHHHHHEEEEEEECCCEEEEEECHHHCCHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHC-CC T ss_conf 34987999973897612030418999961997999831451677899999999984899878984306999999975-98 Q ss_pred CCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 00000-45789886521100000088777654200246752003656544323689999864599999999999999974 Q gi|254780636|r 96 RVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 96 ~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) T Consensus 397 ~l~gi~FDTMLAsYLLnP~~~~h~Ld~La~~yL~~~~~~--------------~e~~ya~~dA~~~~~L~~~L~~~L~~~ 462 (869) T PRK05797 397 EFKGLAFDTAIAAYLIDPSKSEYDLSDLAKEYLSKDVNS--------------EEEEYKIKEVSVMKELYEKLKEKIEEM 462 (869) T ss_pred CCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCC--------------HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 556616689999997289988889999999980877751--------------478999999999999999999999861 Q ss_pred CCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 91899999-996400689998667988884 Q gi|254780636|r 175 GRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 175 ~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 463 ~l~~L~~~IE~PLi~VLa~ME~~GI~-VD~ 491 (869) T PRK05797 463 DMEKLLYEVELPLVEVLASMESEGFK-VDK 491 (869) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 28999999986789999999846809-999 |
|
>PRK08434 consensus | Back alignment and domain information |
---|
Probab=99.96 E-value=1.8e-28 Score=184.76 Aligned_cols=187 Identities=21% Similarity=0.259 Sum_probs=147.8 Q ss_pred CCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC----------HHHHHHHHCCCCCEEE Q ss_conf 88578-424898279971777898544507999984189428997465778570----------6776777323640230 Q gi|254780636|r 11 IPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA----------PNLVGMLVDEKREKIF 79 (207) Q Consensus 11 l~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~----------~~L~~ll~d~~i~KV~ 79 (207) T Consensus 308 l~~~l~~l~~~~~~a~d~Ett~ld~~~a~lvGis~~~~~~~a~YiPi~h~~l~~~~~~~~~~~~~~l~~~~~~---~~Ig 384 (887) T PRK08434 308 LEEILNTLPKESIIAFDTETTGLDTKEAKLVGFSFCFNEEEAYYVPLAHSYLGVGEQISLESAKKAIEKIFNH---FVIG 384 (887) T ss_pred HHHHHHHCCCCCEEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCHHHCCHHHHHHHHHHHHHC---CCHH T ss_conf 9999985311676999951278661334305899995598589997521125773335999999997876337---4036 Q ss_pred CCCCHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCC----EECCCCCCCCCHHHHHHHH Q ss_conf 10000168886542000000-045789886521100000088777654200246752----0036565443236899998 Q gi|254780636|r 80 HYGRFDIAVLFYTFGVRVRP-VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQ----QSSDWSADDLSDEQLQYAA 154 (207) Q Consensus 80 Hn~~~D~~~L~~~~gi~~~~-i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~----q~SdW~~rpLs~~Qi~YAA 154 (207) T Consensus 385 hNlKyDl~vL~~~~gi~l~g~~fDTmLAaYLLdp~-~r~~Ld~La~~yL~~~~i~~e~l~~kg~~f~~v~i-~~a~~YAa 462 (887) T PRK08434 385 HNLKYDFKIIQNNFGLELPQKYADTMILAWLKDPS-SRVGLDDLAKRLFNYEMIHFESVVKKGENFSSVDL-EKACKYAA 462 (887) T ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCC-CCCCHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCH-HHHHHHHH T ss_conf 47799999999856987777314899999866986-66666789999708787748998546777020788-99999999 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCH---HHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 64599999999999999974918---9999-9996400689998667988884 Q gi|254780636|r 155 SDVVHLHALRLQFTEKLQRLGRS---DLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 155 ~Dv~~l~~L~~~l~~~L~~~~~~---~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 463 edA~it~~L~~~l~~~L~~~~~~~L~~Ly~~IElPLi~VLa~ME~~GI~-VD~ 514 (887) T PRK08434 463 EDAWITLRFYKKFLENLEKRGATHLLELAKNVEFPFIKTLLMMEENGIK-LDT 514 (887) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCH T ss_conf 9999999999999999986551779999999886599999999971950-269 |
|
>PRK08076 consensus | Back alignment and domain information |
---|
Probab=99.96 E-value=3.8e-28 Score=182.82 Aligned_cols=180 Identities=16% Similarity=0.130 Sum_probs=146.1 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCC Q ss_conf 98279971777898544507999984189428997465778570677677732364023010000168886542000000 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRP 99 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~ 99 (207) T Consensus 314 ~~~~a~~~Et~~~~~~~a~lvGis~s~~~~-a~yiP~~~~-~~~~~lk~~Led~~i~KighNlK~dl~vL~~~-GI~l~g 390 (877) T PRK08076 314 QQKSALVVEVLEDNYHKADIQGFAIVNENG-CYFIPTEIA-LKSDAFKEWLEDEEKKKWVFDAKRAIVALKWN-GIDLQG 390 (877) T ss_pred CCCCEEEEEECCCCCCCCCEEEEEEECCCC-EEEECCCHH-HHHHHHHHHHCCCCCCEEEECHHHHHHHHHHC-CCCCCC T ss_conf 688549999647885637789999985894-599550044-21589999853976540265479999999968-964477 Q ss_pred H-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE---ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0-457898865211000000887776542002467520---036565443236899998645999999999999999749 Q gi|254780636|r 100 V-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ---SSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 100 i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q---~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) T Consensus 391 i~FDTMLAAYLLdP~~~~~~Ld~La~~yl~~~~~~~e~v~Gkg~k~~~p~~~~~~eYaaedA~~t~~L~~~L~~~L~~~~ 470 (877) T PRK08076 391 IDFDLLLAAYLLNPADSDDDFASVAKMKETHAVKSDEAVYGKGAKRAVPEEEILAEHLARKAHAIYDLKQTFVEELEKNE 470 (877) T ss_pred CCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 64029999987188767666999999855777763476537652224877899999999999999999999999986557 Q ss_pred CHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 1899999-996400689998667988884 Q gi|254780636|r 176 RSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 176 ~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 471 l~~Ly~~IE~PLi~VLa~ME~~GI~-VD~ 498 (877) T PRK08076 471 QLELFEELELPLARVLAEMEVKGVK-VDT 498 (877) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 8999999970488999999854838-989 |
|
>PRK05929 consensus | Back alignment and domain information |
---|
Probab=99.95 E-value=1.3e-26 Score=173.90 Aligned_cols=181 Identities=17% Similarity=0.108 Sum_probs=142.9 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCC-CCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCC Q ss_conf 8982799717778985445079999841894289974657785-706776777323640230100001688865420000 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQK-NAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRV 97 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~-~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~ 97 (207) T Consensus 309 ~~~~~a~~~~~~~~~~~~~~lvGisls~~~-~a~yip~~~~~~~vl~~Lk~~led~~i~kig~NlK~d~~vL~~~-GI~l 386 (870) T PRK05929 309 QGGEVAFCVAYTGNHLPSLKLHGVALAGGS-QVFYIEVEESGDQEIALLKDFFARKDTTFYGYNLKRDNHALKNA-GIDV 386 (870) T ss_pred CCCCEEEEEEECCCCCCCCCEEEEEEECCC-EEEEEECCCCCHHHHHHHHHHHCCCCCCEEECCHHHHHHHHHHC-CCCC T ss_conf 179747999745887677728899997698-08999765555238999999860987745322377799999968-9856 Q ss_pred CCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC----CCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000-4578988652110000008877765420024----67520036565443236899998645999999999999999 Q gi|254780636|r 98 RPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINI----SKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 98 ~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~l----dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) T Consensus 387 ~g~~fDtmLAsYLLn~-~~~~~~~~ll~~~~~~~~~~~~~k~~g~~~l~~~~~~~~~~~yaae~a~~~~~L~~~L~~~L~ 465 (870) T PRK05929 387 HEITADLALAEHLVNG-GAKISFQTLLVEHGHIEEAHRFAKEWGASSLPIQRLPEQPAQYFGEFVSYLPIIKNYLLEELE 465 (870) T ss_pred CCCHHHHHHHHHHHCC-CCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8727799999986299-998883999976667315556555407666642007388999999999999999999999998 Q ss_pred HCCCHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 7491899999-996400689998667988884 Q gi|254780636|r 173 RLGRSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 173 ~~~~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 466 ~~~L~~Ly~eIE~PLi~VLa~ME~~GI~-vD~ 496 (870) T PRK05929 466 EKGLKDIFSNVEMPLEKVLFAMERAGMP-LDV 496 (870) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCEE-EEH T ss_conf 8779999999874489999998738989-819 |
|
>PRK08928 consensus | Back alignment and domain information |
---|
Probab=99.93 E-value=8.7e-25 Score=163.31 Aligned_cols=160 Identities=14% Similarity=0.010 Sum_probs=138.5 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC-CHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHC Q ss_conf 2489827997177789854450799998418942899746577857-067767773236402301000016888654200 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN-APNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~-~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi 95 (207) T Consensus 321 ~~~~~~~a~~le~~-----~~~~vgis~s~~~~~~~~i~~~~~~~~~~~~l~~lLed~~i~KIghNlK~dl~vL~~~-gi 394 (861) T PRK08928 321 CEKEGIFAIYLLQE-----KGTNNAISLSLQNQSYIIIISNEITDAFSDIIFNLLTDKSILKITYDLKPLLKFYANQ-SH 394 (861) T ss_pred HHHCCEEEEEEECC-----CCEEEEEEEEECCCEEEEECCCCCHHHHHHHHHHHHCCCCCCEEECCHHHHHHHHHHC-CC T ss_conf 76579689992057-----8738999999559849995575424789999999843999754454579999999856-96 Q ss_pred CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 00000457898865211000000887776542002467520036565443236899998645999999999999999749 Q gi|254780636|r 96 RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 96 ~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) T Consensus 395 ~l~~i~DTmLasYLLnp~~~~h~Ld~La~~~~~~--------------------~~~aa~~a~~~~~L~~~L~~~L~~~~ 454 (861) T PRK08928 395 DITAIDDLMLMSYSLSAGLHDHSLFNIILKNTNI--------------------INESAKIVCTLISLHKQLILELFDNK 454 (861) T ss_pred CCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7576371889998649998768989999762220--------------------01479999999999999999998866 Q ss_pred CHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 1899999-996400689998667988884 Q gi|254780636|r 176 RSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 176 ~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 455 L~~Ly~eIE~PLi~VLa~ME~~GI~-VD~ 482 (861) T PRK08928 455 LFTIYYRIDLPLCFVLDKMEKIGIK-VDA 482 (861) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC-CCH T ss_conf 8999999887799999999981960-169 |
|
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] | Back alignment and domain information |
---|
Probab=99.92 E-value=1e-24 Score=162.95 Aligned_cols=183 Identities=25% Similarity=0.268 Sum_probs=146.0 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCC---CCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHH Q ss_conf 2489827997177789854450799998418942899746577---8570677677732364023010000168886542 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAG---QKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTF 93 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~---~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~ 93 (207) T Consensus 19 ~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~- 96 (593) T COG0749 19 LNAAANIAFDTETDGLDPHGADLVGLSVASEE-EAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVGQNLKYDYKVLANL- 96 (593) T ss_pred HHHCCCCCEECCCCCCCCCCCCEEEEEEECCC-CCEEEEECCCHHHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHHC- T ss_conf 74223310100014567555874678862365-4236751366555514899999863754103213413669999973- Q ss_pred HCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC-------CCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 000000045789886521100000088777654200246-------7520036565443236899998645999999999 Q gi|254780636|r 94 GVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINIS-------KAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQ 166 (207) Q Consensus 94 gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ld-------K~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~ 166 (207) T Consensus 97 Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~-~~~~~y~a~~a~~~~~L~~~ 175 (593) T COG0749 97 GIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKL-EKATEYAAEDADATLRLESI 175 (593) T ss_pred CCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCHH-HHHHHHHHHHHHHHHHHHHH T ss_conf 97656517899999614867675777899998258774024876325445676100147-78888788888999999999 Q ss_pred HHHHHHHCC-CHHHHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 999999749-1899999-996400689998667988884 Q gi|254780636|r 167 FTEKLQRLG-RSDLATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 167 l~~~L~~~~-~~~~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 176 l~~~l~~~~~L~~l~~~iE~Pl~~VLa~ME~~Gi~-vD~ 213 (593) T COG0749 176 LEPELLKTPVLLELYEEIEMPLVRVLARMERNGIK-VDV 213 (593) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCE-ECH T ss_conf 99876310469999999754089999986862856-429 |
|
>PRK07300 consensus | Back alignment and domain information |
---|
Probab=99.86 E-value=1e-20 Score=139.70 Aligned_cols=173 Identities=16% Similarity=0.071 Sum_probs=130.8 Q ss_pred EEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCH-H Q ss_conf 799717778985445079999841894289974657785706776777323640230100001688865420000000-4 Q gi|254780636|r 23 IAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPV-F 101 (207) Q Consensus 23 iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i-~ 101 (207) T Consensus 322 ~~~~~et~~~~~~~a~lvG~s~~~~~--~~y~~~~~~~l~~~~~~~~~~~~---i~~~nlK~~~~vL~~~-GI~l~~~~f 395 (880) T PRK07300 322 DFFYFETLGDNYHREAIIGFAWGNGE--QIYASTDLSLLATDSFKQVLQKP---IATYDFKRSKVLLSHL-GIELPAPSF 395 (880) T ss_pred CEEEEEECCCCCCCCCEEEEEEECCC--EEEECCCHHHHHCHHHHHHHHHH---HHHHHHHHHHHHHHHC-CCCCCCCHH T ss_conf 02576533798130777999985597--58955813321176888876535---6550378689999977-986677403 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEE-CCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 578988652110000008877765420024675200-3656--5443236899998645999999999999999749189 Q gi|254780636|r 102 CTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS-SDWS--ADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSD 178 (207) Q Consensus 102 DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~-SdW~--~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~ 178 (207) T Consensus 396 DTmLAsYLL~p-~~~~~Ld~La~~yl~~~~~~~e~l~Gkg~k~~~~~~~~~~~yaa~da~~~~~L~~~L~~~L~~~~l~~ 474 (880) T PRK07300 396 DARLAKYLLST-VEDNELSTIARLYTDISLETDDTVYGKGAKRAIPEKEVLLEHLARKVKVLLDSKEQMLDKLTAHEQLD 474 (880) T ss_pred HHHHHHHCCCC-CCCCCHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 48999853687-65587789999946888873376636652103662779999999999999999999899987616999 Q ss_pred HHHH-HHHHHHHHHHHHHCCCCCCCC Q ss_conf 9999-996400689998667988884 Q gi|254780636|r 179 LATS-CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 179 ~~~~-e~~~l~~~~~me~~g~~~~~~ 203 (207) T Consensus 475 L~~~IE~PLi~VLa~ME~~GI~-VD~ 499 (880) T PRK07300 475 LLFDMELPLANVLAKMEIAGIK-VNR 499 (880) T ss_pred HHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 9999986899999999965808-889 |
|
>PRK06309 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=99.41 E-value=4.4e-12 Score=89.50 Aligned_cols=143 Identities=19% Similarity=0.198 Sum_probs=90.8 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECC----CCE-EEECCCCC-C--------------CCCH-------HHHHHHHC Q ss_conf 98279971777898544507999984189----428-99746577-8--------------5706-------77677732 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGD----GTV-DIIRIAAG-Q--------------KNAP-------NLVGMLVD 72 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~----~~~-~l~~~~~~-~--------------~~~~-------~L~~ll~d 72 (207) T Consensus 2 ~~~V~fD~ETTGl~~~~DrI--IEiaav~~~~~e~f~~linP~~pIp~~a~~ihGIt~e~v~~~P~~~ev~~~~~~f~~~ 79 (232) T PRK06309 2 PALIFYDTETTGTQIDKDRI--IEIAAYNGVTSESFQTYVNPEIPIPAEATKIHGITTSEVASAPKFPEAYQKFREFCGT 79 (232) T ss_pred CCEEEEEEECCCCCCCCCEE--EEEEEEECCCCCEEEEEECCCCCCCHHHHCCCCCCHHHHHCCCCHHHHHHHHHHHHCC T ss_conf 96899971179959999458--9999892756768999979989699656210383999980599899999999998579 Q ss_pred CCCCEEECCC-CHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC Q ss_conf 3640230100-00168886542---0000--0004578988652110000008877765420024675200365654432 Q gi|254780636|r 73 EKREKIFHYG-RFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS 146 (207) Q Consensus 73 ~~i~KV~Hn~-~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs 146 (207) T Consensus 80 ~~i-lVaHN~~~FD~~fL~~e~~r~g~~~~~~~~iDTl~lar~l~P~l~~h~L~~L~~~-~gi~~~~a------------ 145 (232) T PRK06309 80 DNI-LVAHNNDGFDFPLLVKECRRHSLEPLTLRTIDSLKWAQKYRPDLPKHNLQYLRQV-YGFAENQA------------ 145 (232) T ss_pred CCE-EEEECCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHH-HCCCCCCC------------ T ss_conf 988-9984896567999999999859986774053799999997589776889999998-09999888------------ Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 368999986459999999999999997491899999 Q gi|254780636|r 147 DEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 (207) Q Consensus 147 ~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~~~ 182 (207) T Consensus 146 ----HrAl~Da~at~~vf~~ll~~~~~~~~~~l~~~ 177 (232) T PRK06309 146 ----HRALDDVITLHRVFSALVGDLSPQQVLDLLNE 177 (232) T ss_pred ----CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC T ss_conf ----88599999999999998721699999999845 |
|
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III | Back alignment and domain information |
---|
Probab=99.19 E-value=1.2e-10 Score=81.13 Aligned_cols=147 Identities=24% Similarity=0.348 Sum_probs=105.5 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCC-CEEEECCC-------CCC--------------CC-------CH Q ss_conf 248982799717778985445079999841---894-28997465-------778--------------57-------06 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDG-TVDIIRIA-------AGQ--------------KN-------AP 64 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~-~~~l~~~~-------~~~--------------~~-------~~ 64 (207) T Consensus 201 l~DaTyVVfD~ETTGLsp~~d~i--IE~gA~k~~nGk~i-i~~~~~FikP~~~l~~~~~elT~ITq~ml~n~~~~~~vL~ 277 (1264) T TIGR01405 201 LKDATYVVFDIETTGLSPQYDEI--IEFGAVKVKNGKRI-IDKFQFFIKPKEPLSAFVTELTGITQDMLENAPEIEEVLE 277 (1264) T ss_pred ECCCEEEEEEEEECCCCCCCCCE--EEEEEEEEECCCEE-EEEHHHHCCCCCCCCCCEEEECCCCHHHHCCCCCHHHHHH T ss_conf 23620799603515888861424--67875887468576-2312323288754675426624664797379841789999 Q ss_pred HHHHHHHCCCCCEEECC-CCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 77677732364023010-000168886542---0000--00045789886521100000088777654200246752003 Q gi|254780636|r 65 NLVGMLVDEKREKIFHY-GRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 65 ~L~~ll~d~~i~KV~Hn-~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) T Consensus 278 k~~~f~~-d~il-VAHNGasFD~~Fl~~~~~k~~~~~~~~p~IDTL~Lar~lnP~y~sh~Lg~~~~K-l~v~~------- 347 (1264) T TIGR01405 278 KFKEFLK-DSIL-VAHNGASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGEIAKK-LGVDL------- 347 (1264) T ss_pred HHHHHHC-CEEE-EECCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHH-CCCCC------- T ss_conf 9999769-7588-862761036688988987627742336511388999983731134454223332-05521------- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHH Q ss_conf 6565443236899998645999999999999999749-18999999 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG-RSDLATSC 183 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~-~~~~~~~e 183 (207) T Consensus 348 -------~~e~~HRA~YDa~~t~~vF~~~~~~~~e~gGi~~l~~ln 386 (1264) T TIGR01405 348 -------DDERHHRADYDAEATAKVFIVMVEQLKEKGGITNLEELN 386 (1264) T ss_pred -------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCC T ss_conf -------533012433479999999999999987503721123405 |
Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm. |
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] | Back alignment and domain information |
---|
Probab=98.97 E-value=3.5e-09 Score=72.59 Aligned_cols=149 Identities=22% Similarity=0.275 Sum_probs=100.1 Q ss_pred HHHHCCCCCCEEEECCCCCCCCCCCEEEEEEEEEC---CCC------EEEECCCCCC--------------CCC------ Q ss_conf 57842489827997177789854450799998418---942------8997465778--------------570------ Q gi|254780636|r 13 AECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPG---DGT------VDIIRIAAGQ--------------KNA------ 63 (207) Q Consensus 13 ~~~~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~---~~~------~~l~~~~~~~--------------~~~------ 63 (207) T Consensus 414 ~d~~l~datyVVfDiETTGLs~~~d~i--IE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~v 491 (1444) T COG2176 414 DDQKLDDATYVVFDIETTGLSPVYDEI--IEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEV 491 (1444) T ss_pred CCCCCCCCCEEEEEEECCCCCCCCCHH--HHHEEEEEECCCCHHHHHHHCCCCCCCCHHHHHCCCCCHHHHCCCCCHHHH T ss_conf 445456550899985537767542015--620004433880437789750899967644542035679987488339999 Q ss_pred -HHHHHHHHCCCCCEEECCCCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEE Q ss_conf -677677732364023010000168886542---0000--0004578988652110000008877765420024675200 Q gi|254780636|r 64 -PNLVGMLVDEKREKIFHYGRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137 (207) Q Consensus 64 -~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~ 137 (207) T Consensus 492 L~kf~~~~~d-~Il-VAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk-~~v~l------ 562 (1444) T COG2176 492 LEKFREFIGD-SIL-VAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKK-LGVEL------ 562 (1444) T ss_pred HHHHHHHHCC-CEE-EECCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCHHHHHCCHHHHHHH-HCCCH------ T ss_conf 9999998448-589-96167556457888899838851027501199999875745432466778887-48637------ Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 365654432368999986459999999999999997491899999 Q gi|254780636|r 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATS 182 (207) Q Consensus 138 SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~~~ 182 (207) T Consensus 563 ----------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l~el 597 (1444) T COG2176 563 ----------ERHHRADYDAEATAKVFFVFLKDLKEKGITNLSEL 597 (1444) T ss_pred ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH T ss_conf ----------87531010089999999999999988455659998 |
|
>cd06129 RNaseD_like The RNase D-like group is composed of RNase D, WRN, and similar proteins | Back alignment and domain information |
---|
Probab=100.00 E-value=8.7e-43 Score=267.92 Aligned_cols=148 Identities=25% Similarity=0.304 Sum_probs=136.5 Q ss_pred HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHC Q ss_conf 42489827997177789854450799998418942899746577857067767773236402301000016888654200 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV 95 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi 95 (207) T Consensus 11 ~~~~~~vig~DtE~~~~~~~~~~v~LiQlat~~-~~~lid~~~~~~~~~~L~~lL~~~~i~Kvgh~~~~D~~~L~~~~g~ 89 (159) T cd06129 11 AKNESIVVALDCEWIPLRLYYGEVTLIQIGTTE-HAFLFDVLSLSAFDGGLKTVLENPSITKVGHGCRGDLAKLLRDFGI 89 (159) T ss_pred HCCCCEEEEEECCCCCCCCCCCCEEEEEEEECC-EEEEEECCCCCCCHHHHHHHHHCCCCEEEEECHHHHHHHHHHHCCC T ss_conf 545980899979768987998978999994599-6899954888767799999982999249995669999999675084 Q ss_pred CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 000004578988652110000008877765420024675200365654432368999986459999999 Q gi|254780636|r 96 RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 96 ~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 90 ~~~~~~Dt~~~~~~l~~~~~~~sL~~l~~~~lg~~ldK~~q~SnW~~rpLt~~Qi~YAA~Da~~ll~ly 158 (159) T cd06129 90 LLRNLFDTQAAHAILGYPEEYWSLNSLVEQYLGPCLDKSRQLSDWAKRPLTEEQMLYAAADVYVLLHIY 158 (159) T ss_pred CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 324303699999995888431659999999808787710245888999999999999999999999976 |
They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of prec |
>pfam01612 3_5_exonuc 3'-5' exonuclease | Back alignment and domain information |
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Probab=100.00 E-value=2.3e-42 Score=265.44 Aligned_cols=161 Identities=33% Similarity=0.479 Sum_probs=142.0 Q ss_pred CCCHHH-HCCCCCCEEEECCCCCCCCC--CCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHH Q ss_conf 888578-42489827997177789854--450799998418942899746577857067767773236402301000016 Q gi|254780636|r 10 DIPAEC-AARYVDAIAVDTETLGLMPR--RDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDI 86 (207) Q Consensus 10 dl~~~~-~l~~~~~iaiDtEt~~l~~~--~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~ 86 (207) T Consensus 9 ~l~~~~~~l~~~~~ia~DtEt~~~~~~~~~~~~~llq~~~~~~-~yli~~~~~~~~~~~L~~ll~~~~i~Kvghn~k~D~ 87 (172) T pfam01612 9 ELEDLIEELLNAKVVAVDTETTSLDTYSYTLVGCLIQISTGEG-AYIIDPLALGDDLEGLKRLLEDPNITKVGHNAKFDL 87 (172) T ss_pred HHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEEECCCC-CEEEECCCCHHHHHHHHHHHCCCCCCEEEEEHHHHH T ss_conf 9999999994099089980628988676134336999967986-077643475667999999975999879997589999 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 88865420000000457898865211000000887776542002467520036565443236899998645999999999 Q gi|254780636|r 87 AVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQ 166 (207) Q Consensus 87 ~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~ 166 (207) T Consensus 88 ~~L~~~~~~~~~~~~Dt~~a~~~l~-~~~~~gL~~L~~~~lg~~~~K~~~~s~w~~rpL~~~qi~YAa~Da~~~~~l~~~ 166 (172) T pfam01612 88 EVLARDFGIKLENLFDTMLAAYLLG-YPRSHSLDDLAEKYLGVELDKSEQCADWRARPLSEEQLRYAAEDADYLLRLYDK 166 (172) T ss_pred HHHHHHCCCCCCCCHHHHHHHHHCC-CCCCCCHHHHHHHHCCCCCCHHHEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 9998854766687327899998819-964356999999980987874415667887898299999999999999999999 Q ss_pred HHHHHH Q ss_conf 999999 Q gi|254780636|r 167 FTEKLQ 172 (207) Q Consensus 167 l~~~L~ 172 (207) T Consensus 167 l~~~l~ 172 (172) T pfam01612 167 LRKELE 172 (172) T ss_pred HHHHHC T ss_conf 999749 |
This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. |
>smart00474 35EXOc 3'-5' exonuclease | Back alignment and domain information |
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Probab=100.00 E-value=5.8e-41 Score=257.31 Aligned_cols=162 Identities=35% Similarity=0.456 Sum_probs=142.2 Q ss_pred CCCHHHH-CC-CCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHH Q ss_conf 8885784-24-898279971777898544507999984189428997465778570677677732364023010000168 Q gi|254780636|r 10 DIPAECA-AR-YVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIA 87 (207) Q Consensus 10 dl~~~~~-l~-~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~ 87 (207) T Consensus 9 ~l~~~~~~l~~~~~~i~~DtE~~~~~~~~~~l~~iql~~~~~~~yi~~~~~~~~~~~~l~~ll~~~~i~kv~hn~k~D~~ 88 (172) T smart00474 9 TLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNAKFDLH 88 (172) T ss_pred HHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCHHHHHHHHHHHCCCCCCEEEECHHHHHH T ss_conf 99999999984299599988306885378758999999689848997012242179999999809998599974599999 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 88654200000004578988652110000008877765420024675200365654432368999986459999999999 Q gi|254780636|r 88 VLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 88 ~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 89 ~L~~-~gi~l~~v~Dt~ia~~l~~~~~~~~~L~~l~~~~~~~~l~k~~~~~~w~~rpl~~~~~~YAa~Da~~~~~l~~~l 167 (172) T smart00474 89 VLAR-FGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKL 167 (172) T ss_pred HHHH-CCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 9997-798567524679987750579864899999999749231555564666789990999999999999999999999 Q ss_pred HHHHH Q ss_conf 99999 Q gi|254780636|r 168 TEKLQ 172 (207) Q Consensus 168 ~~~L~ 172 (207) T Consensus 168 ~~~L~ 172 (172) T smart00474 168 EKELE 172 (172) T ss_pred HHHHC T ss_conf 99729 |
3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes |
>cd06146 mut-7_like_exo The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans | Back alignment and domain information |
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Probab=100.00 E-value=1.9e-39 Score=248.55 Aligned_cols=159 Identities=23% Similarity=0.264 Sum_probs=131.2 Q ss_pred CCCCCHHH---HCCCCCCEEEECCCC--CCCCCCCEEEEEEEEECCCCEEEECCCCCCCC-----CHHHHHHHHCCCCCE Q ss_conf 57888578---424898279971777--89854450799998418942899746577857-----067767773236402 Q gi|254780636|r 8 EGDIPAEC---AARYVDAIAVDTETL--GLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN-----APNLVGMLVDEKREK 77 (207) Q Consensus 8 ~~dl~~~~---~l~~~~~iaiDtEt~--~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~-----~~~L~~ll~d~~i~K 77 (207) T Consensus 7 ~~~l~~~~~~~~l~~~~vvg~D~Ew~~~~~~~~~~~vaLiQlat~~~-~~liD~~~~~~~~~~~~~~~L~~ll~~~~i~K 85 (191) T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDE-VFLLDLLALENLESEDWDRLLKRLFEDPDVLK 85 (191) T ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCEEEEEEECCCC-CEEEEEECCCCCCHHHHHHHHHHHHCCCCEEE T ss_conf 99999999998426898899978757877788889527999952997-58999704565434778999999947999689 Q ss_pred EECCCCHHHHHHHHHHHC------CCCCHHHHHHHHHHHHHH----------CCCHHHHHHHHHHHCCCCCCCCEECCCC Q ss_conf 301000016888654200------000004578988652110----------0000088777654200246752003656 Q gi|254780636|r 78 IFHYGRFDIAVLFYTFGV------RVRPVFCTKIASRLTRTY----------TNQHGLKDNLKELLGINISKAQQSSDWS 141 (207) Q Consensus 78 V~Hn~~~D~~~L~~~~gi------~~~~i~DT~ias~l~~~~----------~~~~~L~~L~~~~lg~~ldK~~q~SdW~ 141 (207) T Consensus 86 vg~~~~~D~~~L~~~~~~~~~~~~~~~~~~Dl~~~a~~~~~~~~~~~~~~~~~~~~gL~~L~~~~lg~~l~K~~q~SnW~ 165 (191) T cd06146 86 LGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQAVLGKPLDKSEQCSNWE 165 (191) T ss_pred EEECHHHHHHHHHHHCCCCCCCCCCCCEEEEHHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99443868999998658643233364403579999999731122101100355675699999999098788565138999 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 54432368999986459999999999 Q gi|254780636|r 142 ADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 142 ~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 166 ~rPLt~~Qi~YAA~Da~~ll~iy~~L 191 (191) T cd06146 166 RRPLREEQILYAALDAYCLLEVFDKL 191 (191) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 99899999999999899999999739 |
Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. |
>cd06141 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity | Back alignment and domain information |
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Probab=100.00 E-value=3.8e-39 Score=246.74 Aligned_cols=150 Identities=24% Similarity=0.275 Sum_probs=133.2 Q ss_pred CCCCCCEEEECCCCCCC--CCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHH Q ss_conf 24898279971777898--5445079999841894289974657785706776777323640230100001688865420 Q gi|254780636|r 17 ARYVDAIAVDTETLGLM--PRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFG 94 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~--~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g 94 (207) T Consensus 15 l~~~~vvG~D~Ew~~~~~~~~~~~~aliQlat~~-~~~l~d~~~~~~~~~~L~~lL~~~~i~Kvg~~~~~D~~~L~~~~g 93 (168) T cd06141 15 LDDEKVVGFDLEWRPSFRKGKRNKVALLQLASES-RCLLFQLSHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLRRDFG 93 (168) T ss_pred HCCCCEEEEECEECCCCCCCCCCCCEEEEEECCC-CEEEEEECCCCHHHHHHHHHHCCCCEEEEEEEEHHHHHHHHHHCC T ss_conf 5689889996645587777888971599982499-659997403312049999997599807999631889999987445 Q ss_pred CCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC--CCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00000045789886521100000088777654200246--75200365654432368999986459999999999 Q gi|254780636|r 95 VRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINIS--KAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 95 i~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ld--K~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 94 ~~~~~~~Dl~~~a~~~~~~~~~~sL~~l~~~~lg~~l~K~k~~q~SdW~~rpLs~~Qi~YAA~Da~~~~~l~~~L 168 (168) T cd06141 94 IEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKDKKVRCSNWEARPLSKEQILYAATDAYASLELYRKL 168 (168) T ss_pred CCCCCEEEHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 024876569999998577777632999999983962154665203888999999999999999999999999739 |
It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability. |
>cd00007 35EXOc 3'-5' exonuclease | Back alignment and domain information |
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Probab=100.00 E-value=7.8e-38 Score=239.13 Aligned_cols=151 Identities=32% Similarity=0.329 Sum_probs=134.7 Q ss_pred CCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCH Q ss_conf 82799717778985445079999841894289974657785706776777323640230100001688865420000000 Q gi|254780636|r 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPV 100 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i 100 (207) T Consensus 1 ~~ia~D~Et~~l~~~~~~i~~iql~~~~~~~yi~~~~~~~~~~~~l~~~l~~~~i~Kv~hn~k~D~~~L~~~~~~~~~~~ 80 (155) T cd00007 1 KEVAFDTETTGLNYHRGKLVGIQIATAGEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNI 80 (155) T ss_pred CEEEEECCCCCCCCCCCCEEEEEEEECCCEEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHCCCCCCCCE T ss_conf 98999898799977888099999998993599981475524699999998299973898734000999986286013501 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 457898865211000000887776542002467520036565----44323689999864599999999999999 Q gi|254780636|r 101 FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSA----DDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 101 ~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~----rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) T Consensus 81 ~Dt~iaa~ll~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 155 (155) T cd00007 81 FDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEEL 155 (155) T ss_pred EHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 149999998477855236999999983987674888617765444479989999999999999999999999659 |
The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). |
>cd06128 DNA_polA_exo The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity | Back alignment and domain information |
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Probab=99.98 E-value=5.8e-32 Score=205.03 Aligned_cols=147 Identities=24% Similarity=0.255 Sum_probs=125.6 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC----------HHHHHHHHCCCCCEEECCCCHHHHHH Q ss_conf 98279971777898544507999984189428997465778570----------67767773236402301000016888 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA----------PNLVGMLVDEKREKIFHYGRFDIAVL 89 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~----------~~L~~ll~d~~i~KV~Hn~~~D~~~L 89 (207) T Consensus 1 a~~~a~DtETt~ld~~~a~iVGis~s~~~~~a~YiP~~h~~~~~~~~l~~~~vl~~L~p~led~~i~KighNlK~D~~vL 80 (166) T cd06128 1 APVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGIL 80 (166) T ss_pred CCEEEEECCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHH T ss_conf 99899978879989043549999998008969999526776675257789999999999973999764531156679999 Q ss_pred HHHHHCCCCCH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC-------CCCCEECCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 65420000000-4578988652110000008877765420024-------675200365654432368999986459999 Q gi|254780636|r 90 FYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINI-------SKAQQSSDWSADDLSDEQLQYAASDVVHLH 161 (207) Q Consensus 90 ~~~~gi~~~~i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~l-------dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~ 161 (207) T Consensus 81 ~~~-Gi~l~g~~fDTMlaaylldp~~~~h~Ld~La~~~L~~~~i~~~dl~GkGk~q~~f~~v~i-~~~~~YA~eDAd~t~ 158 (166) T cd06128 81 ANY-GIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIAL-EEAGRYAAEDADVTL 158 (166) T ss_pred HHC-CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCEEHHHHHCCCCCCCCCCCCCH-HHHHHHHHHHHHHHH T ss_conf 619-966899984576798762899988996999999839987059998378857589322899-999998999999999 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780636|r 162 ALRLQFT 168 (207) Q Consensus 162 ~L~~~l~ 168 (207) T Consensus 159 rL~~~l~ 165 (166) T cd06128 159 QLHLKMW 165 (166) T ss_pred HHHHHHC T ss_conf 9998538 |
Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli pol I, the Thermus aquaticus (Taq) pol I, and Bacillus stearothermophilus (BF) pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF pol I and Taq pol I resemble the fold of the 3'-5' exonuclease domain of KF |
>KOG2206 consensus | Back alignment and domain information |
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Probab=99.94 E-value=1.3e-27 Score=179.76 Aligned_cols=156 Identities=27% Similarity=0.275 Sum_probs=139.2 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCC Q ss_conf 24898279971777898544507999984189428997465778570677677732364023010000168886542000 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVR 96 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~ 96 (207) T Consensus 209 l~~~~Efavdlehhsyrsf~gltclmqISTr~ed~iIDt~~l-~~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiy 287 (687) T KOG2206 209 LDSVIEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTFKL-RDHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIY 287 (687) T ss_pred HHHHHHHHHHCCCCCHHHHCCCEEEEEEECCCHHHEEHHHHH-HHHHHHHHHHCCCCCEEEEEECCCCCHHHHHCCCEEE T ss_conf 855356532036520453337206899530420312114788-8888774221058874789734764034340230489 Q ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0000457898865211000000887776542002467520036565443236899998645999999999999999749 Q gi|254780636|r 97 VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 97 ~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) T Consensus 288 vvnLfdt~~a~r~L~--~~r~sL~~ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a 364 (687) T KOG2206 288 VVNLFDTIQASRLLG--LPRPSLAYLLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLA 364 (687) T ss_pred EEECHHHHHHHHHHC--CCCCCHHHHHHHHHHHHHHHHHHHCHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHH T ss_conf 985110588998857--99400999999987453114664110003658588988875123158999999999999870 |
|
>cd06126 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction | Back alignment and domain information |
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Probab=99.78 E-value=2e-18 Score=126.39 Aligned_cols=143 Identities=22% Similarity=0.246 Sum_probs=112.5 Q ss_pred CEEEECCCCCCCC--CCCEEEEEEEEECCCCEEEECCCCCCCC----------CHHHHHHHHCCCCCEEECCC-CHHHHH Q ss_conf 2799717778985--4450799998418942899746577857----------06776777323640230100-001688 Q gi|254780636|r 22 AIAVDTETLGLMP--RRDRLCIVQLSPGDGTVDIIRIAAGQKN----------APNLVGMLVDEKREKIFHYG-RFDIAV 88 (207) Q Consensus 22 ~iaiDtEt~~l~~--~~~~l~LiQl~~~~~~~~l~~~~~~~~~----------~~~L~~ll~d~~i~KV~Hn~-~~D~~~ 88 (207) T Consensus 1 vl~fDiE~~~~~~~~~~~pI~~i~~~~~~g~~~~~~~~~~~~~~~~~~~E~~ll~~f~~~i~~~~dii~GyN~~~FDlpy 80 (181) T cd06126 1 VVAFDIETTPLVGGGGKGPIILIQLAVSAGEKFLLDVLTLTLDAVDSADEKELLGELKAILEDYDDIKVGYNIDSFDLPY 80 (181) T ss_pred CEEEEEECCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCHHH T ss_conf 92898623798999899988999999659978999862434675567899999999999983089989997997787999 Q ss_pred HHHHHHCCC---------------------CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE---ECCCCCCC Q ss_conf 865420000---------------------000457898865211000000887776542002467520---03656544 Q gi|254780636|r 89 LFYTFGVRV---------------------RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ---SSDWSADD 144 (207) Q Consensus 89 L~~~~gi~~---------------------~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q---~SdW~~rp 144 (207) T Consensus 81 L~~R~~~l~~~~~~~~~~~~~~~~~~~~~gr~~~D~~~~~~~~~~~~~~~~L~~va~~~lg~~K~~~~~~~i~~~w~~~~ 160 (181) T cd06126 81 LLNRAGELGIPLRRGRDRSSGSREEINIKGRILFDLLLAAKRLGVALPSYSLDALAEQLLGEGKEKVDQLAIKQAWRARP 160 (181) T ss_pred HHHHHHHHCCCCHHCCCCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCC T ss_conf 99999995897010226665655048634852321999999841364653599999997499956699999999886798 Q ss_pred CCHHHHHHHHHHHHHHHHHH Q ss_conf 32368999986459999999 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 161 ~~~~~~~Y~~~Da~~tl~l~ 180 (181) T cd06126 161 LLERLAEYAAADAYATLQIY 180 (181) T ss_pred CHHHHHHHHHHHHHHHHHHH T ss_conf 66999999999999999976 |
They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. DEDDy exonucleases include the proofreading domains of DNA polymerases (families A and B), as well as RNases such as RNase D and Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, Bacillus-like DNA polymerases contain inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity. |
>KOG2207 consensus | Back alignment and domain information |
---|
Probab=99.77 E-value=2.9e-19 Score=131.21 Aligned_cols=155 Identities=24% Similarity=0.256 Sum_probs=117.7 Q ss_pred CCCC-CCEEEECCCCCC-CCCCCEEEEEEEEECCCCEEEECCCCCCCCCH-----HHHHHHHCCCCCEEECCCCHHHHHH Q ss_conf 2489-827997177789-85445079999841894289974657785706-----7767773236402301000016888 Q gi|254780636|r 17 ARYV-DAIAVDTETLGL-MPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAP-----NLVGMLVDEKREKIFHYGRFDIAVL 89 (207) Q Consensus 17 l~~~-~~iaiDtEt~~l-~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~-----~L~~ll~d~~i~KV~Hn~~~D~~~L 89 (207) T Consensus 409 l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~~-~v~Lidc~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l 487 (617) T KOG2207 409 LSEELRYVGIDSEWKPSKKVSDSKLAILQIFFKD-CVYLIDCVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVL 487 (617) T ss_pred HHHCCEEEEECCCCCCCCCCCHHHHHHHHHHHCC-EEEEEEHHHHHHCHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHH T ss_conf 6316779987454476567880388999987048-089965687652408999999998706886046603356239999 Q ss_pred HHH-----HHCC---CCCH-HHHHHHHHHHHH-------HCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHH Q ss_conf 654-----2000---0000-457898865211-------00000088777654200246752003656544323689999 Q gi|254780636|r 90 FYT-----FGVR---VRPV-FCTKIASRLTRT-------YTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYA 153 (207) Q Consensus 90 ~~~-----~gi~---~~~i-~DT~ias~l~~~-------~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YA 153 (207) T Consensus 488 ~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~ya 567 (617) T KOG2207 488 EASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYA 567 (617) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCHHHHHHHH T ss_conf 86516666313312318889999999988616325542121110110235777522225200050542587306688998 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 8645999999999999999 Q gi|254780636|r 154 ASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 154 A~Dv~~l~~L~~~l~~~L~ 172 (207) T Consensus 568 alDa~~~~~ifkkv~~vv~ 586 (617) T KOG2207 568 ALDAVVLVEIFKKVCSVVE 586 (617) T ss_pred HHCCHHHHHHHHHHHHHCC T ss_conf 8420266899999985130 |
|
>KOG4373 consensus | Back alignment and domain information |
---|
Probab=99.38 E-value=1.6e-12 Score=91.97 Aligned_cols=129 Identities=20% Similarity=0.202 Sum_probs=100.5 Q ss_pred CCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHH-HHHCCCCCHHHHHH-HHHHHHHH Q ss_conf 45079999841894289974657785706776777323640230100001688865-42000000045789-88652110 Q gi|254780636|r 36 RDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFY-TFGVRVRPVFCTKI-ASRLTRTY 113 (207) Q Consensus 36 ~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~-~~gi~~~~i~DT~i-as~l~~~~ 113 (207) T Consensus 146 ~P~~~~lqlcV~en~C~I~ql~~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr~~~~d~~g~~ 225 (319) T KOG4373 146 DPPPDTLQLCVGENRCLIIQLIHCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLRLLVNDSLGGS 225 (319) T ss_pred CCCCCHHHHHHCCCCEEEEEEECCCCCHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHCCCHHHHHHHHHHCCHHHCCC T ss_conf 99843222442664115677631465559999862387705873055530787766552263776640876503333367 Q ss_pred ---CCCHHHHHHHHHHHC--CCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf ---000008877765420--024675200365654432368999986459999999 Q gi|254780636|r 114 ---TNQHGLKDNLKELLG--INISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 114 ---~~~~~L~~L~~~~lg--~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 226 ~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319) T KOG4373 226 MPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319) T ss_pred CCCCCHHHHHHHHHHCCCCCCCCCHHCCCCCCEEEECCHHHHHHHHHHHHHHHHHH T ss_conf 66761889999874124622025721043565146266889999876788887888 |
|
>PRK07740 hypothetical protein; Provisional | Back alignment and domain information |
---|
Probab=99.31 E-value=4.3e-11 Score=83.74 Aligned_cols=142 Identities=17% Similarity=0.187 Sum_probs=93.8 Q ss_pred CCCCCCEEEECCCCCCCCCC-CEEEEEEEEE---CCC----CE-EEECCCCCC---------------CCCH-------H Q ss_conf 24898279971777898544-5079999841---894----28-997465778---------------5706-------7 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRR-DRLCIVQLSP---GDG----TV-DIIRIAAGQ---------------KNAP-------N 65 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~-~~l~LiQl~~---~~~----~~-~l~~~~~~~---------------~~~~-------~ 65 (207) T Consensus 54 L~~~~fvV~D~ETTGl~p~~gD~I--IeIgAVkv~~g~i~d~F~tLVnP~~~Ip~~i~~ltGIT~emV~~aP~~~eVl~~ 131 (240) T PRK07740 54 LTDLPFVVFDLETTGFSPDQGDEI--LSIAAVKTVGGEVTDLYYSLVKPKKPIPEHILTLTGISAKDVVFAPPLAEVLRT 131 (240) T ss_pred CCCCEEEEEEEECCCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCHHHHHCCCCHHHHHHH T ss_conf 433838999805899898889878--999899999999968877550887989988998609899998379999999999 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHH----HHCCCC-CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCC Q ss_conf 767773236402301000016888654----200000-004578988652110000008877765420024675200365 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYT----FGVRVR-PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~----~gi~~~-~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW 140 (207) T Consensus 132 fl~Fi~~~--vlVaHNa~FD~~FL~~~l~r~~~~~~~~~~iDT~~Lar~l~~-~~~~sL~~l~~~-fgI~~~~------- 200 (240) T PRK07740 132 FYPFINAS--TLVGYHIGHDLAFLRHALWRHYRQKFSHRFIDTQFLTEIIAH-QSFPTLDDALAC-YGITCPR------- 200 (240) T ss_pred HHHHHCCC--EEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCC------- T ss_conf 99983899--899968286399999999984599878876369999998658-998789999997-6999999------- Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH Q ss_conf 6544323689999864599999999999999974918999 Q gi|254780636|r 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 (207) Q Consensus 141 ~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~ 180 (207) T Consensus 201 ---------rHrAl~DA~aTA~lf~~ll~~l~~~Gi~TL~ 231 (240) T PRK07740 201 ---------RHTADGDVEMTAKLWAILIIEARQAGIETLH 231 (240) T ss_pred ---------CCCCHHHHHHHHHHHHHHHHHHHHCCCCCHH T ss_conf ---------9882999999999999999999976999899 |
|
>PRK06310 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=99.28 E-value=4.4e-11 Score=83.64 Aligned_cols=136 Identities=16% Similarity=0.185 Sum_probs=89.4 Q ss_pred HCCCCCCEEEECCCCCCCCCCCEEEEEEEEE----CCCC----EEEECCCCC-C--------------CCCH-------H Q ss_conf 4248982799717778985445079999841----8942----899746577-8--------------5706-------7 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSP----GDGT----VDIIRIAAG-Q--------------KNAP-------N 65 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~----~~~~----~~l~~~~~~-~--------------~~~~-------~ 65 (207) T Consensus 3 ll~~~~yvv~D~ETTGl~~~~DrI--IEI~~vkv~~~~i~~~~~~linP~~~I~~~~~~ihGIt~emV~d~P~f~ev~~~ 80 (250) T PRK06310 3 LLKDTEFVCLDCETTGLDVKKDRI--IEFAAIRFTFDEVIDSMEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQ 80 (250) T ss_pred CCCCCCEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHHH T ss_conf 666898899973379979999627--999999999998868899998928979988987615489998469999999999 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHHH---HCCC----CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 7677732364023010000168886542---0000----00045789886521100000088777654200246752003 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYTF---GVRV----RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~~----~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) T Consensus 81 ~~~fi~~~~il-VaHNa~FD~~fL~~e~~r~g~~~~~~~~~~IDTl~lAr~~~-~~~~~~L~~L~~~-~~i~~~~a---- 153 (250) T PRK06310 81 IKGFFKEGDYI-VGHSVGFDLQVLAQEAERIGETFLSKHYYIIDTLRLAKEYG-DSPNNSLEALAVH-FNVPYDGN---- 153 (250) T ss_pred HHHHHCCCCEE-EEECHHHHHHHHHHHHHHCCCCCCCCCCCEECHHHHHHHCC-CCCCCHHHHHHHH-CCCCCCCC---- T ss_conf 99996799999-99384557999999999769986656795784999997567-6545609999997-09999866---- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6565443236899998645999999999999999 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) T Consensus 154 ------------HrAl~Da~aTa~vf~~l~~r~~ 175 (250) T PRK06310 154 ------------HRAMKDVEININVFKHLCKRFR 175 (250) T ss_pred ------------CCHHHHHHHHHHHHHHHHHHCC T ss_conf ------------6819999999999999998553 |
|
>PRK06631 consensus | Back alignment and domain information |
---|
Probab=99.28 E-value=4.2e-11 Score=83.79 Aligned_cols=130 Identities=25% Similarity=0.334 Sum_probs=82.1 Q ss_pred CCCCEEEECCCCCCCCCC-CEEEEEEEE---------ECCCCE-EEECCCCCCC-C--------------CH-------H Q ss_conf 898279971777898544-507999984---------189428-9974657785-7--------------06-------7 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRR-DRLCIVQLS---------PGDGTV-DIIRIAAGQK-N--------------AP-------N 65 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~-~~l~LiQl~---------~~~~~~-~l~~~~~~~~-~--------------~~-------~ 65 (207) T Consensus 3 ~mr~VvlD~ETTGl~~~~gdrI--IEIgav~~~~~~~t~~-~f~~~inP~r~i~~~~~~ihGIt~e~l~~~P~f~ev~~~ 79 (229) T PRK06631 3 SLREIILDTETTGLDPQQGHRI--VEIGAIEMVNKVLTGR-NFHFYINPERDMPFEAYRIHGISGEFLKDKPLFHTIADD 79 (229) T ss_pred CCCEEEEEEECCCCCCCCCCEE--EEEEEEEEECCEEECC-EEEEEECCCCCCCHHHHHCCCCCHHHHHHCCCHHHHHHH T ss_conf 7888999825799899999879--9999999999988043-799998989979761512018678998538779999999 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHHHH------C---CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE Q ss_conf 76777323640230100001688865420------0---00000457898865211000000887776542002467520 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYTFG------V---RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ 136 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g------i---~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q 136 (207) T Consensus 80 fl~Fi~~s~--LVaHNA~FD~~FLn~El~~l~~~~~~~~~~~~viDTL~lAR~~~Pg-~~~sLdaLc~r-~~I~~----- 150 (229) T PRK06631 80 FLEFISDSK--LIIHNAPFDIKFLNHELSLLKRTEIKLLELANTIDTLVMARSMFPG-SKYNLDALCKR-FKVDN----- 150 (229) T ss_pred HHHHCCCCE--EEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCC-CCCCHHHHHHH-CCCCC----- T ss_conf 999829997--9997638759899999998278888843201101269999986899-88899999998-49999----- Q ss_pred ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 036565443236899998645999999999999 Q gi|254780636|r 137 SSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 137 ~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) T Consensus 151 ---------s~r~~H~AL~DA~llA~Vyl~l~g 174 (229) T PRK06631 151 ---------SGRQLHGALKDAALLAEVYVELTG 174 (229) T ss_pred ---------CCCCCCCCHHHHHHHHHHHHHHHC T ss_conf ---------985556868999999999999717 |
|
>PRK07942 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
---|
Probab=99.22 E-value=3e-10 Score=78.84 Aligned_cols=136 Identities=18% Similarity=0.220 Sum_probs=84.3 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEE----CCC-----CEEEECCCCCC--------------------CCCHHHHH- Q ss_conf 8982799717778985445079999841----894-----28997465778--------------------57067767- Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSP----GDG-----TVDIIRIAAGQ--------------------KNAPNLVG- 68 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~----~~~-----~~~l~~~~~~~--------------------~~~~~L~~- 68 (207) T Consensus 5 ~~~lvvfD~ETTG~d~~~dRII--eia~V~~~~~g~~~~~~~~LvnPg~~IP~~a~~vhGIT~e~~~~~G~p~a~v~~ei 82 (234) T PRK07942 5 DGPLAAFDLETTGVDPETARIV--TAAIVVVDAHGEVVERREWLADPGVEIPEEASAVHGITTERARAHGRPAAEVLAEI 82 (234) T ss_pred CCCEEEEEEECCCCCCCCCEEE--EEEEEEEECCCCEEEEEEEEECCCCCCCHHHHHHHCCCHHHHHHCCCCCHHHHHHH T ss_conf 6978999801699898898389--99999998898546889998695894998897784889999974289830799999 Q ss_pred ------HHHCCCCCEEECCCCHHHHHHHHHH---HCC---CCCHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCC Q ss_conf ------7732364023010000168886542---000---000045789886521100-000088777654200246752 Q gi|254780636|r 69 ------MLVDEKREKIFHYGRFDIAVLFYTF---GVR---VRPVFCTKIASRLTRTYT-NQHGLKDNLKELLGINISKAQ 135 (207) Q Consensus 69 ------ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~---~~~i~DT~ias~l~~~~~-~~~~L~~L~~~~lg~~ldK~~ 135 (207) T Consensus 83 a~~l~~~~~-~g~~lVahNA~FDl~fL~~El~R~g~~~l~~~~viDtl~l~r~l~~~r~gkr~L~aL~~~y-gv~l~~a- 159 (234) T PRK07942 83 AEALRAVWR-AGVPVVVYNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKHVDRYRKGKRTLTALCEHY-GVRLDNA- 159 (234) T ss_pred HHHHHHHHH-CCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHCCCCCCCCCHHHHHHHC-CCCCCCC- T ss_conf 999999972-7987999670764999999999859996777755619998877514777888899999984-9988775- Q ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 003656544323689999864599999999999999974 Q gi|254780636|r 136 QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 136 q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) T Consensus 160 ---------------H~A~aDA~Ata~l~~~l~~r~~~l 183 (234) T PRK07942 160 ---------------HDATADALAAARLAWALARRFPEL 183 (234) T ss_pred ---------------CCCHHHHHHHHHHHHHHHHHHHHH T ss_conf ---------------564152899999999999876887 |
|
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=99.16 E-value=1.3e-09 Score=75.06 Aligned_cols=136 Identities=27% Similarity=0.344 Sum_probs=88.9 Q ss_pred CCCEEEECCCCCCCCCC-CEEEEEEEEE---CCCCE---EEECCCCCCC-----------------C-------CHHHHH Q ss_conf 98279971777898544-5079999841---89428---9974657785-----------------7-------067767 Q gi|254780636|r 20 VDAIAVDTETLGLMPRR-DRLCIVQLSP---GDGTV---DIIRIAAGQK-----------------N-------APNLVG 68 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~-~~l~LiQl~~---~~~~~---~l~~~~~~~~-----------------~-------~~~L~~ 68 (207) T Consensus 3 ~~~~vvDlETTG~~~~~~d~I--Iqig~v~i~~~~i~~~f~t~vnP~~~iP~~I~~LTgI~~~~v~~AP~f~eva~~i~~ 80 (932) T PRK08074 3 KRFVVVDLETTGNSPKKGDKI--IQIAAVVVEDGEILERFSTFVNPERPIPPFITELTGISEEMVKNAPLFEDVAPMIVE 80 (932) T ss_pred CEEEEEEEECCCCCCCCCCEE--EEEEEEEEECCEEEEEEECCCCCCCCCCHHHHHHCCCCHHHHCCCCCHHHHHHHHHH T ss_conf 708999988889897779889--999799999999989985325899989977886069898998059998999999999 Q ss_pred HHHCCCCCEEECCCCHHHHHHHHHH---HCC-CC-CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCC Q ss_conf 7732364023010000168886542---000-00-004578988652110000008877765420024675200365654 Q gi|254780636|r 69 MLVDEKREKIFHYGRFDIAVLFYTF---GVR-VR-PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSAD 143 (207) Q Consensus 69 ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~-~~-~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~r 143 (207) T Consensus 81 ~l~~~--~~VaHNv~FD~~FL~~~l~~~G~~~~~~~~~DTveLa~i~~P~~~sy~L~~L~~~-l~i~~~~~--------- 148 (932) T PRK08074 81 LLEGA--YFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTADSYKLSDLSEE-LELEHDQP--------- 148 (932) T ss_pred HHCCC--EEEECCHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHCCCCCCCCHHHHHHH-CCCCCCCC--------- T ss_conf 96699--5994780540999999999739986668765199999997788788888999986-49999998--------- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 432368999986459999999999999997491 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALRLQFTEKLQRLGR 176 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~ 176 (207) T Consensus 149 -------HrA~sDa~aTa~l~~~l~~~l~~lp~ 174 (932) T PRK08074 149 -------HRADSDAEVTAELFLQLLHKLERLPL 174 (932) T ss_pred -------CCCHHHHHHHHHHHHHHHHHHHHCCH T ss_conf -------75178899999999999999983799 |
|
>PRK06022 consensus | Back alignment and domain information |
---|
Probab=99.14 E-value=4.3e-10 Score=77.88 Aligned_cols=127 Identities=21% Similarity=0.275 Sum_probs=79.3 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE-----C--C-CCE-EEECCC-CC-CCC--------------C-------HHHHHH Q ss_conf 2799717778985445079999841-----8--9-428-997465-77-857--------------0-------677677 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP-----G--D-GTV-DIIRIA-AG-QKN--------------A-------PNLVGM 69 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~-----~--~-~~~-~l~~~~-~~-~~~--------------~-------~~L~~l 69 (207) T Consensus 3 ~IvlDtETTGl~~~~dRI--IEIg~vel~~~~~t~~~f~~~inP~~r~I~~~a~~IHGIt~e~L~~~P~F~eva~~fl~F 80 (234) T PRK06022 3 EIIFDTETTGLERREDRV--IEIGGVELVNRFPTGRTFHKFINPQGRQVHPDALAVHGISDEQLLDKPVFAEILDEFLEF 80 (234) T ss_pred EEEEEEECCCCCCCCCCE--EEEEEEEEECCCCCCCEEEEEECCCCCCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHH T ss_conf 699982279989989707--999999997786336578999899998689889988560899870599799999999998 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH---HCC---CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCC Q ss_conf 732364023010000168886542---000---00004578988652110000008877765420024675200365654 Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF---GVR---VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSAD 143 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~---gi~---~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~r 143 (207) T Consensus 81 i~~a~--LVaHNA~FD~gFLn~El~r~G~~~~~~~~viDTL~LAR~~~P-g~~~sLdaLc~r-~~Id~~---------~R 147 (234) T PRK06022 81 FDGAR--LVAHNATFDLGFINAEFARLGQPEITSERVVDTLALARRKHP-MGPNSLDALCRR-YGIDNS---------HR 147 (234) T ss_pred HCCCE--EEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCC-CCCCCHHHHHHH-CCCCCC---------CC T ss_conf 18985--999557872999999999859987778887469999998688-998898999998-399977---------73 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4323689999864599999999999 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 148 ~-----~HgAL~Da~lLa~VyleL~ 167 (234) T PRK06022 148 T-----KHGALLDSELLAEVYIELI 167 (234) T ss_pred C-----CCCCHHHHHHHHHHHHHHC T ss_conf 5-----3762888999999999972 |
|
>PRK08517 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
---|
Probab=99.14 E-value=6.7e-10 Score=76.81 Aligned_cols=135 Identities=19% Similarity=0.193 Sum_probs=88.0 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCCCE-----EEECCCCCC--------------CCC-------HHHH Q ss_conf 248982799717778985445079999841---89428-----997465778--------------570-------6776 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDGTV-----DIIRIAAGQ--------------KNA-------PNLV 67 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~~-----~l~~~~~~~--------------~~~-------~~L~ 67 (207) T Consensus 67 ~ke~~fvvvDlETTGl~~~~d~I--IEIgavkv~~g~iid~f~tlVnp~~Ip~~It~lTGIt~emv~~aP~~~evl~~f~ 144 (259) T PRK08517 67 IKEQVFCFVDIETNGSKPKKGQI--IEIGAVKVKGGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEDFR 144 (259) T ss_pred CCCCCEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHCCCCHHHHHCCCCHHHHHHHHH T ss_conf 67883899996589989999824--9999999999999998743239898998882213899899827998899999999 Q ss_pred HHHHCCCCCEEECCCCHHHHHHHHHHH---CC-C-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCC Q ss_conf 777323640230100001688865420---00-0-000457898865211000000887776542002467520036565 Q gi|254780636|r 68 GMLVDEKREKIFHYGRFDIAVLFYTFG---VR-V-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSA 142 (207) Q Consensus 68 ~ll~d~~i~KV~Hn~~~D~~~L~~~~g---i~-~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~ 142 (207) T Consensus 145 ~Fi~d~--ilVaHNa~FD~~FL~~~l~r~g~~~l~n~~lDTl~LAR~~~p~-~~ykL~~La~~-~~I~~~~~-------- 212 (259) T PRK08517 145 LFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKEL-LGIETEVH-------- 212 (259) T ss_pred HHHCCC--EEEEECCHHHHHHHHHHHHHCCCCCCCCCEEEEHHHHHHHCCC-CCCCHHHHHHH-CCCCCCCC-------- T ss_conf 996889--5999372760999999999839997689856608999987587-78788999997-59899999-------- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4432368999986459999999999999997 Q gi|254780636|r 143 DDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 143 rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) T Consensus 213 --------HRAl~DA~aTaevF~~~L~~l~~ 235 (259) T PRK08517 213 --------HRAYADALAAYEIFEICLLNLPS 235 (259) T ss_pred --------CCCHHHHHHHHHHHHHHHHHCCC T ss_conf --------78458899999999999985665 |
|
>PRK08858 consensus | Back alignment and domain information |
---|
Probab=99.13 E-value=6.2e-10 Score=77.00 Aligned_cols=133 Identities=18% Similarity=0.229 Sum_probs=83.5 Q ss_pred CCCCCEEEECCCCCCCCCC----CEEEEEEEEEC---C-----CCE-EEECCCCCCC---------------CC------ Q ss_conf 4898279971777898544----50799998418---9-----428-9974657785---------------70------ Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRR----DRLCIVQLSPG---D-----GTV-DIIRIAAGQK---------------NA------ 63 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~----~~l~LiQl~~~---~-----~~~-~l~~~~~~~~---------------~~------ 63 (207) T Consensus 8 ~~~R~VVlDtETTGl~~~~~~~~~gdRIIEIgaV~i~~~~~t~~~f~~~InP~r~Ip~~a~~ihGIT~e~L~daP~F~eI 87 (246) T PRK08858 8 EYQRIVVLDTETTGMNREGGPHYEGHRIIEIGAVEIINRKLTGRHFHVYLKPDREIQPEAIDVHGITDEFLVDKPEYKDV 87 (246) T ss_pred CCCEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEEECCEEECCEEEEEECCCCCCCHHHHHHCCCCHHHHHCCCCHHHH T ss_conf 60479999857899997656777898799999999999998221478888979969988997739289998359758999 Q ss_pred -HHHHHHHHCCCCCEEECCCCHHHHHHHHHHHC---CC------CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC Q ss_conf -67767773236402301000016888654200---00------000457898865211000000887776542002467 Q gi|254780636|r 64 -PNLVGMLVDEKREKIFHYGRFDIAVLFYTFGV---RV------RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 (207) Q Consensus 64 -~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi---~~------~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK 133 (207) T Consensus 88 ~~efl~FI~d~~L--VaHNa~FD~~FLn~El~r~~~~~~~~~~~~~viDTL~lAR~~~P-g~~~sLdaLc~r-~~Id~-- 161 (246) T PRK08858 88 HQEFLEFIKGAEL--VAHNAPFDVGFMDYEFEKLNPAIGKTDDYCKVTDTLAMAKKIFP-GKRNNLDVLCER-YGIDN-- 161 (246) T ss_pred HHHHHHHHCCCEE--EEECCHHHHHHHHHHHHHHCCCCCCHHHHCCCEEHHHHHHHHCC-CCCCCHHHHHHH-CCCCC-- T ss_conf 9999999589989--99722888999999999828776751342010029999998689-998888999998-19898-- Q ss_pred CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 52003656544323689999864599999999999 Q gi|254780636|r 134 AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 134 ~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 162 ------------s~R~~HgALlDa~lLa~Vyl~mt 184 (246) T PRK08858 162 ------------SHRTLHGALLDAEILADVYLLMT 184 (246) T ss_pred ------------CCCCCCCHHHHHHHHHHHHHHHC T ss_conf ------------88340230888999999999972 |
|
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=99.13 E-value=2.5e-09 Score=73.47 Aligned_cols=136 Identities=19% Similarity=0.223 Sum_probs=89.2 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEE---CCCCE---EEECCCCCCCC------------------------CHHHHH Q ss_conf 8982799717778985445079999841---89428---99746577857------------------------067767 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSP---GDGTV---DIIRIAAGQKN------------------------APNLVG 68 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~~---~l~~~~~~~~~------------------------~~~L~~ 68 (207) T Consensus 6 ~~~~~vvDlETTG~~~~-~--~Iiqi~~v~~~~~~i~~~f~t~vnP~~~ip~~I~~LTgI~~~~v~~ap~f~~v~~~~~~ 82 (820) T PRK07246 6 LRKYAVVDLEATGAGPN-A--SIIQVGIVIIQGNKIIDSYETDVNPHESLDEHIVHLTGITDKQLAQAPDFSQVAHHIYQ 82 (820) T ss_pred CCCEEEEEEECCCCCCC-C--CEEEEEEEEEECCEEEEEEEECCCCCCCCCHHHHHHCCCCHHHHHCCCCHHHHHHHHHH T ss_conf 67189999887898999-8--77999999999999989987311889979978886469898998529998999999999 Q ss_pred HHHCCCCCEEECCCCHHHHHHHHHH---HCCC-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCC Q ss_conf 7732364023010000168886542---0000-00045789886521100000088777654200246752003656544 Q gi|254780636|r 69 MLVDEKREKIFHYGRFDIAVLFYTF---GVRV-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADD 144 (207) Q Consensus 69 ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rp 144 (207) T Consensus 83 ~l~~~--~~VaHNv~FD~~fl~~~~~~~g~~~~~~~~DTv~La~i~~P~~~~y~L~~L~~~-l~~~~~~~H--------- 150 (820) T PRK07246 83 LIEDC--IFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPRLEKYSLSHLSRQ-LNIDLAEAH--------- 150 (820) T ss_pred HHCCC--EEEEECCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHH-CCCCCCCCC--------- T ss_conf 96798--599837201699999999975898899826099999997798788888999997-399999887--------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 32368999986459999999999999997491 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEKLQRLGR 176 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~ 176 (207) T Consensus 151 -------rA~~Da~ata~l~~~l~~~l~~lp~ 175 (820) T PRK07246 151 -------TAIADARATAILFLRLLQKIESLPK 175 (820) T ss_pred -------CHHHHHHHHHHHHHHHHHHHHCCCH T ss_conf -------6188999999999999999861999 |
|
>PRK07009 consensus | Back alignment and domain information |
---|
Probab=99.12 E-value=8.6e-10 Score=76.16 Aligned_cols=127 Identities=24% Similarity=0.338 Sum_probs=79.1 Q ss_pred CEEEECCCCCCCCCC-CEEEEEEEE---------ECCCCEEEECCCCCC-CC--------------CH-------HHHHH Q ss_conf 279971777898544-507999984---------189428997465778-57--------------06-------77677 Q gi|254780636|r 22 AIAVDTETLGLMPRR-DRLCIVQLS---------PGDGTVDIIRIAAGQ-KN--------------AP-------NLVGM 69 (207) Q Consensus 22 ~iaiDtEt~~l~~~~-~~l~LiQl~---------~~~~~~~l~~~~~~~-~~--------------~~-------~L~~l 69 (207) T Consensus 3 ~VvlDtETTGl~~~~gdRI--IEIg~v~l~~~~~t~~~~~~yiNP~r~I~~~a~~IHGIt~e~L~~kP~F~eia~efl~F 80 (241) T PRK07009 3 QIILDTETTGLNARTGDRI--IEIGCVELLNRRLTGNNLHFYVNPERDSDPGALAVHGLTTEFLSDKPKFAEVVDQIRDF 80 (241) T ss_pred EEEEEEECCCCCCCCCCEE--EEEEEEEEECCEEECEEEEEEECCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHHH T ss_conf 7999825799799999878--99999999999780406899878899799757651225799872585599999999999 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH---HCCC-C----CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCC Q ss_conf 732364023010000168886542---0000-0----0045789886521100000088777654200246752003656 Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF---GVRV-R----PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWS 141 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~---gi~~-~----~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~ 141 (207) T Consensus 81 i~~a~L--VaHNA~FD~~FLn~EL~r~G~~~~~~~~~~viDTL~lAR~~~P-g~~~sLdaLc~R-~~I~~---------- 146 (241) T PRK07009 81 VQDAEL--IIHNAPFDLGFLDAEFALLGLPPFTEHCAGVIDTLVQAKQMFP-GKRNSLDALCDR-FGISN---------- 146 (241) T ss_pred HCCCEE--EEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHH-CCCCC---------- T ss_conf 669927--8867699999999999983997310244447679999999789-998788999998-28698---------- Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 544323689999864599999999999 Q gi|254780636|r 142 ADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 142 ~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 147 ----~~r~~HgAL~Da~lLa~vyl~mt 169 (241) T PRK07009 147 ----AHRTLHGALLDSELLAEVYLAMT 169 (241) T ss_pred ----CCCCCCCCHHHHHHHHHHHHHHH T ss_conf ----87330242877999999999983 |
|
>PRK05711 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
---|
Probab=99.09 E-value=1.2e-09 Score=75.42 Aligned_cols=129 Identities=27% Similarity=0.344 Sum_probs=77.6 Q ss_pred CCEEEECCCCCCCCCC-CEEEEEEEE---------ECCCCEEEECCCCCC---------------CCCH-------HHHH Q ss_conf 8279971777898544-507999984---------189428997465778---------------5706-------7767 Q gi|254780636|r 21 DAIAVDTETLGLMPRR-DRLCIVQLS---------PGDGTVDIIRIAAGQ---------------KNAP-------NLVG 68 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~-~~l~LiQl~---------~~~~~~~l~~~~~~~---------------~~~~-------~L~~ 68 (207) T Consensus 5 R~VvlDtETTGl~~~~gdRI--IEIgav~~~~~~~t~~~f~~~inP~r~i~~~a~~IhGIT~e~L~~~P~F~ei~~efl~ 82 (240) T PRK05711 5 RQIVLDTETTGLNQREGHRI--IEIGAVELINRRLTGRNFHVYIKPDRDVDPEALAVHGITDEFLADKPTFAEVADEFLD 82 (240) T ss_pred CEEEEEEECCCCCCCCCCEE--EEEEEEEEECCEECCCEEEEEECCCCCCCHHHHHHCCCCHHHHCCCCCHHHHHHHHHH T ss_conf 28999866899699999878--9999999999988143578998968959977875408688996458759999999999 Q ss_pred HHHCCCCCEEECCCCHHHHHHHHHH---HCC---CC---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECC Q ss_conf 7732364023010000168886542---000---00---00457898865211000000887776542002467520036 Q gi|254780636|r 69 MLVDEKREKIFHYGRFDIAVLFYTF---GVR---VR---PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139 (207) Q Consensus 69 ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~---~~---~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~Sd 139 (207) T Consensus 83 Fi~~s--~lVaHNa~FD~~FLn~El~r~g~~~~~~~~~~~viDTL~lAR~~~P-g~~~sLdaLc~r-~~I~~-------- 150 (240) T PRK05711 83 FIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTTTFCKVTDTLAMARRMFP-GKRNSLDALCKR-YGIDN-------- 150 (240) T ss_pred HHCCC--EEEEECCHHHHHHHHHHHHHHCCCCCCHHHHCCHHHHHHHHHHHCC-CCCCCHHHHHHH-CCCCC-------- T ss_conf 81899--7999661998999999999868998764452121019999998789-998899999998-09898-------- Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 565443236899998645999999999999 Q gi|254780636|r 140 WSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 140 W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) T Consensus 151 -s~R~-----~HgAL~Da~llA~Vyl~l~g 174 (240) T PRK05711 151 -SHRT-----LHGALLDAEILAEVYLAMTG 174 (240) T ss_pred -CCCC-----CCCHHHHHHHHHHHHHHHCC T ss_conf -8756-----57648889999999999717 |
|
>PRK08816 consensus | Back alignment and domain information |
---|
Probab=99.08 E-value=1.5e-09 Score=74.74 Aligned_cols=128 Identities=23% Similarity=0.309 Sum_probs=76.3 Q ss_pred CCEEEECCCCCCCCCC-CEEEEEEEE---------ECCCCEEEECCCCCC-CC--------------C-------HHHHH Q ss_conf 8279971777898544-507999984---------189428997465778-57--------------0-------67767 Q gi|254780636|r 21 DAIAVDTETLGLMPRR-DRLCIVQLS---------PGDGTVDIIRIAAGQ-KN--------------A-------PNLVG 68 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~-~~l~LiQl~---------~~~~~~~l~~~~~~~-~~--------------~-------~~L~~ 68 (207) T Consensus 2 R~VVlDtETTGl~~~~gdRI--IEIgaV~~~~~~~~~~~f~~~inP~r~I~~~a~~vhGIT~e~L~dkP~F~eV~~efl~ 79 (244) T PRK08816 2 RQIILDTETTGLEWRKGNRV--VEIGAVELLERRPSGNNFHRYLKPDCDFEPGAQEVTGLTLEFLADKPLFGEVVDEFLA 79 (244) T ss_pred CEEEEEEECCCCCCCCCCEE--EEEEEEEEECCEECCCEEEEEECCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHH T ss_conf 87999722799899899889--9999999999968143789986889969988987525178998409989999999999 Q ss_pred HHHCCCCCEEECCCCHHHHHHHHHHHC---C------CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECC Q ss_conf 773236402301000016888654200---0------0000457898865211000000887776542002467520036 Q gi|254780636|r 69 MLVDEKREKIFHYGRFDIAVLFYTFGV---R------VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139 (207) Q Consensus 69 ll~d~~i~KV~Hn~~~D~~~L~~~~gi---~------~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~Sd 139 (207) T Consensus 80 Fi~ds~--LVaHNa~FDi~FLn~El~r~g~~~~~~~~~~~v~DTl~lAr~~~P-g~~nsLDaLc~r~-~id~-------- 147 (244) T PRK08816 80 YIDGAE--LIIHNAAFDLGFLDNELSLLGDQYGRIVDRATVVDTLMMARERYP-GQRNSLDALCKRL-GVDN-------- 147 (244) T ss_pred HHCCCE--EEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCC-CCCCCHHHHHHHC-CCCC-------- T ss_conf 828998--999663652989999999848875676431010438999998787-9977899999974-9788-------- Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56544323689999864599999999999 Q gi|254780636|r 140 WSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 140 W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 148 ------~~R~~HgALlDa~lLa~VYl~mt 170 (244) T PRK08816 148 ------SHRQLHGALLDAQILADVYIALT 170 (244) T ss_pred ------CCCCCCCHHHHHHHHHHHHHHHC T ss_conf ------77350148887999999999974 |
|
>cd06131 DNA_pol_III_epsilon_Ecoli_like This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (polIII) and similar proteins | Back alignment and domain information |
---|
Probab=99.07 E-value=1.3e-09 Score=75.14 Aligned_cols=125 Identities=25% Similarity=0.320 Sum_probs=75.4 Q ss_pred EEEECCCCCCCCCC-CEEEEEEEEE-----C---CCCE-EEECCCCCC-C--------------CC-------HHHHHHH Q ss_conf 79971777898544-5079999841-----8---9428-997465778-5--------------70-------6776777 Q gi|254780636|r 23 IAVDTETLGLMPRR-DRLCIVQLSP-----G---DGTV-DIIRIAAGQ-K--------------NA-------PNLVGML 70 (207) Q Consensus 23 iaiDtEt~~l~~~~-~~l~LiQl~~-----~---~~~~-~l~~~~~~~-~--------------~~-------~~L~~ll 70 (207) T Consensus 2 Vv~D~ETTGl~p~~~d~I--ieigav~~~~~~~~~~~~~~lv~P~~~i~~~~~~ihGIt~e~l~~~p~~~ev~~~f~~~l 79 (167) T cd06131 2 IVLDTETTGLDPREGHRI--IEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79 (167) T ss_pred EEEECCCCCCCCCCCCEE--EEEEEEEEECCEEECCEEEEEECCCCCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHC T ss_conf 899760698898899837--999999999999924478999897898998899780968589835975899999998635 Q ss_pred HCCCCCEEECCCCHHHHHHHHHH---HCCC-----CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCC Q ss_conf 32364023010000168886542---0000-----000457898865211000000887776542002467520036565 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTF---GVRV-----RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSA 142 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~---gi~~-----~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~ 142 (207) T Consensus 80 ~~~--~lVaHN~~FD~~fL~~~~~r~~~~~~~~~~~~~~Dtl~l~r~~~p-~~~~~L~~l~~~-~gi~~~---------- 145 (167) T cd06131 80 RGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFP-GKPNSLDALCKR-FGIDNS---------- 145 (167) T ss_pred CCC--EEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCHHHHHHH-CCCCCC---------- T ss_conf 699--999837187899999999981899777765541139999999849-998889999987-697999---------- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4432368999986459999999999 Q gi|254780636|r 143 DDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 143 rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 146 ----~~~~H~Al~Da~~ta~vf~~l 166 (167) T cd06131 146 ----HRTLHGALLDAELLAEVYLEL 166 (167) T ss_pred ----CCCCCCHHHHHHHHHHHHHHH T ss_conf ----998758899999999999976 |
PolIII is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The polIII epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of polIII also functions as a stabilizer of the holoenzyme complex. |
>PRK06807 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=99.07 E-value=2.9e-09 Score=73.05 Aligned_cols=133 Identities=20% Similarity=0.289 Sum_probs=84.7 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEE---CCCC----E-EEECCCCC-C--------------CCCH-------HHHHH Q ss_conf 982799717778985445079999841---8942----8-99746577-8--------------5706-------77677 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSP---GDGT----V-DIIRIAAG-Q--------------KNAP-------NLVGM 69 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~----~-~l~~~~~~-~--------------~~~~-------~L~~l 69 (207) T Consensus 8 ~~fVV~DiETTGl~p~~D~II--EIgAVkv~ng~Ivd~f~tLInP~~~Ip~~It~ItGIT~emV~dAP~f~EVl~~f~~F 85 (313) T PRK06807 8 LDYVVIDFETTGFNPYNDKII--QVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85 (313) T ss_pred CCEEEEEEECCCCCCCCCEEE--EEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH T ss_conf 878999978899799998789--999999999979899999989489799667653397999982699899999999987 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH---HC-CCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCC Q ss_conf 732364023010000168886542---00-0000-045789886521100000088777654200246752003656544 Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF---GV-RVRP-VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADD 144 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~---gi-~~~~-i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rp 144 (207) T Consensus 86 i~d-~iL-VAHNA~FD~~FL~~~L~r~gl~~~~n~~IDTL~LAR~l~P~L~NhKLnTVa~-~LgI~l~------------ 150 (313) T PRK06807 86 LHT-NVI-VAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKR-MLGIRLS------------ 150 (313) T ss_pred CCC-CEE-EEECCHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCHHHHHH-HHCCCCC------------ T ss_conf 389-989-9955366199999999974998889987765999998647876566789999-8399834------------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 323689999864599999999999999974 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) T Consensus 151 -----HHrAldDA~acAeI~~k~~~~~~~~ 175 (313) T PRK06807 151 -----SHNAFDDCITCAAVYQKCASIEEEA 175 (313) T ss_pred -----CCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf -----3671778999999999999988616 |
|
>PRK07982 consensus | Back alignment and domain information |
---|
Probab=99.02 E-value=3e-09 Score=73.04 Aligned_cols=130 Identities=19% Similarity=0.227 Sum_probs=79.0 Q ss_pred CCEEEECCCCCCCCC---CCEEEEEEEE---------ECCCCEEEECCCCCCC---------------CC-------HHH Q ss_conf 827997177789854---4507999984---------1894289974657785---------------70-------677 Q gi|254780636|r 21 DAIAVDTETLGLMPR---RDRLCIVQLS---------PGDGTVDIIRIAAGQK---------------NA-------PNL 66 (207) Q Consensus 21 ~~iaiDtEt~~l~~~---~~~l~LiQl~---------~~~~~~~l~~~~~~~~---------------~~-------~~L 66 (207) T Consensus 7 R~ivlDtETTGL~p~~~~~~gdRIIEIgaVei~~~~~t~~~fh~yiNP~r~I~~~a~~VHGIT~e~L~dkP~F~eI~~ef 86 (243) T PRK07982 7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 86 (243) T ss_pred EEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCHHHHHHEEECHHHHHCCCCHHHHHHHH T ss_conf 58999711799998776778987999999999999882523437888899799889852115778871699899999999 Q ss_pred HHHHHCCCCCEEECCCCHHHHHHHHHHHC---C--C-C---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEE Q ss_conf 67773236402301000016888654200---0--0-0---004578988652110000008877765420024675200 Q gi|254780636|r 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGV---R--V-R---PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQS 137 (207) Q Consensus 67 ~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi---~--~-~---~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~ 137 (207) T Consensus 87 l~Fi~~a~L--VaHNA~FD~~FLn~El~r~g~~~~~~~~~~~v~DTL~lAR~~~P-g~~~sLDaLc~R-~~Id~------ 156 (243) T PRK07982 87 LDYIRGAEL--VIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLALARKMFP-GKRNSLDALCDR-YEIDN------ 156 (243) T ss_pred HHHHCCCEE--EEECCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEHHHHHHHHCC-CCCCCHHHHHHH-CCCCC------ T ss_conf 999679989--99733888999999999708898861012431349999888788-986899999875-48776------ Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3656544323689999864599999999999 Q gi|254780636|r 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 138 SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 157 --------s~R~~HgALlDa~lLAeVYl~lt 179 (243) T PRK07982 157 --------SKRTLHGALLDAQILAEVYLAMT 179 (243) T ss_pred --------CCCCCCCHHHHHHHHHHHHHHHC T ss_conf --------56552333774889999999972 |
|
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit; InterPro: IPR006309 These represent DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria | Back alignment and domain information |
---|
Probab=99.01 E-value=4.6e-09 Score=71.92 Aligned_cols=130 Identities=26% Similarity=0.345 Sum_probs=84.0 Q ss_pred CEEEECCCCCCCCCC-----CEEEEEEEE---------ECCCCEEEECCCCCC-----------------CCCHH----- Q ss_conf 279971777898544-----507999984---------189428997465778-----------------57067----- Q gi|254780636|r 22 AIAVDTETLGLMPRR-----DRLCIVQLS---------PGDGTVDIIRIAAGQ-----------------KNAPN----- 65 (207) Q Consensus 22 ~iaiDtEt~~l~~~~-----~~l~LiQl~---------~~~~~~~l~~~~~~~-----------------~~~~~----- 65 (207) T Consensus 2 ~IiLDTETTGl~~~~G~~~~G-hRivEIGavE~vnr~~tG~~fH~Y~~P~Rd~p~eA~kVHGiT~efL~dKnaP~Fk~Ia 80 (246) T TIGR01406 2 EIILDTETTGLDPKGGLPYIG-HRIVEIGAVELVNRMLTGKNFHVYVKPERDIPAEAAKVHGITDEFLKDKNAPKFKEIA 80 (246) T ss_pred EEEECCCCCCCCCCCCCCCCC-CEEEEEEEEEEECCCCCCCCEEEEECCCCCCHHHCEECCCCCHHHHCCCCCCCHHHHH T ss_conf 267115556877667768568-6268882185673503887312433688877300210137646884688989525789 Q ss_pred --HHHHHHCCCCCEEECCCCHHHHHHHHH---HH---CC----CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC Q ss_conf --767773236402301000016888654---20---00----0000457898865211000000887776542002467 Q gi|254780636|r 66 --LVGMLVDEKREKIFHYGRFDIAVLFYT---FG---VR----VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 (207) Q Consensus 66 --L~~ll~d~~i~KV~Hn~~~D~~~L~~~---~g---i~----~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK 133 (207) T Consensus 81 ~~Fl~Fi~~~~L--vIHNA~FD~gFlN~EL~~Lg~~~~~~~~~~~~~~DTL~mAR~~-FPG~~~sLDALCkR-f~vD--- 153 (246) T TIGR01406 81 DEFLDFIKGSEL--VIHNAAFDVGFLNYELERLGLKEIKKISDFCRVIDTLAMARER-FPGKRNSLDALCKR-FKVD--- 153 (246) T ss_pred HHHHHHHCCCEE--EEECCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHC-CCCCCCCHHHHHHH-HCCC--- T ss_conf 999998459889--9975702167899999872873210001366786568999723-78986646787743-0425--- Q ss_pred CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5200365654432368999986459999999999999 Q gi|254780636|r 134 AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 134 ~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) T Consensus 154 -----------ns~R~LHGAL~DA~LLAeVYl~ltGG 179 (246) T TIGR01406 154 -----------NSHRQLHGALLDAELLAEVYLALTGG 179 (246) T ss_pred -----------CCCCHHHHHHHHHHHHHHHHHHHCCC T ss_conf -----------00021347899999999999986288 |
It consists largely of an exonuclease region as described in IPR006055 from INTERPRO. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are not included in this set of sequences, as they are smaller proteins.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication. |
>cd06134 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA | Back alignment and domain information |
---|
Probab=99.01 E-value=3.6e-09 Score=72.53 Aligned_cols=132 Identities=22% Similarity=0.299 Sum_probs=77.6 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEE------CCC------CE-EEECCCCC-------------C---------CCC Q ss_conf 8982799717778985445079999841------894------28-99746577-------------8---------570 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSP------GDG------TV-DIIRIAAG-------------Q---------KNA 63 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~------~~~------~~-~l~~~~~~-------------~---------~~~ 63 (207) T Consensus 4 ~~~~VV~D~ETTGL~p~~d~I--IEIgav~v~~d~~g~i~~~~~~~~~v~P~~~~~i~~~~~~itGIt~~~~~~~~~~~~ 81 (189) T cd06134 4 GFLPVVVDVETGGFNPQTDAL--LEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEK 81 (189) T ss_pred CCCCEEEEEECCCCCCCCCEE--EEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCCHHHHCCCCCHH T ss_conf 985079995289999889807--999999999768785324516899778988998985566550777001100167577 Q ss_pred HHHHHHHH---C----C---CCCEEECCCCHHHHHHHHHH---HCC--C-CC--HHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 67767773---2----3---64023010000168886542---000--0-00--04578988652110000008877765 Q gi|254780636|r 64 PNLVGMLV---D----E---KREKIFHYGRFDIAVLFYTF---GVR--V-RP--VFCTKIASRLTRTYTNQHGLKDNLKE 125 (207) Q Consensus 64 ~~L~~ll~---d----~---~i~KV~Hn~~~D~~~L~~~~---gi~--~-~~--i~DT~ias~l~~~~~~~~~L~~L~~~ 125 (207) T Consensus 82 ~~~~~~~~~i~~~~~~~~~~~avlVaHNa~FD~~FL~~~~~r~g~~~~p~~~~~~~DTl~La~~~--~-~~~~L~~l~~~ 158 (189) T cd06134 82 EALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLA--Y-GQTVLAKACQA 158 (189) T ss_pred HHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHH--H-CCCCHHHHHHH T ss_conf 88999999999998751675556875177772999999999849988888777656699998677--3-80019999998 Q ss_pred HHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 420024675200365654432368999986459999999999999 Q gi|254780636|r 126 LLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 126 ~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) T Consensus 159 -~gi~~~--------------~~~~HrAl~DA~~ta~lf~~l~~k 188 (189) T cd06134 159 -AGIEFD--------------NKEAHSALYDTQKTAELFCKIVNR 188 (189) T ss_pred -CCCCCC--------------CCCCCCCHHHHHHHHHHHHHHHHH T ss_conf -799999--------------987887299999999999999964 |
It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site. |
>PRK00448 polC DNA polymerase III PolC; Validated | Back alignment and domain information |
---|
Probab=99.01 E-value=8.1e-09 Score=70.50 Aligned_cols=145 Identities=22% Similarity=0.351 Sum_probs=94.5 Q ss_pred HHHCCCCCCEEEECCCCCCCCCCCEEEEEEEEEC---CCCE-----EEECCCC---------------CCCCC------- Q ss_conf 7842489827997177789854450799998418---9428-----9974657---------------78570------- Q gi|254780636|r 14 ECAARYVDAIAVDTETLGLMPRRDRLCIVQLSPG---DGTV-----DIIRIAA---------------GQKNA------- 63 (207) Q Consensus 14 ~~~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~---~~~~-----~l~~~~~---------------~~~~~------- 63 (207) T Consensus 412 ~~~l~~~~yVvFDiETTGls~~~d~I--iEigAvki~~g~iid~f~~fi~P~~~i~~~i~~lT~Itd~mv~~~~~~~evl 489 (1436) T PRK00448 412 DRDLKDATYVVFDVETTGLSAVYDEI--IEIGAVKIKNGEIIDKFEEFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVL 489 (1436) T ss_pred CCCCCCCCEEEEEECCCCCCCCCCCE--EEEEEEEEECCEEEEEEHHHCCCCCCCCHHHHHCCCCCHHHHCCCCCHHHHH T ss_conf 77467663799860068888666723--6875798637817541021038999797545321478847863898789999 Q ss_pred HHHHHHHHCCCCCEEECCCCHHHHHHHHHH---HCC-C-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 677677732364023010000168886542---000-0-00045789886521100000088777654200246752003 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTF---GVR-V-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~-~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) T Consensus 490 ~~f~~f~~d-~-vlVAHNa~FD~~Fi~~~~~~~~~~~~~~p~iDTl~lsr~l~p~~k~~~L~~l~k~-~~v~~~~h---- 562 (1436) T PRK00448 490 PKFKEFCGD-S-VLVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPEYKSHRLNTLAKK-FGVELEHH---- 562 (1436) T ss_pred HHHHHHHCC-C-EEEEECCCCCHHHHHHHHHHCCCCCCCCCEECHHHHHHHHCCCCCCCCHHHHHHH-HCCCCCCC---- T ss_conf 999998289-7-7998458656889999999808986679723029989875510111447889988-48886545---- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 65654432368999986459999999999999997491899 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~ 179 (207) T Consensus 563 ------------HRA~~Da~~t~~i~~~~l~~~~~~~i~~~ 591 (1436) T PRK00448 563 ------------HRADYDAEATAYLLIKFLKDLKEKGITNL 591 (1436) T ss_pred ------------CCCCCCHHHHHHHHHHHHHHHHHCCCCCH T ss_conf ------------44322388899999999999987487437 |
|
>PRK07883 hypothetical protein; Validated | Back alignment and domain information |
---|
Probab=98.99 E-value=1.4e-08 Score=69.15 Aligned_cols=143 Identities=22% Similarity=0.274 Sum_probs=90.1 Q ss_pred HCCCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCCCE-----EEECCCCC---------------CCCCH-------H Q ss_conf 4248982799717778985445079999841---89428-----99746577---------------85706-------7 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDGTV-----DIIRIAAG---------------QKNAP-------N 65 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~~-----~l~~~~~~---------------~~~~~-------~ 65 (207) T Consensus 20 pL~~~tfVVvDlETTG~s~~~d~I--iEIgAVkv~~g~vv~~f~tLVnP~~~Ip~~I~~LTGIt~~mV~~AP~~~~vl~~ 97 (575) T PRK07883 20 PLRDTTFVVVDLETTGGSPTGDAI--TEIGAVKVRGGEVLGEFATLVNPGRSIPPFIVVLTGITTAMVADAPPIDAVLPA 97 (575) T ss_pred CCCCCEEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEECCCCCCCCCCHHHHCCCCCCHHHHCCCCCHHHHHHH T ss_conf 356784899995079999889705--999999998999999971001938989854400369698998079999999999 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHHH---HCC-CCC-HHHHHHHHHHHHH--HCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 7677732364023010000168886542---000-000-0457898865211--00000088777654200246752003 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYTF---GVR-VRP-VFCTKIASRLTRT--YTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~-~~~-i~DT~ias~l~~~--~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) T Consensus 98 f~~F~~~--~vlVAHNa~FD~~FL~~~~~r~g~~~~~~~~ldTl~LARrl~p~~e~~~~kL~tLa~~-~g~~~~~~---- 170 (575) T PRK07883 98 FLEFARG--SVLVAHNAPFDIGFLRAAAERCGYPWPQPEVLCTVRLARRVLSRDEAPNVRLSALARL-FGAATTPT---- 170 (575) T ss_pred HHHHHCC--CEEEEECCHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCCCHHHHHHH-CCCCCCCC---- T ss_conf 9999689--9899908345299999999975999878978648999998669211468998999997-59999998---- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 65654432368999986459999999999999997491899 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~ 179 (207) T Consensus 171 ------------HRAl~DA~AT~~vl~~l~~~~~~~gv~t~ 199 (575) T PRK07883 171 ------------HRALDDARATVDVLHGLIERLGNQGVHTL 199 (575) T ss_pred ------------CCHHHHHHHHHHHHHHHHHHHHHCCCCCH T ss_conf ------------66045299999999999998542242209 |
|
>PRK06859 consensus | Back alignment and domain information |
---|
Probab=98.99 E-value=6.6e-09 Score=71.01 Aligned_cols=132 Identities=23% Similarity=0.322 Sum_probs=79.0 Q ss_pred CCCCCEEEECCCCCCCCCC---CEEEEEEEE---------ECCCCE-EEECCCCCCC---------------CCH----- Q ss_conf 4898279971777898544---507999984---------189428-9974657785---------------706----- Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRR---DRLCIVQLS---------PGDGTV-DIIRIAAGQK---------------NAP----- 64 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~---~~l~LiQl~---------~~~~~~-~l~~~~~~~~---------------~~~----- 64 (207) T Consensus 3 n~~R~VvlDtETTGl~p~~~~~~g~RIIEIgaVel~~~~~t~~-~f~~yinP~r~I~~~a~~vhGIT~e~L~~kP~F~ei 81 (253) T PRK06859 3 NPNRQIVLDTETTGMNQFGAHYEGHCIIEIGAVELINRRYTGN-NFHIYIKPDRPVDPDAIKVHGITDEMLADKPEFKEV 81 (253) T ss_pred CCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEECCC-EEEEEECCCCCCCHHHHHHHCCCHHHHHCCCCHHHH T ss_conf 8883799972179999876666898689999999999978240-467887869949988998745089998369979999 Q ss_pred --HHHHHHHCCCCCEEECCCCHHHHHHHHHH---HCCC--C---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCC Q ss_conf --77677732364023010000168886542---0000--0---004578988652110000008877765420024675 Q gi|254780636|r 65 --NLVGMLVDEKREKIFHYGRFDIAVLFYTF---GVRV--R---PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134 (207) Q Consensus 65 --~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~~--~---~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~ 134 (207) T Consensus 82 a~efl~Fi~~a~L--VaHNa~FD~~FLn~El~r~g~~~~~~~~~~viDTL~lAR~~~P-g~~~sLdaLc~r~-~id~--- 154 (253) T PRK06859 82 AQEFIDYIKGAEL--LIHNAPFDVGFMDYEFRKLNLNVKTDDICLVTDTLQMARQMYP-GKRNNLDALCDRL-GIDN--- 154 (253) T ss_pred HHHHHHHHCCCEE--EEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCC-CCCCCHHHHHHHC-CCCC--- T ss_conf 9999999679979--9957188899999999974999653220011339999998787-9977999999973-9987--- Q ss_pred CEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2003656544323689999864599999999999 Q gi|254780636|r 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 135 ~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 155 ------~~R-----~~HgAllDa~lLa~VYl~mt 177 (253) T PRK06859 155 ------SKR-----TLHGALLDAEILADVYLMMT 177 (253) T ss_pred ------CCC-----CCCCHHHHHHHHHHHHHHHC T ss_conf ------663-----30132888999999999872 |
|
>PRK05168 ribonuclease T; Provisional | Back alignment and domain information |
---|
Probab=98.98 E-value=6.2e-09 Score=71.18 Aligned_cols=140 Identities=19% Similarity=0.240 Sum_probs=86.4 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEEC------C------CCE-EEECCCC-------------C---------CCCCH Q ss_conf 9827997177789854450799998418------9------428-9974657-------------7---------85706 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPG------D------GTV-DIIRIAA-------------G---------QKNAP 64 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~------~------~~~-~l~~~~~-------------~---------~~~~~ 64 (207) T Consensus 17 ~~pVV~D~ETTGl~p~~D~I--IEIGAV~v~~~e~g~i~~~~~f~~~V~P~~g~~I~~~~~~ltGI~~~~~l~~a~~~~~ 94 (213) T PRK05168 17 FLPVVIDVETAGFNAQTDAL--LEIAAITLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEKE 94 (213) T ss_pred CCCEEEEEECCCCCCCCCCE--EEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCCCCCCCCCCCHHH T ss_conf 88759983079988778855--8888899886378867247548898788878878866751126786532223666788 Q ss_pred HHHHHHH---C-------CCCCEEECCCCHHHHHHHHHH---HCCCC-----CHHHHHHHHHHHHHHCCCHHHHHHHHHH Q ss_conf 7767773---2-------364023010000168886542---00000-----0045789886521100000088777654 Q gi|254780636|r 65 NLVGMLV---D-------EKREKIFHYGRFDIAVLFYTF---GVRVR-----PVFCTKIASRLTRTYTNQHGLKDNLKEL 126 (207) Q Consensus 65 ~L~~ll~---d-------~~i~KV~Hn~~~D~~~L~~~~---gi~~~-----~i~DT~ias~l~~~~~~~~~L~~L~~~~ 126 (207) T Consensus 95 al~~~~~~i~~~~~~~~c~~avLVaHNA~FD~~FLn~~~~r~g~~~~P~~~~~viDTl~Lar~~~---~~~~L~~lc~~- 170 (213) T PRK05168 95 ALHEIFKPVRKGIKAAGCQRAILVAHNAHFDLGFLNAAAERTGLKRNPFHPFSTFDTATLAGLAY---GQTVLAKACQA- 170 (213) T ss_pred HHHHHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHH---CCCCHHHHHHH- T ss_conf 78999999999987504675637763418749999999998499778888776335899868874---87409999998- Q ss_pred HCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 20024675200365654432368999986459999999999999997491899 Q gi|254780636|r 127 LGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 (207) Q Consensus 127 lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~ 179 (207) T Consensus 171 ~gi~~~--------------~~~~HrAl~DA~~tA~vFl~ll~~l~~~g~~~~ 209 (213) T PRK05168 171 AGIEFD--------------NKEAHSALYDTEKTAELFCEIVNRWKRLGGWPL 209 (213) T ss_pred CCCCCC--------------CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 699999--------------977777389999999999999999997389999 |
|
>PRK09145 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=98.97 E-value=4e-09 Score=72.30 Aligned_cols=131 Identities=20% Similarity=0.281 Sum_probs=77.3 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCC------CE-EEECCCCCCC---------------CC-------HH Q ss_conf 48982799717778985445079999841---894------28-9974657785---------------70-------67 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDG------TV-DIIRIAAGQK---------------NA-------PN 65 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~------~~-~l~~~~~~~~---------------~~-------~~ 65 (207) T Consensus 27 ~~~~fVv~D~ETTGL~~~~D~I--ieIgav~v~~~~i~~~~~f~~lV~P~~~i~~~~~~IhGIt~~~l~~ap~~~evl~~ 104 (203) T PRK09145 27 PPDEWVALDCETTGLDPRRAEI--VSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEHGLSEEEALRQ 104 (203) T ss_pred CCCCEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEECCCEEEEEECCCCCCCHHHHCCCCCCHHHHCCCCCHHHHHHH T ss_conf 9998999985689999999706--99999999999993175289998979959864520138787998139999999999 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHH----HHCCC-CCHHHHHH--HHHHHHH---HCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 767773236402301000016888654----20000-00045789--8865211---00000088777654200246752 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYT----FGVRV-RPVFCTKI--ASRLTRT---YTNQHGLKDNLKELLGINISKAQ 135 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~----~gi~~-~~i~DT~i--as~l~~~---~~~~~~L~~L~~~~lg~~ldK~~ 135 (207) T Consensus 105 f~~fi~~~--~lVgHNa~FD~~fL~~~~~r~~g~~l~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~---- 177 (203) T PRK09145 105 LLAFIGNR--PLVGYYLEFDVAMLNRYVRPLLGIGLPNPLIEVSSLYHDKKERHLPDAYIDLRFDAILKH-LDLPV---- 177 (203) T ss_pred HHHHCCCC--EEEEECHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHH-CCCCC---- T ss_conf 99882999--899987899999999999996299999987760987999999667698778899999985-79878---- Q ss_pred EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0036565443236899998645999999999999 Q gi|254780636|r 136 QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 136 q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) T Consensus 178 ------------~~~HrAL~DA~aTa~lfl~L~k 199 (203) T PRK09145 178 ------------LGRHDALNDAIMTALIYLRLRK 199 (203) T ss_pred ------------CCCCCHHHHHHHHHHHHHHHHC T ss_conf ------------9997989999999999999867 |
|
>cd06127 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction | Back alignment and domain information |
---|
Probab=98.90 E-value=6.7e-09 Score=70.96 Aligned_cols=122 Identities=22% Similarity=0.236 Sum_probs=73.6 Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEC---C-----CCE-EEECCCCCCCC----------------------CHHHHHHHH Q ss_conf 7997177789854450799998418---9-----428-99746577857----------------------067767773 Q gi|254780636|r 23 IAVDTETLGLMPRRDRLCIVQLSPG---D-----GTV-DIIRIAAGQKN----------------------APNLVGMLV 71 (207) Q Consensus 23 iaiDtEt~~l~~~~~~l~LiQl~~~---~-----~~~-~l~~~~~~~~~----------------------~~~L~~ll~ 71 (207) T Consensus 1 v~~D~ETTGl~~~~~~I--ieia~v~~~~~~~~~~~~~~~i~P~~~~~~~~~~i~gi~~~~~~~~~~~~~~~~~~~~~l~ 78 (159) T cd06127 1 VVLDTETTGLDPKGDRI--IEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLG 78 (159) T ss_pred CEEEEECCCCCCCCCCE--EEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHCC T ss_conf 98982679999999846--9999999999956520079998899999988987606778995899968999999987315 Q ss_pred CCCCCEEECCCCHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC Q ss_conf 236402301000016888654200-----000004578988652110000008877765420024675200365654432 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTFGV-----RVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS 146 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~gi-----~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs 146 (207) T Consensus 79 ~-~-~lv~hN~~FD~~~L~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------- 140 (159) T cd06127 79 G-R-VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAARYGIP---------------- 140 (159) T ss_pred C-C-EEEECCHHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCHHHHHHHHCCCC---------------- T ss_conf 6-3-465158889999999999983999889966647999999738888999999999976988---------------- Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 368999986459999999 Q gi|254780636|r 147 DEQLQYAASDVVHLHALR 164 (207) Q Consensus 147 ~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 141 ~~~aH~Al~D~~at~~l~ 158 (159) T cd06127 141 LEGAHRALADALATAELL 158 (159) T ss_pred CCCCCCHHHHHHHHHHHH T ss_conf 798959899999999996 |
These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others. |
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are a family of proteins in Gram-positive bacteria | Back alignment and domain information |
---|
Probab=98.85 E-value=7e-08 Score=65.04 Aligned_cols=134 Identities=24% Similarity=0.292 Sum_probs=84.9 Q ss_pred CEEEECCCCCCCCCC-CEEEEEEEEE---CCCCE---EEECCCCCCCCC-----------------H-------HHHHHH Q ss_conf 279971777898544-5079999841---89428---997465778570-----------------6-------776777 Q gi|254780636|r 22 AIAVDTETLGLMPRR-DRLCIVQLSP---GDGTV---DIIRIAAGQKNA-----------------P-------NLVGML 70 (207) Q Consensus 22 ~iaiDtEt~~l~~~~-~~l~LiQl~~---~~~~~---~l~~~~~~~~~~-----------------~-------~L~~ll 70 (207) T Consensus 2 YaVVDLEtTg~~~~~~d~I--IqiGiV~v~DgeIv~~f~T~VNP~~~~pp~I~eLTGisd~~l~~AP~F~qVA~~i~~~l 79 (944) T TIGR01407 2 YAVVDLETTGTDSSEFDKI--IQIGIVLVEDGEIVDTFATDVNPNEPIPPFIQELTGISDEQLKQAPYFSQVAQEIYDLL 79 (944) T ss_pred EEEEEEEECCCCCCCCCCE--EEEEEEEEECCCEEEECCCCCCCCCCCCCHHHHHCCCCHHHHCCCCCHHHHHHHHHHHH T ss_conf 6899874168886455766--89988998558143201267788987761145422877686404888879999999874 Q ss_pred HCCCCCEEECCCCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCC Q ss_conf 32364023010000168886542---0000--000457898865211000000887776542002467520036565443 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDL 145 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpL 145 (207) T Consensus 80 ~D~--iFVAHNV~FD~nfL~k~l~~~G~~~~~~~~iDTVELa~if~PT~esY~Ls~L~E~-LGl~h~npH~--------- 147 (944) T TIGR01407 80 EDG--IFVAHNVHFDLNFLAKELVDEGYEPLEVPRIDTVELARIFFPTEESYKLSELSEE-LGLEHENPHR--------- 147 (944) T ss_pred CCC--EEEEECHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHH-HCCCCCCCCC--------- T ss_conf 297--2776101506789999998568974343520056799874674435561489997-1987146676--------- Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 2368999986459999999999999997491 Q gi|254780636|r 146 SDEQLQYAASDVVHLHALRLQFTEKLQRLGR 176 (207) Q Consensus 146 s~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~ 176 (207) T Consensus 148 -------AdSDA~~TAeLLLl~~~K~~~LPl 171 (944) T TIGR01407 148 -------ADSDAQVTAELLLLLEEKMKKLPL 171 (944) T ss_pred -------CCHHHHHHHHHHHHHHHHHHHHHH T ss_conf -------105789999999999999875108 |
The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of Escherichia coli. . |
>cd06144 REX4_like This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins | Back alignment and domain information |
---|
Probab=98.84 E-value=1.1e-08 Score=69.73 Aligned_cols=123 Identities=24% Similarity=0.254 Sum_probs=71.1 Q ss_pred EEEECCCCCCCCCCCE--EEEEEEEECCCCEEEECCCCCC------------------CCC-------HHHHHHHHCCCC Q ss_conf 7997177789854450--7999984189428997465778------------------570-------677677732364 Q gi|254780636|r 23 IAVDTETLGLMPRRDR--LCIVQLSPGDGTVDIIRIAAGQ------------------KNA-------PNLVGMLVDEKR 75 (207) Q Consensus 23 iaiDtEt~~l~~~~~~--l~LiQl~~~~~~~~l~~~~~~~------------------~~~-------~~L~~ll~d~~i 75 (207) T Consensus 1 valDcEm~g~~~~~~~~~larv~vvd~~g~~v~d~~V~P~~~V~d~~T~~sGIt~~~l~~a~~~~~v~~~~~~~l~~~-i 79 (152) T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGR-I 79 (152) T ss_pred CEEEEEECCCCCCCCEEEEEEEEEEECCCCEEEEEEECCCCCCCCCCEEECCCCHHHHCCCCCHHHHHHHHHHHHCCC-E T ss_conf 989876033528998789999999967899998872369976787635624857999738999999999999985388-7 Q ss_pred CEEECCCCHHHHHHHHHHHCCCC-CHHHHHHHHHHHH-HHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHH Q ss_conf 02301000016888654200000-0045789886521-100000088777654200246752003656544323689999 Q gi|254780636|r 76 EKIFHYGRFDIAVLFYTFGVRVR-PVFCTKIASRLTR-TYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYA 153 (207) Q Consensus 76 ~KV~Hn~~~D~~~L~~~~gi~~~-~i~DT~ias~l~~-~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YA 153 (207) T Consensus 80 -lVGH~l~~Dl~~L~l~---~~~~~i~DT~~~~~~~~~~~~~~~sLk~L~~~~Lg~~Iq~~~---------------H~s 140 (152) T cd06144 80 -LVGHALKNDLKVLKLD---HPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE---------------HSS 140 (152) T ss_pred -EEECCHHHHHHHHHCC---CCCCEEEEEEEEHHHHHCCCCCCCCHHHHHHHHCCCCCCCCC---------------CCC T ss_conf -9860646469996243---887606885564224541688992799999998588589979---------------696 Q ss_pred HHHHHHHHHHHH Q ss_conf 864599999999 Q gi|254780636|r 154 ASDVVHLHALRL 165 (207) Q Consensus 154 A~Dv~~l~~L~~ 165 (207) T Consensus 141 ~eDA~at~~Lfk 152 (152) T cd06144 141 VEDARAAMRLYR 152 (152) T ss_pred HHHHHHHHHHHC T ss_conf 999999999859 |
REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required fo |
>PRK09146 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=98.83 E-value=2e-08 Score=68.28 Aligned_cols=150 Identities=19% Similarity=0.179 Sum_probs=84.9 Q ss_pred HCCCCCCEEEECCCCCCCCCCCEEE---EEEEE-----ECCCCEEEECCCCCCC-C--------------CH----HHHH Q ss_conf 4248982799717778985445079---99984-----1894289974657785-7--------------06----7767 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRRDRLC---IVQLS-----PGDGTVDIIRIAAGQK-N--------------AP----NLVG 68 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~~~l~---LiQl~-----~~~~~~~l~~~~~~~~-~--------------~~----~L~~ 68 (207) T Consensus 43 pl~d~~fvalD~ETTGLdp~~D~IiSIGaV~i~~~~I~l~~a~~~lV~p~~~i~~~s~~IHGIt~~~l~~ap~l~evl~~ 122 (239) T PRK09146 43 PLSEVPFVALDFETTGLDPEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLNEESVVIHGITHSDLQDAPDLERILDE 122 (239) T ss_pred CCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEECCEEEECCEEEEEECCCCCCCCCCEEECCCCHHHHHCCCCHHHHHHH T ss_conf 32108789996415788878885489989998788886534158998899978764511069698998569999999999 Q ss_pred HHHC-CCCCEEECCCCHHHHHHHHH----HHCCC-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCC Q ss_conf 7732-36402301000016888654----20000-000457898865211000000887776542002467520036565 Q gi|254780636|r 69 MLVD-EKREKIFHYGRFDIAVLFYT----FGVRV-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSA 142 (207) Q Consensus 69 ll~d-~~i~KV~Hn~~~D~~~L~~~----~gi~~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~ 142 (207) T Consensus 123 ll~~l~g~VLVaH~a~~D~~FL~~a~~~~~g~~l~~P~IDTl~Le~~~~~----~~~~~~~~r~~~~~~~-slrL~~~r~ 197 (239) T PRK09146 123 LLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQR----KQAGGLWNRLKGKKPE-SIRLADSRL 197 (239) T ss_pred HHHHHCCCEEEEECCHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH----HHHHHHHHHHCCCCCC-CCCHHHHHH T ss_conf 99981899899968399999999999996288988746448999999988----5420044431358986-763899999 Q ss_pred C-CCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4-432368999986459999999999999 Q gi|254780636|r 143 D-DLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 143 r-pLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) T Consensus 198 rYgLP~y~aH~AL~DAlATAELflAQi~~ 226 (239) T PRK09146 198 RYGLPAYPPHHALTDAIATAELLQAQIAH 226 (239) T ss_pred HCCCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 81989888767199999999999999998 |
|
>PRK06063 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
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Probab=98.80 E-value=1.2e-07 Score=63.64 Aligned_cols=131 Identities=21% Similarity=0.240 Sum_probs=80.0 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEE----CCCC----E-EEECCCCCC-------------CCC-------HHHHHH Q ss_conf 8982799717778985445079999841----8942----8-997465778-------------570-------677677 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSP----GDGT----V-DIIRIAAGQ-------------KNA-------PNLVGM 69 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~----~~~~----~-~l~~~~~~~-------------~~~-------~~L~~l 69 (207) T Consensus 14 ~~~fvvvD~ETTGl~p~~drIi--eig~v~~~~~g~i~~~~~tlvnP~~dp~~~~IhGIt~~~v~~aP~f~ev~~~l~~~ 91 (313) T PRK06063 14 GQGWAVVDVETSGFRPGQARII--SVAVLGLDADGNVEQSVVSLLNPGVDPGPTHVHGLTAAMLEGQPQFADIAGELAEV 91 (313) T ss_pred CCCEEEEEEECCCCCCCCCEEE--EEEEEEEECCCEEEEEEEEEECCCCCCCCEEEECCCHHHHCCCCCHHHHHHHHHHH T ss_conf 9997999976899999897069--99999998997888999997591999898434187999981799899999999999 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH---HCC-C-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCC Q ss_conf 732364023010000168886542---000-0-00045789886521100000088777654200246752003656544 Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF---GVR-V-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADD 144 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~---gi~-~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rp 144 (207) T Consensus 92 l~g-~-vlVAHNa~FD~~FL~~e~~r~g~~~p~~~~lcTl~lARr~~~~l~~~kL~tla~~-~Gi~~~~~H~-------- 160 (313) T PRK06063 92 LRG-R-TLVAHNVAFDYSFLAAEAELAGAELPVDQVMCTVELARRLDLGLPNLRLETLAAH-WGVVQQRPHD-------- 160 (313) T ss_pred HCC-C-EEEEECCHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCHHHHHHH-CCCCCCCCCC-------- T ss_conf 789-9-7999685652999999999739988999667689988654489999747889998-0999887655-------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 32368999986459999999999999 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) T Consensus 161 --------Al~DAra~a~il~~~l~~ 178 (313) T PRK06063 161 --------ALDDARVLAGILAPALER 178 (313) T ss_pred --------CHHHHHHHHHHHHHHHHH T ss_conf --------067789999998999986 |
|
>pfam00929 Exonuc_X-T Exonuclease | Back alignment and domain information |
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Probab=98.79 E-value=8.1e-08 Score=64.69 Aligned_cols=124 Identities=21% Similarity=0.258 Sum_probs=74.0 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE----CCC----CE-EEECCCCCC-CC---------------------CHHHHHHH Q ss_conf 2799717778985445079999841----894----28-997465778-57---------------------06776777 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP----GDG----TV-DIIRIAAGQ-KN---------------------APNLVGML 70 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~----~~~----~~-~l~~~~~~~-~~---------------------~~~L~~ll 70 (207) T Consensus 1 ~v~~D~ETTGl~~~~~~I--ieigav~~~~~~~~~~~~~~~v~P~~~i~~~~~~i~GIt~~~l~~~~~~~~~~~~~~~~l 78 (162) T pfam00929 1 LVVIDCETTGLDPEKDRI--IEIAAVSIVGGENIGPVFDTYVKPERLITDEATKFHGITPEMLRNAPSFEEVLEAFLEFL 78 (162) T ss_pred CEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHHHCCCCHHHHHHCCCHHHHHHHHHHHH T ss_conf 989998689998999758--999999999997765556787778888899999873978777541531177999999984 Q ss_pred HCCCCCEEECCCCHHHHHHHHHHH---CC----CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCC Q ss_conf 323640230100001688865420---00----00004578988652110000008877765420024675200365654 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTFG---VR----VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSAD 143 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~g---i~----~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~r 143 (207) T Consensus 79 ~~~~-~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~~~~dt~~~~~~~~~~~~~~~L~~l~~~-~~i~~~---------~~ 147 (162) T pfam00929 79 KKLK-ILVGHNASFDVGFLLYDDLRFLKLPHPKLNDVIDTLILDKATYKGFKRRSLDALAEK-LGLEKI---------QR 147 (162) T ss_pred CCCC-EEECCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHH-CCCCCC---------CC T ss_conf 2585-777788778999999999985863366333304489999997504467998999988-599998---------88 Q ss_pred CCCHHHHHHHHHHHHHHHHHH Q ss_conf 432368999986459999999 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 148 ------aH~Al~Da~~t~~lf 162 (162) T pfam00929 148 ------AHRALDDARATAELF 162 (162) T ss_pred ------CCCHHHHHHHHHHHC T ss_conf ------678299999999879 |
This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; |
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases | Back alignment and domain information |
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Probab=98.77 E-value=4.4e-08 Score=66.22 Aligned_cols=131 Identities=20% Similarity=0.266 Sum_probs=80.6 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE----CCCC---E-EEECCCC-CC--------------CC-------CHHHHHHHH Q ss_conf 2799717778985445079999841----8942---8-9974657-78--------------57-------067767773 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP----GDGT---V-DIIRIAA-GQ--------------KN-------APNLVGMLV 71 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~----~~~~---~-~l~~~~~-~~--------------~~-------~~~L~~ll~ 71 (207) T Consensus 2 ~v~~D~ETTGl~~~~~~I--ieigav~~~~~~~~~~~~~~i~P~~~i~~~~~~i~GIt~~~l~~~~~~~~v~~~~~~~l~ 79 (169) T smart00479 2 LVVIDCETTGLDPGKDEI--IEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLK 79 (169) T ss_pred EEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCCHHCCCCCCHHHHHHHHHHHHC T ss_conf 999998527999999869--999999999998878889887999999989986318472120458669999999998604 Q ss_pred CCCCCEEECCCCHHHHHHHHHHH---CC---CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCC Q ss_conf 23640230100001688865420---00---0000457898865211000000887776542002467520036565443 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTFG---VR---VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDL 145 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~g---i~---~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpL 145 (207) T Consensus 80 ~~~~-v~~~~~~fD~~~L~~~~~~~~~~~~~~~~~~dt~~~~~~~~~-~~~~~L~~l~~~-~~i~~~---------~--- 144 (169) T smart00479 80 GKIL-VAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNP-GRKYSLKKLAER-LGLEVI---------G--- 144 (169) T ss_pred CCCC-HHCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCC-CCCHHHHHHHHH-CCCCCC---------C--- T ss_conf 8745-103679999999999999818998866524629999999758-854589999998-599989---------9--- Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 236899998645999999999999999 Q gi|254780636|r 146 SDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 146 s~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) T Consensus 145 ---~~H~Al~Da~~t~~v~~~l~~~~~ 168 (169) T smart00479 145 ---RAHRALDDARATAKLFKKLVERLL 168 (169) T ss_pred ---CCCCHHHHHHHHHHHHHHHHHHCC T ss_conf ---992979999999999999997724 |
|
>PRK07247 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=98.67 E-value=5e-07 Score=60.08 Aligned_cols=136 Identities=16% Similarity=0.050 Sum_probs=81.8 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEEC---CC-CE----EEECCCCC-C--------------CCC-------HHHHHH Q ss_conf 9827997177789854450799998418---94-28----99746577-8--------------570-------677677 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPG---DG-TV----DIIRIAAG-Q--------------KNA-------PNLVGM 69 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~---~~-~~----~l~~~~~~-~--------------~~~-------~~L~~l 69 (207) T Consensus 5 ~~yvv~DlETTg~~~~-~~--IIEIgAVk~~~g~ivd~F~slVnP~~~I~~~i~~lTGIt~~~v~~aP~~~eVl~~f~~F 81 (195) T PRK07247 5 ETYIAFDLEFNTVNDV-SH--IIQVSAVKYDHHKEVDSFDTYVYTDVPLQSFINGLTGITADKIAAAPKVEEVLAAFKNF 81 (195) T ss_pred CEEEEEEEECCCCCCC-CE--EEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHCCCCCHHHHHCCCCHHHHHHHHHHH T ss_conf 8499999778999999-80--69999999989989999983566989999555413598999983599999999999999 Q ss_pred HHCCCCCEEECCC-CHHHHHHHHHH---HCCC-CCHHHHHHHHH-HHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCC Q ss_conf 7323640230100-00168886542---0000-00045789886-52110000008877765420024675200365654 Q gi|254780636|r 70 LVDEKREKIFHYG-RFDIAVLFYTF---GVRV-RPVFCTKIASR-LTRTYTNQHGLKDNLKELLGINISKAQQSSDWSAD 143 (207) Q Consensus 70 l~d~~i~KV~Hn~-~~D~~~L~~~~---gi~~-~~i~DT~ias~-l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~r 143 (207) T Consensus 82 igd~~--lVaHNa~~FD~~fL~~~~~~~~~~~~~~~~~~~~~~r~~~~p~l~n~kL~tLa~~-f~I~-~----------- 146 (195) T PRK07247 82 VGELP--LIGYNAQKSDLPILAENGLDLRDQYQVDLFDEAFDRRSSDLNGIANLKLQTVATF-LGIK-G----------- 146 (195) T ss_pred HCCCE--EEEECCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHH-CCCC-C----------- T ss_conf 68991--8990884514999999877415776685699999998860588767778999997-4999-9----------- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH Q ss_conf 43236899998645999999999999999749189 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSD 178 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~ 178 (207) T Consensus 147 ---~~--HRAl~DA~aTa~If~klLe~~~~~~~~~ 176 (195) T PRK07247 147 ---RG--HNSLEDARMTARIYESFLETDTNKAYLS 176 (195) T ss_pred ---CC--CCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf ---89--0818999999999999999766433677 |
|
>PRK06195 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
---|
Probab=98.60 E-value=6.7e-07 Score=59.37 Aligned_cols=139 Identities=19% Similarity=0.279 Sum_probs=81.8 Q ss_pred CCEEEECCCCCCCCCCCEEEEEEEE-ECC-----CCEEEECCCCCC----------------CCC-------HHHHHHHH Q ss_conf 8279971777898544507999984-189-----428997465778----------------570-------67767773 Q gi|254780636|r 21 DAIAVDTETLGLMPRRDRLCIVQLS-PGD-----GTVDIIRIAAGQ----------------KNA-------PNLVGMLV 71 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~l~LiQl~-~~~-----~~~~l~~~~~~~----------------~~~-------~~L~~ll~ 71 (207) T Consensus 2 ~fvviD~ETt~--~~~d~iieIg~v~v~~g~iv~~~~~Li~P~~~~~~p~~i~ihGIt~~~v~~aP~f~ev~~~~~~fi~ 79 (309) T PRK06195 2 DFVAIDFETAN--EKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVQDELEFDKIWEKIKDYFN 79 (309) T ss_pred CEEEEEEECCC--CCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCCCCCEEEECCCCHHHHHCCCCHHHHHHHHHHHHC T ss_conf 29999978999--9998059999999999999999999989999888874464037799999659999999999999857 Q ss_pred CCCCCEEECCCCHHHHHHHHH---HHCCC-C-CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC Q ss_conf 236402301000016888654---20000-0-004578988652110000008877765420024675200365654432 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYT---FGVRV-R-PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS 146 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~---~gi~~-~-~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs 146 (207) T Consensus 80 ~~--vlVaHNa~FD~~fL~~~~~r~gl~~~~~~~~cTl~LAR~~~p~l~~~kL~~La~~-~gi~~~-------------- 142 (309) T PRK06195 80 DN--LVIAHNASFDISVLRKTLELYNIPMPDFEYICTMKLAKNFYSNIPNARLNTVNNF-LGYEFK-------------- 142 (309) T ss_pred CC--EEEEECCHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCHHHHHHH-HCCCCC-------------- T ss_conf 99--7999562888999999999849999999777479999986557765788899998-598801-------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH Q ss_conf 36899998645999999999999999749189999 Q gi|254780636|r 147 DEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLAT 181 (207) Q Consensus 147 ~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~~ 181 (207) T Consensus 143 --h-H~Al~DA~A~a~I~~~~~~~~~~~~l~el~~ 174 (309) T PRK06195 143 --H-HDALEDAMACSNILLNISKELNSKSIEEISK 174 (309) T ss_pred --C-CCCCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf --1-6851019999999999999818877899976 |
|
>cd06137 DEDDh_RNase This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins | Back alignment and domain information |
---|
Probab=98.58 E-value=1.3e-07 Score=63.43 Aligned_cols=124 Identities=19% Similarity=0.182 Sum_probs=71.6 Q ss_pred EEEECCCCCCCCCCCEEEEEEEEEC-CCCEEEECCCCCC------------CCCH--------------------HHHHH Q ss_conf 7997177789854450799998418-9428997465778------------5706--------------------77677 Q gi|254780636|r 23 IAVDTETLGLMPRRDRLCIVQLSPG-DGTVDIIRIAAGQ------------KNAP--------------------NLVGM 69 (207) Q Consensus 23 iaiDtEt~~l~~~~~~l~LiQl~~~-~~~~~l~~~~~~~------------~~~~--------------------~L~~l 69 (207) T Consensus 1 VAlDCEMv~~~~~~~el~rvs~Vd~~~g~vl~d~~VkP~~~V~Dy~T~~SGIt~~~l~~a~~~~~~~~~~~~a~~~l~~~ 80 (161) T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALWKF 80 (161) T ss_pred CEEEEEEECCCCCCCEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 97964523322997258999999727991999863359843230143325799999854342153333199999999974 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH---HCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC Q ss_conf 7323640230100001688865420000000457898865211---0000008877765420024675200365654432 Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRT---YTNQHGLKDNLKELLGINISKAQQSSDWSADDLS 146 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~---~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs 146 (207) T Consensus 81 i-~~~tIlVGH~L~nDL~aL~----~~H~~viDTa~l~~~~~~~~~~~~~~sLk~La~~~L~~~IQ~g~----------- 144 (161) T cd06137 81 I-DPDTILVGHSLQNDLDALR----MIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGG----------- 144 (161) T ss_pred C-CCCCEEEECCHHHHHHHHC----CCCCCEEECEEECCHHCCCCCCCCCHHHHHHHHHHHCHHHCCCC----------- T ss_conf 5-8996798510131087862----77983543203320011578888886699999998287752899----------- Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 368999986459999999 Q gi|254780636|r 147 DEQLQYAASDVVHLHALR 164 (207) Q Consensus 147 ~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 145 --~gHds~EDA~aam~L~ 160 (161) T cd06137 145 --EGHDSLEDALAAREVV 160 (161) T ss_pred --CCCCCHHHHHHHHHHH T ss_conf --8849199999999985 |
They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA. |
>KOG2249 consensus | Back alignment and domain information |
---|
Probab=98.50 E-value=1.7e-06 Score=57.00 Aligned_cols=134 Identities=19% Similarity=0.203 Sum_probs=83.3 Q ss_pred CCCEEEECCCCCCCCC-C-CEEEEEEEEECCCCEEEECCCCCC------------------CCCHH-------HHHHHHC Q ss_conf 9827997177789854-4-507999984189428997465778------------------57067-------7677732 Q gi|254780636|r 20 VDAIAVDTETLGLMPR-R-DRLCIVQLSPGDGTVDIIRIAAGQ------------------KNAPN-------LVGMLVD 72 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~-~-~~l~LiQl~~~~~~~~l~~~~~~~------------------~~~~~-------L~~ll~d 72 (207) T Consensus 105 ~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g 184 (280) T KOG2249 105 TRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG 184 (280) T ss_pred CEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 23899740475147997600034788861468676555037886633103322365877851575389999999999708 Q ss_pred CCCCEEECCCCHHHHHHHHHHHCCCCC-HHHHHHHHHHHH--HHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHH Q ss_conf 364023010000168886542000000-045789886521--10000008877765420024675200365654432368 Q gi|254780636|r 73 EKREKIFHYGRFDIAVLFYTFGVRVRP-VFCTKIASRLTR--TYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQ 149 (207) Q Consensus 73 ~~i~KV~Hn~~~D~~~L~~~~gi~~~~-i~DT~ias~l~~--~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Q 149 (207) T Consensus 185 -RIl-VGHaLhnDl~~L~l~---hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeH------------- 246 (280) T KOG2249 185 -RIL-VGHALHNDLQALKLE---HPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEH------------- 246 (280) T ss_pred -CEE-ECCCCCCHHHHHHHH---CCHHHHCCCCCCCHHHHHHHCCCCCCHHHHHHHHHCHHHHCCCC------------- T ss_conf -777-512200079998553---74355314312754877752159831999999984525431566------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999986459999999999999997 Q gi|254780636|r 150 LQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 150 i~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) T Consensus 247 --sSvEDA~AtM~LY~~vk~qwe~ 268 (280) T KOG2249 247 --SSVEDARATMELYKRVKVQWEK 268 (280) T ss_pred --CCHHHHHHHHHHHHHHHHHHHH T ss_conf --8588999999999999999999 |
|
>cd06130 DNA_pol_III_epsilon_like This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (polIII), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase | Back alignment and domain information |
---|
Probab=98.40 E-value=1.5e-06 Score=57.30 Aligned_cols=119 Identities=23% Similarity=0.288 Sum_probs=70.1 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE---CCCCE-----EEECCCCC-CC--------------C-------CHHHHHHHH Q ss_conf 2799717778985445079999841---89428-----99746577-85--------------7-------067767773 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP---GDGTV-----DIIRIAAG-QK--------------N-------APNLVGMLV 71 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~~-----~l~~~~~~-~~--------------~-------~~~L~~ll~ 71 (207) T Consensus 1 fvv~D~ETT~~~--~d~I--ieIgav~i~~g~i~~~f~~lv~P~~~i~~~~~~ihGIt~~~v~~~p~~~~v~~~l~~~l~ 76 (156) T cd06130 1 FVAIDFETANAD--RASA--CSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76 (156) T ss_pred CEEEEEECCCCC--CCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHHHHHHHCC T ss_conf 989997789899--9969--999999999999989999987789879988932208887998409999999999998558 Q ss_pred CCCCCEEECCCCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC Q ss_conf 2364023010000168886542---0000--0004578988652110000008877765420024675200365654432 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS 146 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs 146 (207) T Consensus 77 ~~--~lVaHn~~FD~~fL~~~~~~~~~~~~~~~~iDtl~l~r~~~~~~~~~~L~~l~~~-~gi~~~-~------------ 140 (156) T cd06130 77 GS--LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN-H------------ 140 (156) T ss_pred CC--EEEEECHHHHHHHHHHHHHHCCCCCCCCCEECHHHHHHHHCCCCCCCCHHHHHHH-CCCCCC-C------------ T ss_conf 98--8999577889999999999819999898588189999997388888999999998-599987-8------------ Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 368999986459999999 Q gi|254780636|r 147 DEQLQYAASDVVHLHALR 164 (207) Q Consensus 147 ~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 141 ----H~Al~DA~ata~l~ 154 (156) T cd06130 141 ----HDALEDARACAEIL 154 (156) T ss_pred ----CCCHHHHHHHHHHH T ss_conf ----79689999999998 |
The pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The polIII epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of polIII also functions as a stabilizer of the holoenzyme complex |
>cd06138 ExoI_N This subfamily is composed of the N-terminal domain of E | Back alignment and domain information |
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Probab=98.35 E-value=8.9e-06 Score=52.84 Aligned_cols=123 Identities=22% Similarity=0.153 Sum_probs=65.5 Q ss_pred EEEECCCCCCCCCCCEEEEEEEEE----CC----CCE-EEECCCCCCCC-------------------------CHHHHH Q ss_conf 799717778985445079999841----89----428-99746577857-------------------------067767 Q gi|254780636|r 23 IAVDTETLGLMPRRDRLCIVQLSP----GD----GTV-DIIRIAAGQKN-------------------------APNLVG 68 (207) Q Consensus 23 iaiDtEt~~l~~~~~~l~LiQl~~----~~----~~~-~l~~~~~~~~~-------------------------~~~L~~ 68 (207) T Consensus 1 i~fD~ETTGl~~~~d~I--iqiaai~~d~~~~~~~~~~~~i~p~~~~~p~p~a~~v~git~~~~~~~~~s~~e~~~~i~~ 78 (183) T cd06138 1 LFYDYETFGLNPSFDQI--LQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHR 78 (183) T ss_pred CEEEECCCCCCCCCCCE--EEEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHHHCCCCHHHHHHCCCCHHHHHHHHHH T ss_conf 98970389979998760--6999999989987864468874048999988479987188999975318877899999999 Q ss_pred HHHCCCCCEEECC-CCHHHHHHHHHH---HCCCC-------C-HHHHH---HHHHHHHHH----------CCCHHHHHHH Q ss_conf 7732364023010-000168886542---00000-------0-04578---988652110----------0000088777 Q gi|254780636|r 69 MLVDEKREKIFHY-GRFDIAVLFYTF---GVRVR-------P-VFCTK---IASRLTRTY----------TNQHGLKDNL 123 (207) Q Consensus 69 ll~d~~i~KV~Hn-~~~D~~~L~~~~---gi~~~-------~-i~DT~---ias~l~~~~----------~~~~~L~~L~ 123 (207) T Consensus 79 ~~~~~~~i~vg~N~~~FD~~fL~~~~~r~~~~p~~~~~~~~~~~~D~l~~~r~~~~~~p~~i~~~~~~~g~~s~kL~~l~ 158 (183) T cd06138 79 LFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLA 158 (183) T ss_pred HHCCCCCEEEEECCHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH T ss_conf 86169977998453556899999999982787156675278712307889999999782014476556897411299999 Q ss_pred HHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 65420024675200365654432368999986459999999 Q gi|254780636|r 124 KELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 124 ~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 159 ~~-~gi~~~----------------~aH~Al~Dv~aT~~l~ 182 (183) T cd06138 159 QA-NGIEHS----------------NAHDALSDVEATIALA 182 (183) T ss_pred HH-CCCCCC----------------CCCCCHHHHHHHHHHH T ss_conf 98-499998----------------8868289999999986 |
coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site. |
>cd06149 ISG20 Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA | Back alignment and domain information |
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Probab=98.34 E-value=1.9e-06 Score=56.76 Aligned_cols=125 Identities=20% Similarity=0.130 Sum_probs=71.0 Q ss_pred EEEECCCCCCCCCCC--EEEEEEEEECCCCEEEECCCCCCCC------------------C-------HHHHHHHHCCCC Q ss_conf 799717778985445--0799998418942899746577857------------------0-------677677732364 Q gi|254780636|r 23 IAVDTETLGLMPRRD--RLCIVQLSPGDGTVDIIRIAAGQKN------------------A-------PNLVGMLVDEKR 75 (207) Q Consensus 23 iaiDtEt~~l~~~~~--~l~LiQl~~~~~~~~l~~~~~~~~~------------------~-------~~L~~ll~d~~i 75 (207) T Consensus 1 vAlDCEMv~t~~g~~~~~LaRvsvVd~~G~vl~D~~VkP~~~V~dy~T~~SGIt~~~l~~a~~~~~~~~~l~~~l~~~-I 79 (157) T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGK-V 79 (157) T ss_pred CEEECEEEEECCCCCEEEEEEEEEEECCCCEEEEEEECCCCCCCCCEEECCCCCHHHHCCCCCHHHHHHHHHHHHCCC-E T ss_conf 979365342748998468999999927898986743388987786365626788889579984999999999971698-8 Q ss_pred CEEECCCCHHHHHHHHHHHCCCC-CHHHHHHH---HHHHH-HHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHH Q ss_conf 02301000016888654200000-00457898---86521-100000088777654200246752003656544323689 Q gi|254780636|r 76 EKIFHYGRFDIAVLFYTFGVRVR-PVFCTKIA---SRLTR-TYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQL 150 (207) Q Consensus 76 ~KV~Hn~~~D~~~L~~~~gi~~~-~i~DT~ia---s~l~~-~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi 150 (207) T Consensus 80 l-VGH~L~nDL~aL~l---~h~~~~i~DT~~~~~~~~~~~~p~~~~~sLk~L~~~~L~~~IQ~~~~-------------g 142 (157) T cd06149 80 V-VGHAIHNDFKALKY---FHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQ-------------G 142 (157) T ss_pred E-EEECCHHHHHHHHC---CCCCCCEEECCCCEEHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCC-------------C T ss_conf 9-98260766988603---38987267771110013324898766875999999984850259998-------------8 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999864599999999 Q gi|254780636|r 151 QYAASDVVHLHALRL 165 (207) Q Consensus 151 ~YAA~Dv~~l~~L~~ 165 (207) T Consensus 143 Hds~EDA~aa~~L~k 157 (157) T cd06149 143 HSSVEDARATMELYK 157 (157) T ss_pred CCHHHHHHHHHHHHC T ss_conf 080999999999859 |
It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral r |
>cd06145 REX1_like This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins | Back alignment and domain information |
---|
Probab=98.29 E-value=1.5e-06 Score=57.26 Aligned_cols=123 Identities=20% Similarity=0.128 Sum_probs=68.4 Q ss_pred EEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCC------------------CC--------HHHHHHHHCCCCC Q ss_conf 799717778985445079999841894289974657785------------------70--------6776777323640 Q gi|254780636|r 23 IAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQK------------------NA--------PNLVGMLVDEKRE 76 (207) Q Consensus 23 iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~------------------~~--------~~L~~ll~d~~i~ 76 (207) T Consensus 1 ~AlDCEMv~t~~g-~~LaRvsvVd~~g~vl~D~~V~P~~~V~DyrT~~SGIt~~~l~~a~~~~~~~~~~l~~li-~~~~I 78 (150) T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLI-SPDTI 78 (150) T ss_pred CCCCCEEEEECCC-CEEEEEEEECCCCCEEEEEEECCCCCCEECCCCCCCCCHHHHHCCCCCHHHHHHHHHHHC-CCCCE T ss_conf 9561367752799-889999999389989877433499772132010457898898546588999999999875-99988 Q ss_pred EEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHH Q ss_conf 23010000168886542000000045789886521100000088777654200246752003656544323689999864 Q gi|254780636|r 77 KIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASD 156 (207) Q Consensus 77 KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~D 156 (207) T Consensus 79 lVGH~L~nDL~aL~----i~H~~v~DTa~l~~~~~~~~~~~sLk~L~~~~L~~~IQ~~~~-------------gHdsvED 141 (150) T cd06145 79 LVGHSLENDLKALK----LIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEG-------------GHDSVED 141 (150) T ss_pred EEECCCCCCHHHHH----CCCCCEEEHHHHHHHCCCCCCCHHHHHHHHHHHCHHHCCCCC-------------CCCCHHH T ss_conf 99626434777761----558761571662110379998978999999982877439998-------------8183999 Q ss_pred HHHHHHHH Q ss_conf 59999999 Q gi|254780636|r 157 VVHLHALR 164 (207) Q Consensus 157 v~~l~~L~ 164 (207) T Consensus 142 A~aam~L~ 149 (150) T cd06145 142 ARAALELV 149 (150) T ss_pred HHHHHHHH T ss_conf 99999975 |
In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of E.coli RNase T. |
>KOG2405 consensus | Back alignment and domain information |
---|
Probab=98.24 E-value=4.8e-07 Score=60.17 Aligned_cols=150 Identities=15% Similarity=0.074 Sum_probs=95.1 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC-HHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCH Q ss_conf 279971777898544507999984189428997465778570-6776777323640230100001688865420000000 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA-PNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPV 100 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~-~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i 100 (207) T Consensus 197 ~i~~~~~s~-~~~~~~e~~~m~ia~~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nV 272 (458) T KOG2405 197 FIRPVSPSL-LKILALEATYMNIADGNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNV 272 (458) T ss_pred EEECCCHHH-HHHHHHHHHHHHHCCCCHHHHHHHCCCCCEEECCCCHHHHHHCCE--EH-HHHHHHHHHHHHHHHHHHHH T ss_conf 860376447-776234532001125303332232357847750222055662321--04-23300488776889999856 Q ss_pred HHHHHHHHHHHH--HCCCHHHHHHHH--------HHHCCCCCC-------CCEEC-CCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 457898865211--000000887776--------542002467-------52003-656544323689999864599999 Q gi|254780636|r 101 FCTKIASRLTRT--YTNQHGLKDNLK--------ELLGINISK-------AQQSS-DWSADDLSDEQLQYAASDVVHLHA 162 (207) Q Consensus 101 ~DT~ias~l~~~--~~~~~~L~~L~~--------~~lg~~ldK-------~~q~S-dW~~rpLs~~Qi~YAA~Dv~~l~~ 162 (207) T Consensus 273 kDtQia~sLve~~e~grr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~ 352 (458) T KOG2405 273 KDTQIASSLVEPSEYGRRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLG 352 (458) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCEEEHHHHHHHHHHHHHHHCCCCCCEECCCHHHHHHHHHHHHHHHHH T ss_conf 88999998751687455687655056675266514403345468888888723897633366378999998888999999 Q ss_pred HHHHHHHHHHHCCCHHH Q ss_conf 99999999997491899 Q gi|254780636|r 163 LRLQFTEKLQRLGRSDL 179 (207) Q Consensus 163 L~~~l~~~L~~~~~~~~ 179 (207) T Consensus 353 ~~~~----l~a~~l~HL 365 (458) T KOG2405 353 IFDT----LVAVCLSHL 365 (458) T ss_pred HHHH----HHHHCHHHH T ss_conf 9865----764083753 |
|
>PRK07983 exodeoxyribonuclease X; Provisional | Back alignment and domain information |
---|
Probab=98.21 E-value=2e-05 Score=50.74 Aligned_cols=125 Identities=22% Similarity=0.193 Sum_probs=71.5 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE---CCCCE-----EEECCCCC---------------CCCCHHHHHH---HHCCCC Q ss_conf 2799717778985445079999841---89428-----99746577---------------8570677677---732364 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP---GDGTV-----DIIRIAAG---------------QKNAPNLVGM---LVDEKR 75 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~~-----~l~~~~~~---------------~~~~~~L~~l---l~d~~i 75 (207) T Consensus 2 ~~VlDtETTGl~~~-----IiEia~v~v~~g~i~~~~~~linP~~pI~~~a~~ihgIT~emv~~aP~f~ev~~~~~~~~~ 76 (219) T PRK07983 2 LRIIDTETCGLQGG-----IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGSEW 76 (219) T ss_pred EEEEEEECCCCCCC-----CEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCHHHHCCCCCHHHHHHHHCCCCE T ss_conf 59996347999998-----4899999999999976689998968969888998729899998689988999998628987 Q ss_pred CEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHH Q ss_conf 02301000016888654200000004578988652110000008877765420024675200365654432368999986 Q gi|254780636|r 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAAS 155 (207) Q Consensus 76 ~KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~ 155 (207) T Consensus 77 l-VaHNa~FD~~~L~~~-~---~~~IcTl~lAR~l~p~-~~~~l~~Lry-~~~~~~~~~~~--------~---~AHrAl~ 138 (219) T PRK07983 77 Y-VAHNASFDRRVLPEM-P---GEWICTMKLARRLWPG-IKYSNMALYK-SRKLNVQTPPG--------L---HHHRALY 138 (219) T ss_pred E-EECCCCCCHHHHCCC-C---CCEEEHHHHHHHHCCC-CCHHHHHHHH-HHCCCCCCCCC--------C---CCCCHHH T ss_conf 8-753651038664155-8---7566578999987677-4241899999-84276133244--------3---3343078 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 45999999999999 Q gi|254780636|r 156 DVVHLHALRLQFTE 169 (207) Q Consensus 156 Dv~~l~~L~~~l~~ 169 (207) T Consensus 139 Dv~v~~~ll~~l~~ 152 (219) T PRK07983 139 DCYITAALLIDIMR 152 (219) T ss_pred HHHHHHHHHHHHHH T ss_conf 79999999999998 |
|
>cd06133 ERI-1_3'hExo_like This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria | Back alignment and domain information |
---|
Probab=98.19 E-value=4.4e-05 Score=48.82 Aligned_cols=130 Identities=13% Similarity=0.169 Sum_probs=74.7 Q ss_pred CEEEECCCCCCCCCCCE---EEEEEEEE-----CCCCE-----EEECCCCCCCC-----------------C-------H Q ss_conf 27997177789854450---79999841-----89428-----99746577857-----------------0-------6 Q gi|254780636|r 22 AIAVDTETLGLMPRRDR---LCIVQLSP-----GDGTV-----DIIRIAAGQKN-----------------A-------P 64 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~---l~LiQl~~-----~~~~~-----~l~~~~~~~~~-----------------~-------~ 64 (207) T Consensus 1 yvv~D~EtTg~~~~~~~~~~~eIIeIgav~vd~~~~~i~~~f~~lI~P~~~~~i~~~i~~itGIt~~~l~~ap~~~~v~~ 80 (176) T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176) T ss_pred CEEEEEECCCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHCCCCHHHHHH T ss_conf 98999726899878898999707999999998799979899999975876887898899773818878707863999999 Q ss_pred HHHHHHHCCCCCEEECCCCHHHHHHHHHH---HCC-C----CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE Q ss_conf 77677732364023010000168886542---000-0----000457898865211000000887776542002467520 Q gi|254780636|r 65 NLVGMLVDEKREKIFHYGRFDIAVLFYTF---GVR-V----RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ 136 (207) Q Consensus 65 ~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~-~----~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q 136 (207) T Consensus 81 ~f~~~i~~~~~~~~~~~~~fD~~~l~~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~sL~~l~~~-~gi~~~~--- 156 (176) T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFEG--- 156 (176) T ss_pred HHHHHHCCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHH-CCCCCCC--- T ss_conf 999997269857999606002999999999978998873011120499999998188889899999998-6999999--- Q ss_pred ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0365654432368999986459999999999 Q gi|254780636|r 137 SSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 137 ~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 157 ------------~~H~AL~DA~~ta~v~~~l 175 (176) T cd06133 157 ------------RHHRGLDDARNIARILKRL 175 (176) T ss_pred ------------CCCCCHHHHHHHHHHHHHH T ss_conf ------------8858599999999999987 |
These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo. |
>cd05781 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3 | Back alignment and domain information |
---|
Probab=98.15 E-value=3.4e-05 Score=49.43 Aligned_cols=145 Identities=19% Similarity=0.234 Sum_probs=81.1 Q ss_pred CCCEEEECCCCCC----CCCCCEEEEEEEEECCCCEEEECCCCCC--CCCHHHHHHH--HCCCCCEEECCC-CHHHHHHH Q ss_conf 9827997177789----8544507999984189428997465778--5706776777--323640230100-00168886 Q gi|254780636|r 20 VDAIAVDTETLGL----MPRRDRLCIVQLSPGDGTVDIIRIAAGQ--KNAPNLVGML--VDEKREKIFHYG-RFDIAVLF 90 (207) Q Consensus 20 ~~~iaiDtEt~~l----~~~~~~l~LiQl~~~~~~~~l~~~~~~~--~~~~~L~~ll--~d~~i~KV~Hn~-~~D~~~L~ 90 (207) T Consensus 3 lk~lsfDIE~~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~ll~~f~~~i~~~~Pdii-~gyN~~~FD~pyl~ 81 (188) T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAFDWPYLV 81 (188) T ss_pred CEEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHHHH T ss_conf 41999998876899989988897899999968997699984799989999999999987299999-96698675789999 Q ss_pred HHH---HCCC--------------------CC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCCE-----EC Q ss_conf 542---0000--------------------00--0457898865211000000887776542002--467520-----03 Q gi|254780636|r 91 YTF---GVRV--------------------RP--VFCTKIASRLTRTYTNQHGLKDNLKELLGIN--ISKAQQ-----SS 138 (207) Q Consensus 91 ~~~---gi~~--------------------~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~--ldK~~q-----~S 138 (207) T Consensus 82 ~Ra~~~~i~l~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~-~~l~sysL~~Va~-~lg~~~k~e~~~~~~~~I~~ 159 (188) T cd05781 82 ERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEI-PEVKVKTLENVAE-YLGVMKKSERVLIEWYRIYE 159 (188) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHH-CCCCCCCHHHHHH-HHCCCCCCCCCCCCHHHHHH T ss_conf 999996998501556776512254206998789999778999762-4756457999999-85412245446579999999 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 65654432368999986459999999999 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 160 ~~~~~~~r~~l~~YnlqDa~L~~~L~~KL 188 (188) T cd05781 160 YWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188) T ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 87084121699999788799999998429 |
B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarch |
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] | Back alignment and domain information |
---|
Probab=98.10 E-value=5.9e-05 Score=48.07 Aligned_cols=140 Identities=22% Similarity=0.291 Sum_probs=81.2 Q ss_pred CCCEEEECCCCCCCCCCCEE---EEEEEEEC---CCCE-EEECCCCC-CCC--------------CH-------HHHHHH Q ss_conf 98279971777898544507---99998418---9428-99746577-857--------------06-------776777 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRL---CIVQLSPG---DGTV-DIIRIAAG-QKN--------------AP-------NLVGML 70 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l---~LiQl~~~---~~~~-~l~~~~~~-~~~--------------~~-------~L~~ll 70 (207) T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~~i 92 (243) T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLDFI 92 (243) T ss_pred CCEEEEECCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHH T ss_conf 75799966148988778854899659967784024311146688987875431147738899747863899999999984 Q ss_pred HCCCCCEEECCCCHHHHHHHHHHHC---CC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCC Q ss_conf 3236402301000016888654200---00--000457898865211000000887776542002467520036565443 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTFGV---RV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDL 145 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~gi---~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpL 145 (207) T Consensus 93 ~~~~-~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~-------~- 161 (243) T COG0847 93 GGLR-LLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFH-------P- 161 (243) T ss_pred CCCC-EEEEEEHHHCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHH-HCCCCCC-CCC-------C- T ss_conf 7888-699950530889999899970898757642007999998769976134899999-6298877-777-------6- Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH-HHHCC Q ss_conf 2368999986459999999999999-99749 Q gi|254780636|r 146 SDEQLQYAASDVVHLHALRLQFTEK-LQRLG 175 (207) Q Consensus 146 s~~Qi~YAA~Dv~~l~~L~~~l~~~-L~~~~ 175 (207) T Consensus 162 -----H~Al~Da~~~a~~~~~~~~~~~~~~~ 187 (243) T COG0847 162 -----HRALFDALALAELFLLLQTGLLLKAP 187 (243) T ss_pred -----CCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf -----61678899999999998620001011 |
|
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] | Back alignment and domain information |
---|
Probab=97.88 E-value=0.00027 Score=44.18 Aligned_cols=153 Identities=20% Similarity=0.189 Sum_probs=91.5 Q ss_pred CCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEE-CCCCC--CCCCHHHHHHHHCCCC-CEE-ECCCCHHHHHHHH---- Q ss_conf 8279971777898544507999984189428997-46577--8570677677732364-023-0100001688865---- Q gi|254780636|r 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDII-RIAAG--QKNAPNLVGMLVDEKR-EKI-FHYGRFDIAVLFY---- 91 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~-~~~~~--~~~~~~L~~ll~d~~i-~KV-~Hn~~~D~~~L~~---- 91 (207) T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~v~~ 178 (278) T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRMVRD 178 (278) T ss_pred CEEEEEEECCCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHC T ss_conf 25899633146688898599998887357569997512798413568999975389845599746832670899998751 Q ss_pred HHHCCCCC-HHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCCCCCCCEE-------CCCCC---CCCCHHHHHHHHHHHHH Q ss_conf 42000000-04578988652110-000008877765420024675200-------36565---44323689999864599 Q gi|254780636|r 92 TFGVRVRP-VFCTKIASRLTRTY-TNQHGLKDNLKELLGINISKAQQS-------SDWSA---DDLSDEQLQYAASDVVH 159 (207) Q Consensus 92 ~~gi~~~~-i~DT~ias~l~~~~-~~~~~L~~L~~~~lg~~ldK~~q~-------SdW~~---rpLs~~Qi~YAA~Dv~~ 159 (207) T Consensus 179 ~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~V-Er~LGi~R~edtdG~~~p~lyr~~~~~~dp~ll~~l~~hN~eDvln 257 (278) T COG3359 179 RLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTV-ERILGIRREEDTDGYDGPELYRLYRRYGDPGLLDGLVLHNREDVLN 257 (278) T ss_pred CCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHH-HHHHCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHCCHHHHHH T ss_conf 644476666312210344531202878881367-8885755011589850199999998709877778988706998875 Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999999999974 Q gi|254780636|r 160 LHALRLQFTEKLQRL 174 (207) Q Consensus 160 l~~L~~~l~~~L~~~ 174 (207) T Consensus 258 L~~i~~h~~~~i~~~ 272 (278) T COG3359 258 LPTIIKHVSKKILED 272 (278) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999999987 |
|
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family; InterPro: IPR006054 All proteins in this entry for which functions are known are components of the DNA polymerase III complex (epsilon subunit) | Back alignment and domain information |
---|
Probab=97.80 E-value=0.00054 Score=42.45 Aligned_cols=136 Identities=21% Similarity=0.236 Sum_probs=82.2 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEE---------ECCC-CEEEECCCCCCCC--------------CHH-------HHH Q ss_conf 98279971777898544507999984---------1894-2899746577857--------------067-------767 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLS---------PGDG-TVDIIRIAAGQKN--------------APN-------LVG 68 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~---------~~~~-~~~l~~~~~~~~~--------------~~~-------L~~ 68 (207) T Consensus 7 ~t~t~~d~e~tgl~~~~~~I--I~IGAv~~i~rr~~~~~~~~~~~P~R~~~~~~~k~hGItDd~L~dkP~F~eia~dF~~ 84 (228) T TIGR00573 7 DTFTTGDNETTGLYAKHDEI--IEIGAVEIINRRIIGNKFHTYIKPDRLIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 84 (228) T ss_pred EEEEEEECCCCCCCCCCCCE--EEEEEEEEECCCEEECCEEEEECCCCCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHH T ss_conf 42687521106763224304--5453376644614401005776188888964255248882884689851378899999 Q ss_pred HHHCCCCCEEECCCCHHHHHHHHHHHCC-C------CCHHHHHHHHHHHHHH--CCCHHHHHHHHHHHCCCCCCCCEECC Q ss_conf 7732364023010000168886542000-0------0004578988652110--00000887776542002467520036 Q gi|254780636|r 69 MLVDEKREKIFHYGRFDIAVLFYTFGVR-V------RPVFCTKIASRLTRTY--TNQHGLKDNLKELLGINISKAQQSSD 139 (207) Q Consensus 69 ll~d~~i~KV~Hn~~~D~~~L~~~~gi~-~------~~i~DT~ias~l~~~~--~~~~~L~~L~~~~lg~~ldK~~q~Sd 139 (207) T Consensus 85 ~I~g~-~L-v~HNA~FD~GFl~~e~~~LG~~~~~~~~~v~~~~~~~~~~~~~~p~~~~~Ld~L~~~-~~~~~-------- 153 (228) T TIGR00573 85 YIKGA-VL-VIHNASFDVGFLNYEFSKLGLKKEPKTNDVIDTTDTLQAARPEFPGKRNTLDALALR-YEITN-------- 153 (228) T ss_pred HHCCC-EE-EEEHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH-CCCCH-------- T ss_conf 83794-78-752003057789999985145011001144449999999972058843027777878-05440-------- Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 56544323689999864599999999999999974 Q gi|254780636|r 140 WSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 140 W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) T Consensus 154 ------s~R~~H~A~~DA~~l~~~~~~~~~~~~~~ 182 (228) T TIGR00573 154 ------SHRALHGALLDAFILAKLYLVMTGKQTKY 182 (228) T ss_pred ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf ------37777317788999999999998612203 |
There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the N-terminal region of DinG from some low GC Gram-positive bacteria. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication. |
>cd05780 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D | Back alignment and domain information |
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Probab=97.76 E-value=0.00014 Score=45.91 Aligned_cols=145 Identities=16% Similarity=0.246 Sum_probs=81.2 Q ss_pred CCCEEEECCCCCC----CCCCCEEEEEEEEECCCCEEEECCCCC-----------CCCCHHHHHHH--HCCCCCEEECCC Q ss_conf 9827997177789----854450799998418942899746577-----------85706776777--323640230100 Q gi|254780636|r 20 VDAIAVDTETLGL----MPRRDRLCIVQLSPGDGTVDIIRIAAG-----------QKNAPNLVGML--VDEKREKIFHYG 82 (207) Q Consensus 20 ~~~iaiDtEt~~l----~~~~~~l~LiQl~~~~~~~~l~~~~~~-----------~~~~~~L~~ll--~d~~i~KV~Hn~ 82 (207) T Consensus 3 lkilsfDIE~~~~~g~P~p~~d~Ii~Is~~~~~~~~vi~-~~~~~~~~v~~~~tE~eLL~~F~~~i~~~dPDii-~GyN~ 80 (195) T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVIT-WKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVI-YTYNG 80 (195) T ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEE-ECCCCCCCEEEECCHHHHHHHHHHHHHHCCCCEE-EECCC T ss_conf 429999999758999989888828999999689978998-1798877456738999999999999987299999-95798 Q ss_pred -CHHHHHHHHHHH---CCC----------------------C--CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC- Q ss_conf -001688865420---000----------------------0--00457898865211000000887776542002467- Q gi|254780636|r 83 -RFDIAVLFYTFG---VRV----------------------R--PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK- 133 (207) Q Consensus 83 -~~D~~~L~~~~g---i~~----------------------~--~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK- 133 (207) T Consensus 81 ~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~-~~l~sy~L~~Va~~~Lg~~K~d~ 159 (195) T cd05780 81 DNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT-LNLTRYTLERVYEELFGIEKEDV 159 (195) T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHH-CCCCCCCHHHHHHHHHCCCCCCC T ss_conf 78768999999999589864578886047997785079987686885549999752-56240159999999839997889 Q ss_pred C-CEECC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5-20036-5654432368999986459999999999 Q gi|254780636|r 134 A-QQSSD-WSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 134 ~-~q~Sd-W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 160 ~~~~i~~~~~~~~~~~~l~~Yn~~D~~L~~~L~~K~ 195 (195) T cd05780 160 PGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195) T ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999759753888844599899999998529 |
Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B D |
>cd05160 DNA_polB_exo The 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
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Probab=97.74 E-value=0.00018 Score=45.23 Aligned_cols=142 Identities=18% Similarity=0.188 Sum_probs=76.1 Q ss_pred CEEEECCCCCCC----CCCCEEEEEEEEEC-CCCEEEE----------------------CCCCCCCCCHHHHHHH--HC Q ss_conf 279971777898----54450799998418-9428997----------------------4657785706776777--32 Q gi|254780636|r 22 AIAVDTETLGLM----PRRDRLCIVQLSPG-DGTVDII----------------------RIAAGQKNAPNLVGML--VD 72 (207) Q Consensus 22 ~iaiDtEt~~l~----~~~~~l~LiQl~~~-~~~~~l~----------------------~~~~~~~~~~~L~~ll--~d 72 (207) T Consensus 1 vlsfDIE~~~~~gfP~p~~d~Ii~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~eLL~~F~~~i~~~d 80 (200) T cd05160 1 VLSFDIETLPNVGGPEPSRDPIICISYADSFQGHKVVFLLKVSTHGDDIEAGFIDGIEVEYFDDEKELLKRFFDIIREYD 80 (200) T ss_pred CEEEEEEECCCCCCCCCCCCEEEEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCC T ss_conf 97999832799997899988089999999359999998864355676765467799699996999999999999999709 Q ss_pred CCCCEEECCC-CHHHHHHHHHH---HCCCCC-----------------------HHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 3640230100-00168886542---000000-----------------------04578988652110000008877765 Q gi|254780636|r 73 EKREKIFHYG-RFDIAVLFYTF---GVRVRP-----------------------VFCTKIASRLTRTYTNQHGLKDNLKE 125 (207) Q Consensus 73 ~~i~KV~Hn~-~~D~~~L~~~~---gi~~~~-----------------------i~DT~ias~l~~~~~~~~~L~~L~~~ 125 (207) T Consensus 81 PDii-~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~-~~l~sy~Ld~Va~~ 158 (200) T cd05160 81 PDIL-TGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVKRD-FKLKSYTLDAVAEE 158 (200) T ss_pred CCEE-EECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHHHH-HCCCCCCHHHHHHH T ss_conf 9999-972677784889999999969885554673454543575059973677860289999975-32466539999999 Q ss_pred HHCCCCCC-C-CEECCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 42002467-5-2003656544323689999864599999999 Q gi|254780636|r 126 LLGINISK-A-QQSSDWSADDLSDEQLQYAASDVVHLHALRL 165 (207) Q Consensus 126 ~lg~~ldK-~-~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~ 165 (207) T Consensus 159 ~Lg~~K~d~~~~~~~~~~~~~d~~k~~~Y~~~D~~L~~~L~e 200 (200) T cd05160 159 LLGEGKEKVDGEIIEDLEWEEDLERLLEYNLKDAELTLQILE 200 (200) T ss_pred HHCCCCCCCCHHHHHHHHHCCCCHHHHHEEHHHHHHHHHHHC T ss_conf 849997878989999998738914866025999998999759 |
This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and |
>cd05785 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
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Probab=97.42 E-value=0.0031 Score=38.09 Aligned_cols=142 Identities=25% Similarity=0.277 Sum_probs=76.4 Q ss_pred CCCCCCEEEECCCCCCCCC--------CCEEEEEEEEECCCCEEEECCCCCCCCCHHHHH---HH--HCCCCCEEECCC- Q ss_conf 2489827997177789854--------450799998418942899746577857067767---77--323640230100- Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPR--------RDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVG---ML--VDEKREKIFHYG- 82 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~--------~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~---ll--~d~~i~KV~Hn~- 82 (207) T Consensus 6 ~~~lr~lsfDIE~~~~~g~~~p~p~~~~d~Ii~I~~~~~~~~~~v~~~~~-~~E~~lL~~F~~~i~~~dPDII-tGyNi~ 83 (207) T cd05785 6 FDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAED-AAEKELLEELVAIIRERDPDVI-EGHNIF 83 (207) T ss_pred HHHEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECC-CCHHHHHHHHHHHHHHCCCCEE-EECCCC T ss_conf 20405999999747889977999888999789999885899779876269-9999999999999987399999-867987 Q ss_pred CHHHHHHHHHHH---CC------------------------------CCC--HHHHHHHHHHHH--H-HCCCHHHHHHHH Q ss_conf 001688865420---00------------------------------000--045789886521--1-000000887776 Q gi|254780636|r 83 RFDIAVLFYTFG---VR------------------------------VRP--VFCTKIASRLTR--T-YTNQHGLKDNLK 124 (207) Q Consensus 83 ~~D~~~L~~~~g---i~------------------------------~~~--i~DT~ias~l~~--~-~~~~~~L~~L~~ 124 (207) T Consensus 84 ~FD~pYL~~Ra~~~~i~~~lgR~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~~~~~~~L~SY~L~~Va~ 163 (207) T cd05785 84 RFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAK 163 (207) T ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCEEECCEEEECCCCCCEEEEEECCEEEEEHHHHHHHHCCCCCCCCCCCHHHHHH T ss_conf 75889999999995997222578987446403021223555304998736488654999986421114677652899999 Q ss_pred HHHCCC-CCCCC----EECC-CCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 542002-46752----0036-565443236899998645999999 Q gi|254780636|r 125 ELLGIN-ISKAQ----QSSD-WSADDLSDEQLQYAASDVVHLHAL 163 (207) Q Consensus 125 ~~lg~~-ldK~~----q~Sd-W~~rpLs~~Qi~YAA~Dv~~l~~L 163 (207) T Consensus 164 ~~-~l~~~~k~~~~~~~i~~~~~~d~--~~l~~Yni~Dv~~t~~L 205 (207) T cd05785 164 HF-GLASPDRTYIDGRQIAEVWRSDP--ARLLAYALDDVRETEGL 205 (207) T ss_pred HH-HHCCCCCCCCCHHHHHHHHHCCH--HHHHHHHHHHHHHHHHH T ss_conf 87-31366656388999999995298--99999829999999986 |
This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. |
>PRK05762 DNA polymerase II; Reviewed | Back alignment and domain information |
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Probab=97.37 E-value=0.0021 Score=38.98 Aligned_cols=139 Identities=15% Similarity=0.106 Sum_probs=75.5 Q ss_pred CCEEEECCCCCCCCCCCEEEEEEEEE--CCCCE-EEE----------CCCCCCCCCHHHHHHH--HCCCCCEEECCC-CH Q ss_conf 82799717778985445079999841--89428-997----------4657785706776777--323640230100-00 Q gi|254780636|r 21 DAIAVDTETLGLMPRRDRLCIVQLSP--GDGTV-DII----------RIAAGQKNAPNLVGML--VDEKREKIFHYG-RF 84 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~l~LiQl~~--~~~~~-~l~----------~~~~~~~~~~~L~~ll--~d~~i~KV~Hn~-~~ 84 (207) T Consensus 156 rvlSfDIEc~~~g----~--ii~I~l~~~~~~~v~~~g~~~~~~~v~~~~~E~eLL~~F~~~i~~~DPDII-~GyNi~~F 228 (785) T PRK05762 156 KVVSLDIETSNKG----E--LYSIGLEGCGQRQVYMLGEANGDAELEYVADEKALLERFNAWFAEFDPDVI-IGWNVVQF 228 (785) T ss_pred EEEEEEEEECCCC----C--EEEEEECCCCCCEEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHHCCCEE-EECCCCCC T ss_conf 6999998977999----8--899995179984689966889985389909999999999999998599989-96274787 Q ss_pred HHHHHHHHH---HCC-------------------------CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC--C Q ss_conf 168886542---000-------------------------000--04578988652110000008877765420024--6 Q gi|254780636|r 85 DIAVLFYTF---GVR-------------------------VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGINI--S 132 (207) Q Consensus 85 D~~~L~~~~---gi~-------------------------~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~l--d 132 (207) T Consensus 229 DlpyL~~Ra~~~gi~l~lgR~~~~~~~~~~~~~~~~~~~~i~GRv~iD~~~~~k~~~~~l~sYsL~~Va~~~Lge~K~~~ 308 (785) T PRK05762 229 DLRLLQERAERYGIPLRLGRGGSELSWRVHGHKRGHFFASVPGRLVLDGIDALKSAFYEFKSFSLENVAQELLGEGKAID 308 (785) T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCEEEEEEEEEEEEEEHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCC T ss_conf 77999999999499854687888653331565566059998428999709999875203676629999999854455556 Q ss_pred CCC-E---E-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 752-0---0-3656544323689999864599999999999 Q gi|254780636|r 133 KAQ-Q---S-SDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 133 K~~-q---~-SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 309 ~~~~r~~eI~~~~~~~r--~~l~~Y~l~Da~L~~~L~~kl~ 347 (785) T PRK05762 309 NPYDRMDEIDRYFADDK--PALAKYNLKDCELVTRIFEKTE 347 (785) T ss_pred CHHHHHHHHHHHHHCCH--HHHHHHHHHHHHHHHHHHHHHH T ss_conf 66666888899885468--9999999999999999999870 |
|
>cd05784 DNA_polB_II_exo The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (PolII) and similar bacterial proteins | Back alignment and domain information |
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Probab=97.08 E-value=0.0019 Score=39.28 Aligned_cols=139 Identities=17% Similarity=0.096 Sum_probs=72.2 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECC-CCEEEEC------------CCCCCCCCHHHHHHHH--CCCCCEEECCC-C Q ss_conf 98279971777898544507999984189-4289974------------6577857067767773--23640230100-0 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGD-GTVDIIR------------IAAGQKNAPNLVGMLV--DEKREKIFHYG-R 83 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~-~~~~l~~------------~~~~~~~~~~L~~ll~--d~~i~KV~Hn~-~ 83 (207) T Consensus 3 lki~s~DIE~~~~~----~i~~I~~~~~~~~~v~~~~~~~~~~~~~v~~~~sE~eLL~~F~~~i~~~dPDiI-tG~N~~~ 77 (193) T cd05784 3 LKVVSLDIETSMDG----ELYSIGLYGEGQERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDII-IGWNVIN 77 (193) T ss_pred CEEEEEEECCCCCC----CEEEEEEECCCCCEEEEEECCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEE-EECCCCC T ss_conf 30999996327988----888999986999989999789888997799989999999999999986299999-9779877 Q ss_pred HHHHHHHHHHH---CC------------------------CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC-C Q ss_conf 01688865420---00------------------------000--045789886521100000088777654200246-7 Q gi|254780636|r 84 FDIAVLFYTFG---VR------------------------VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGINIS-K 133 (207) Q Consensus 84 ~D~~~L~~~~g---i~------------------------~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ld-K 133 (207) T Consensus 78 FDiPYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~~~l~sy~Ld~Va~~~LGe~K~~~ 157 (193) T cd05784 78 FDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLIH 157 (193) T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCC T ss_conf 76789999999858864336578850598768562699997887841729999760735114348889999838775445 Q ss_pred CC--EEC----CCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 52--003----656544323689999864599999999 Q gi|254780636|r 134 AQ--QSS----DWSADDLSDEQLQYAASDVVHLHALRL 165 (207) Q Consensus 134 ~~--q~S----dW~~rpLs~~Qi~YAA~Dv~~l~~L~~ 165 (207) T Consensus 158 ~~~~~~~~i~~l~~~d~--~k~~~Yni~D~~Lv~rLf~ 193 (193) T cd05784 158 DVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193) T ss_pred CCCCCHHHHHHHHHCCC--HHHEEEHHHHHHHHHHHHC T ss_conf 65555888999886590--3610320277999999749 |
PolII is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. PolII is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in a |
>PRK11779 sbcB exonuclease I; Provisional | Back alignment and domain information |
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Probab=96.51 E-value=0.058 Score=30.68 Aligned_cols=145 Identities=21% Similarity=0.153 Sum_probs=75.1 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEEC--CCCE--------EEECCCCCC-----------CC--------------C Q ss_conf 89827997177789854450799998418--9428--------997465778-----------57--------------0 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSPG--DGTV--------DIIRIAAGQ-----------KN--------------A 63 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~~--~~~~--------~l~~~~~~~-----------~~--------------~ 63 (207) T Consensus 6 ~~~f~fyD~ETtG~~~~~dqi--~Qfa~i~td~~ln~i~~~~~~~c~~~~~~lP~p~A~lvt~itp~~~~~~~~~~~~~~ 83 (477) T PRK11779 6 QPTFLWHDYETFGANPALDRP--AQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 83 (477) T ss_pred CCCEEEEECCCCCCCCCCCCC--CEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCHHHCCCCCHHHHHHCCCCHHHHH T ss_conf 785799945368999877650--125778987753725774105644799989993043114889999986699879999 Q ss_pred HHHHHHHHCCCCCEEECC-CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHC-----CC--C-CCC Q ss_conf 677677732364023010-00016888654200000004578988652110000008877765420-----02--4-675 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHY-GRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLG-----IN--I-SKA 134 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn-~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg-----~~--l-dK~ 134 (207) T Consensus 84 ~~i~~~~~~~~t~~iGyNsi~FDee~~R~~f---y~nl~dPY~~~~~-ng-NsR~Dll~~~r~~~~~~p~~i~~p~~~~G 158 (477) T PRK11779 84 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIF---YRNFYDPYAREWQ-NG-NSRWDLLDVVRACYALRPEGINWPENEDG 158 (477) T ss_pred HHHHHHHCCCCCEEEECCCCCCCHHHHHHHH---HHHCCCHHHHHCC-CC-CCHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 9999996689848982277544899999999---9861345766424-89-70579999999998748366116737999 Q ss_pred C---EECCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2---003656-54432368999986459999999999999 Q gi|254780636|r 135 Q---QSSDWS-ADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 135 ~---q~SdW~-~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) T Consensus 159 ~~sfKLe~la~aNgi~h~~AHDAl~Dv~aTi~laklIk~k 198 (477) T PRK11779 159 LPSFKLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 198 (477) T ss_pred CEEEEHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 8544499999855987655410688999999999999876 |
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>PTZ00166 DNA polymerase delta catalytic subunit; Provisional | Back alignment and domain information |
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Probab=96.46 E-value=0.031 Score=32.26 Aligned_cols=150 Identities=15% Similarity=0.088 Sum_probs=78.1 Q ss_pred CCCCEEEECCCCCCC----C--CCCEEEEEEEEE-----CCC-CE---EEECCCCCC--------------CCCHHHHHH Q ss_conf 898279971777898----5--445079999841-----894-28---997465778--------------570677677 Q gi|254780636|r 19 YVDAIAVDTETLGLM----P--RRDRLCIVQLSP-----GDG-TV---DIIRIAAGQ--------------KNAPNLVGM 69 (207) Q Consensus 19 ~~~~iaiDtEt~~l~----~--~~~~l~LiQl~~-----~~~-~~---~l~~~~~~~--------------~~~~~L~~l 69 (207) T Consensus 289 PlrilSfDIEC~~~~G~gFP~~~~Dp--VIqIs~~~~~~g~~~~~~~~~~ftl~~C~~I~g~~V~~F~tE~eLL~aF~~f 366 (1081) T PTZ00166 289 PIRILSFDIECIKLDGKGFPEANNDP--VIQISSVLHTHGDPLDSCKNFIFTLKECASLAGANVLWFDNEKTLLLAWNDF 366 (1081) T ss_pred CCEEEEEEEEECCCCCCCCCCCCCCC--EEEEEEEEEECCCCCCCCCCEEEECCCCCCCCCCEEEEECCHHHHHHHHHHH T ss_conf 81699986784588899898999995--7998579881478887646446674787788997799709999999999999 Q ss_pred H--HCCCCCEEECCC-CHHHHHHHHHHHC---C----------------------------------CCC--HHHHHHHH Q ss_conf 7--323640230100-0016888654200---0----------------------------------000--04578988 Q gi|254780636|r 70 L--VDEKREKIFHYG-RFDIAVLFYTFGV---R----------------------------------VRP--VFCTKIAS 107 (207) Q Consensus 70 l--~d~~i~KV~Hn~-~~D~~~L~~~~gi---~----------------------------------~~~--i~DT~ias 107 (207) T Consensus 367 i~~~DPDII-TGYNI~nFDlpYLl~Ra~~L~i~~f~~lgRlk~~~~~~~~~~~~s~a~G~~~~k~i~i~GRv~~Dl~~~v 445 (1081) T PTZ00166 367 IIAVDPDFL-TGYNIINFDLPYLLNRATALNLKKFKFLTRIKSVKSTVKDSIFSSNQFGTHENKEINIEGRILFDVYDLI 445 (1081) T ss_pred HHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCEEEEECCEEEEEHHHHH T ss_conf 987099899-9668788888999999999588643323611577652202656655556665506867578996469999 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCC-CC-EECC-CCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 65211000000887776542002467-52-0036-565443-236899998645999999999999999 Q gi|254780636|r 108 RLTRTYTNQHGLKDNLKELLGINISK-AQ-QSSD-WSADDL-SDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 108 ~l~~~~~~~~~L~~L~~~~lg~~ldK-~~-q~Sd-W~~rpL-s~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) T Consensus 446 ~r-~~kL~SYkLntVs~~fLgeqKeDV~~~~I~~l~~~~~e~r~rla~YClkDa~L~lrL~~KL~~l~n 513 (1081) T PTZ00166 446 RR-DYKLKSYSLNYVSFEFLKEQKEDVHYSTINKLQNGNPEDRKRIASYCLKDSILPLRLIDKLLLLYN 513 (1081) T ss_pred HH-HCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 87-558785768889999818875337999999998149378899999989989999999999989999 |
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>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3 | Back alignment and domain information |
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Probab=94.58 E-value=0.2 Score=27.50 Aligned_cols=135 Identities=21% Similarity=0.280 Sum_probs=73.2 Q ss_pred CCEEEECCCCCCCCCCC---EEEEEEEEE-------CCCC--EEEECCCCCCCCCH---------------------HHH Q ss_conf 82799717778985445---079999841-------8942--89974657785706---------------------776 Q gi|254780636|r 21 DAIAVDTETLGLMPRRD---RLCIVQLSP-------GDGT--VDIIRIAAGQKNAP---------------------NLV 67 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~---~l~LiQl~~-------~~~~--~~l~~~~~~~~~~~---------------------~L~ 67 (207) T Consensus 9 lPVVvDVET~GfN~~~dALLEiAait~~MDe~G~L~P~~~~~~~~~P~~Gani~P~~L~~~GI~~d~P~R~A~~E~~Al~ 88 (201) T TIGR01298 9 LPVVVDVETAGFNAKTDALLEIAAITLKMDEQGYLVPDETLHFHVEPFEGANIEPEALEFTGIDLDHPLRGAVEEKLALE 88 (201) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCEEEEEEECCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHH T ss_conf 43488610677660134555554200011673001478525788522679988712002206544887522466889999 Q ss_pred HHHH----------CCCCCEEECCCCHHHHHHHHHH----HC-----CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHH-- Q ss_conf 7773----------2364023010000168886542----00-----0000045789886521100000088777654-- Q gi|254780636|r 68 GMLV----------DEKREKIFHYGRFDIAVLFYTF----GV-----RVRPVFCTKIASRLTRTYTNQHGLKDNLKEL-- 126 (207) Q Consensus 68 ~ll~----------d~~i~KV~Hn~~~D~~~L~~~~----gi-----~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~-- 126 (207) T Consensus 89 ~iF~~vR~~~K~~gC~RailV~HNa~fD~~Fl~~AA~~R~~~KRnPFH~F~~FDTatLAGl~--y----GQTVL~kA~Q~ 162 (201) T TIGR01298 89 EIFKVVRKALKASGCQRAILVAHNASFDLGFLNRAAVKRTALKRNPFHPFSVFDTATLAGLA--Y----GQTVLAKACQA 162 (201) T ss_pred HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH--H----HHHHHHHHHHH T ss_conf 99999999997557960367600320466689999999861157898765224689998886--4----17999988864 Q ss_pred HCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 2002467520036565443236899998645999999999999999749 Q gi|254780636|r 127 LGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 127 lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) T Consensus 163 Ag~---------~f-----d~~~AHSA~YDtE~TA~LFC~ivN~wk~~g 197 (201) T TIGR01298 163 AGL---------DF-----DAKQAHSALYDTEKTAELFCEIVNRWKELG 197 (201) T ss_pred CCC---------CC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 278---------86-----754431012003568999998863045504 |
1.13 from EC) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases.; GO: 0004540 ribonuclease activity, 0006396 RNA processing. |
>cd05783 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins | Back alignment and domain information |
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Probab=92.70 E-value=0.62 Score=24.70 Aligned_cols=140 Identities=17% Similarity=0.202 Sum_probs=68.1 Q ss_pred CCCEEEECCCCCC----CC--CCCEEEEEEEEEC--CC--CEEEECCC-------------------CCCCCCHHHHHHH Q ss_conf 9827997177789----85--4450799998418--94--28997465-------------------7785706776777 Q gi|254780636|r 20 VDAIAVDTETLGL----MP--RRDRLCIVQLSPG--DG--TVDIIRIA-------------------AGQKNAPNLVGML 70 (207) Q Consensus 20 ~~~iaiDtEt~~l----~~--~~~~l~LiQl~~~--~~--~~~l~~~~-------------------~~~~~~~~L~~ll 70 (207) T Consensus 5 lrvlsfDIEv~s~~~~~FP~p~~~~~~iisI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~f~~E~~LL~~F~~~i 84 (204) T cd05783 5 LKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKII 84 (204) T ss_pred CEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHH T ss_conf 74999998878899997979555886199999992799889999950871257655789989999599999999999997 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCC---CC--C-------------H-HHHH-------HHHHHHHHHCCCHHHHHHH Q ss_conf 323640230100-00168886542000---00--0-------------0-4578-------9886521100000088777 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVR---VR--P-------------V-FCTK-------IASRLTRTYTNQHGLKDNL 123 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~---~~--~-------------i-~DT~-------ias~l~~~~~~~~~L~~L~ 123 (207) T Consensus 85 ~~~p~I-i~wN~~~FDiPYL~~R~~~Lg~~~~~~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~y~~~~k~~sY~Ld~Va 163 (204) T cd05783 85 SEYPIV-LTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREYTLDAVA 163 (204) T ss_pred HCCCEE-EECCCCCCCHHHHHHHHHHHCCCCEEEEEEECCEEEEEEEEEEEEEHHHCCCCHHHHHHCCCCCCCCCHHHHH T ss_conf 439979-9817867788999999998599820456673436999934499986463573135441202421225288999 Q ss_pred HHHHCCC-CCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 6542002-4675200365654432368999986459999999 Q gi|254780636|r 124 KELLGIN-ISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 124 ~~~lg~~-ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 164 ~~~LGe~K~d~~~~~--~~~-d~-~k~i~YNi~D~~Lv~~L~ 201 (204) T cd05783 164 KALLGEGKVELEKNI--SEL-NL-YELAEYNYRDAELTLELT 201 (204) T ss_pred HHHHCCCCCCCCCCC--CCC-CH-HHHHEEEHHHHHHHHHHH T ss_conf 998388860067644--425-86-785514267767777862 |
B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthes |
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion | Back alignment and domain information |
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Probab=99.52 E-value=2.6e-14 Score=102.46 Aligned_cols=134 Identities=19% Similarity=0.212 Sum_probs=102.3 Q ss_pred HHHHHHCCCCCEEE-------------CCCCHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC Q ss_conf 76777323640230-------------1000016888654200000---0045789886521100000088777654200 Q gi|254780636|r 66 LVGMLVDEKREKIF-------------HYGRFDIAVLFYTFGVRVR---PVFCTKIASRLTRTYTNQHGLKDNLKELLGI 129 (207) Q Consensus 66 L~~ll~d~~i~KV~-------------Hn~~~D~~~L~~~~gi~~~---~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~ 129 (207) T Consensus 444 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~K~~~~~L~~~-g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~ 522 (1005) T TIGR00593 444 FAEWLLKETIKKALEELLVSASKVKVAHDAKFLMHLLKRK-GIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVE 522 (1005) T ss_pred HHHHHHHCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCC T ss_conf 8998740001455521002341012288999999999743-773344211454899999843035640278999871343 Q ss_pred CCCCC----C--EEC--CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HCCCHHHHHH Q ss_conf 24675----2--003--6565443236899998645999999999999999-------------------7491899999 Q gi|254780636|r 130 NISKA----Q--QSS--DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ-------------------RLGRSDLATS 182 (207) Q Consensus 130 ~ldK~----~--q~S--dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~-------------------~~~~~~~~~~ 182 (207) T Consensus 523 ~~~~d~~~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~L~~~l~~~L~~eDaDitfrlyhylklrle~~~~~~L~~e 601 (1005) T TIGR00593 523 ELILDDDRKEEGIKKLAKFADPD-LEEAIEYLARKAAATARLAEELLKELDAEDADITFRLYHYLKLRLEENKLLSLYEE 601 (1005) T ss_pred CCCCCCCHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 46778731345544334441121-77889999999999999999988873113220466777788865163889999988 Q ss_pred -HHHHHHHHHHHHHCCCCCCC Q ss_conf -99640068999866798888 Q gi|254780636|r 183 -CCNFLMDRAELDLLGWENVD 202 (207) Q Consensus 183 -e~~~l~~~~~me~~g~~~~~ 202 (207) T Consensus 602 iE~Pl~~VL~~ME~~Gi~-~D 621 (1005) T TIGR00593 602 IELPLSKVLAEMEKTGIK-VD 621 (1005) T ss_pred HCCCHHHHHHHHHHHHHH-HH T ss_conf 420078999998776678-70 |
Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication. |
>KOG1275 consensus | Back alignment and domain information |
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Probab=97.24 E-value=0.00045 Score=42.93 Aligned_cols=95 Identities=21% Similarity=0.118 Sum_probs=63.1 Q ss_pred HHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCH Q ss_conf 77732364023010000168886542000000045789886521100000088777654200246752003656544323 Q gi|254780636|r 68 GMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSD 147 (207) Q Consensus 68 ~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~ 147 (207) T Consensus 1008 ~~Li~~GviFVGHGL~nDFrvINi--~Vp~~QiiDTv~lf~~--~s~R~LSLrfLa~~lLg~~I----Q~~~-------- 1071 (1118) T KOG1275 1008 RLLIQRGVIFVGHGLQNDFRVINI--HVPEEQIIDTVTLFRL--GSQRMLSLRFLAWELLGETI----QMEA-------- 1071 (1118) T ss_pred HHHHHCCCEEECCCCCCCCEEEEE--ECCHHHHEEEEEEEEC--CCCCEEEHHHHHHHHHCCHH----HCCC-------- T ss_conf 999973828972244666159998--3484560103577861--66627877999999814132----0134-------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 68999986459999999999999997491899999996 Q gi|254780636|r 148 EQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCN 185 (207) Q Consensus 148 ~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~~~~e~~ 185 (207) T Consensus 1072 ---HDSIeDA~taLkLYk~Yl~-lkeq~~---~~~~l~ 1102 (1118) T KOG1275 1072 ---HDSIEDARTALKLYKKYLK-LKEQGK---LESELR 1102 (1118) T ss_pred ---CCCHHHHHHHHHHHHHHHH-HHHHHH---HHHHHH T ss_conf ---5537879999999999998-887668---999987 |
|
>cd06125 DnaQ_like_exo The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction | Back alignment and domain information |
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Probab=99.05 E-value=2.5e-10 Score=79.32 Aligned_cols=85 Identities=25% Similarity=0.235 Sum_probs=56.0 Q ss_pred EEEECCCCCCCC-CCCEEEEEEEEEC-CCCEEEECCCCCCC------------------------CCHHHHHHHHCCCCC Q ss_conf 799717778985-4450799998418-94289974657785------------------------706776777323640 Q gi|254780636|r 23 IAVDTETLGLMP-RRDRLCIVQLSPG-DGTVDIIRIAAGQK------------------------NAPNLVGMLVDEKRE 76 (207) Q Consensus 23 iaiDtEt~~l~~-~~~~l~LiQl~~~-~~~~~l~~~~~~~~------------------------~~~~L~~ll~d~~i~ 76 (207) T Consensus 1 Vv~D~ETTGl~~~~~d~Iiei~~v~~~~~~~~~~~v~p~~~i~~~~~~i~gi~~~~v~~~p~~~~~~~~~~~f~~~~~~i 80 (130) T cd06125 1 VAFDIETTGLNGNARDEIIEIALVVVHIGEKFVFDVKPDDLIDPYAFTISGITDEVVERAATEAELLIELLAFLRDKDDI 80 (130) T ss_pred CEEEEECCCCCCCCCCEEEEEEEEEEECCCEEEEEECCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCE T ss_conf 98980189969999985899999997189889999799998997794103759999833060899999999997699999 Q ss_pred EEECCCCHHHHHHHHHHH---CC----CCCHHHHHHHH Q ss_conf 230100001688865420---00----00004578988 Q gi|254780636|r 77 KIFHYGRFDIAVLFYTFG---VR----VRPVFCTKIAS 107 (207) Q Consensus 77 KV~Hn~~~D~~~L~~~~g---i~----~~~i~DT~ias 107 (207) T Consensus 81 lVgHN~~FD~~fL~~~~~r~g~~~~~~~~~~iDTl~la 118 (130) T cd06125 81 LVGHNISFDLPYLLNRAAELGIPYPILGRIVFDTLALA 118 (130) T ss_pred EEEECHHHHHHHHHHHHHHCCCCCCCCCCCEEECHHHH T ss_conf 99919477499999999984999987899686860984 |
It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif |
>PRK09182 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
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Probab=97.57 E-value=0.00017 Score=45.36 Aligned_cols=82 Identities=24% Similarity=0.390 Sum_probs=48.2 Q ss_pred CEEEECCCCCCCCCCCEEE---EEEEE-ECCCCEE-EECC-CC----CCCC---------------------CHHHHHHH Q ss_conf 2799717778985445079---99984-1894289-9746-57----7857---------------------06776777 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLC---IVQLS-PGDGTVD-IIRI-AA----GQKN---------------------APNLVGML 70 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~---LiQl~-~~~~~~~-l~~~-~~----~~~~---------------------~~~L~~ll 70 (207) T Consensus 39 g~~lD~ETTGl~~~~d~IIElg~v~f~~~~~G~i~~i~~~~~~~~dP~~pIp~~it~lTGItd~mV~Gq~id~~~V~~~~ 118 (293) T PRK09182 39 GVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVVDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAEVDALI 118 (293) T ss_pred EEEEECCCCCCCCCCCEEEEEEEEEEEECCCCCEEEEECCEECCCCCCCCCCHHHHHHCCCCHHHHCCCCCCHHHHHHHH T ss_conf 99995305788977877999768999986998587764323110389998998798751888899688827999999986 Q ss_pred HCCCCCEEECCCCHHHHHHHHHHHCCCC-CHHHHH Q ss_conf 3236402301000016888654200000-004578 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTFGVRVR-PVFCTK 104 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~gi~~~-~i~DT~ 104 (207) T Consensus 119 ~~adli-iAHNA~FDR~F~E~~~p~f~~k~WaCS~ 152 (293) T PRK09182 119 APADLI-IAHNAGFDRPFLERFSPVFANKPWACSV 152 (293) T ss_pred CCCCEE-EECCCCCCHHHHHHHCCCCCCCCEEEEC T ss_conf 449899-9817754677898509532587505316 |
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>pfam04857 CAF1 CAF1 family ribonuclease | Back alignment and domain information |
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Probab=97.48 E-value=0.0006 Score=42.19 Aligned_cols=113 Identities=25% Similarity=0.340 Sum_probs=65.0 Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECCCC------EEEECC-----CCCCC Q ss_conf 424898279971777898544-------------------507999984----18942------899746-----57785 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGDGT------VDIIRI-----AAGQK 61 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~~~------~~l~~~-----~~~~~ 61 (207) T Consensus 18 ~i~~~~fVaiDtEFpG~v~~p~~~~~~t~~~~Y~~lk~nVd~l~iiQlGlt~~~~~g~~p~~~~~wqfNf~~F~~~~d~~ 97 (235) T pfam04857 18 AIDSYDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEEDFY 97 (235) T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCC T ss_conf 98319989995142752468988888987899999984300123146898887468878987437850155679732211 Q ss_pred CCH-----------------------HH------HHHHHC-CCCCEEECCCCHHHHHHHHHH-H-CC------------- Q ss_conf 706-----------------------77------677732-364023010000168886542-0-00------------- Q gi|254780636|r 62 NAP-----------------------NL------VGMLVD-EKREKIFHYGRFDIAVLFYTF-G-VR------------- 96 (207) Q Consensus 62 ~~~-----------------------~L------~~ll~d-~~i~KV~Hn~~~D~~~L~~~~-g-i~------------- 96 (207) T Consensus 98 ~~~Si~fL~~~G~DF~~~~~~GI~~~~f~e~l~~S~lv~~~~~~~wv~f~g~yD~~yl~k~l~g~~LP~~~~eF~~~l~~ 177 (235) T pfam04857 98 APSSIEFLAKQGFDFNKHRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLELLRE 177 (235) T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCHHHHHHHHHHHHHEECCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHH T ss_conf 68899999985988899987099989999899870302057998799817277899999997499899989999999999 Q ss_pred -CCCHHHHHHHHHHHHHH--CCCHHHHHHHHHHHCC Q ss_conf -00004578988652110--0000088777654200 Q gi|254780636|r 97 -VRPVFCTKIASRLTRTY--TNQHGLKDNLKELLGI 129 (207) Q Consensus 97 -~~~i~DT~ias~l~~~~--~~~~~L~~L~~~~lg~ 129 (207) T Consensus 178 ~FP~vyD~K~la~~~~~~~~~~~~gL~~lA~~-L~v 212 (235) T pfam04857 178 LFPRVYDTKYLAKFCFELDGGSNGGLQELADL-LGV 212 (235) T ss_pred HCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHH-CCC T ss_conf 77717509999985221358755789999997-499 |
The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution. |
>KOG2405 consensus | Back alignment and domain information |
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Probab=96.66 E-value=4.3e-05 Score=48.87 Aligned_cols=88 Identities=24% Similarity=0.315 Sum_probs=63.8 Q ss_pred CCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCC--HHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCC Q ss_conf 898279971777898544507999984189428997465778570--677677732364023010000168886542000 Q gi|254780636|r 19 YVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA--PNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVR 96 (207) Q Consensus 19 ~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~--~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~ 96 (207) T Consensus 58 ~qn~~-~~~e~a~~~~-~~~l~~~q~~~-~~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~ 134 (458) T KOG2405 58 KQNVL-VAAEGANVCR-HGKLCWLQVAT-NCRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGIL 134 (458) T ss_pred HHCCC-CCCCCCCCCC-CCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE T ss_conf 61676-5566754025-67633588888-899999999986159999899998604667655799999998740302244 Q ss_pred CCCHHHHHHHHHH Q ss_conf 0000457898865 Q gi|254780636|r 97 VRPVFCTKIASRL 109 (207) Q Consensus 97 ~~~i~DT~ias~l 109 (207) T Consensus 135 ~n~v~~~q~~d~~ 147 (458) T KOG2405 135 LNNVFDTQVADVL 147 (458) T ss_pred ECCHHHHHHHHHH T ss_conf 3320333320665 |
|
>cd06136 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases | Back alignment and domain information |
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Probab=98.55 E-value=1.1e-06 Score=58.18 Aligned_cols=79 Identities=24% Similarity=0.256 Sum_probs=51.4 Q ss_pred HHHHHHC--CCCCEEECCC-CHHHHHHHHHH---HCC-CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCE Q ss_conf 7677732--3640230100-00168886542---000-000--0457898865211000000887776542002467520 Q gi|254780636|r 66 LVGMLVD--EKREKIFHYG-RFDIAVLFYTF---GVR-VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQ 136 (207) Q Consensus 66 L~~ll~d--~~i~KV~Hn~-~~D~~~L~~~~---gi~-~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q 136 (207) T Consensus 88 ~~~F~~~~~~~~~LVAHNa~~FD~~fL~~e~~r~g~~~p~~~~~iDtL~l~r---~--~~~~L~~l~~~~~gi~~~~a-- 160 (177) T cd06136 88 IKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFR---E--LDQSLGSLYKRLFGQEPKNS-- 160 (177) T ss_pred HHHHHHHCCCCCEEEECCCHHCCHHHHHHHHHHCCCCCCCCCEEEEEHHHHH---H--HCCCHHHHHHHHCCCCCCCC-- T ss_conf 9999962677867996485123799999999986998998988998607645---5--06999999999759999877-- Q ss_pred ECCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 03656544323689999864599999999 Q gi|254780636|r 137 SSDWSADDLSDEQLQYAASDVVHLHALRL 165 (207) Q Consensus 137 ~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~ 165 (207) T Consensus 161 --------------HRAl~Da~at~~vfl 175 (177) T cd06136 161 --------------HTAEGDVLALLKCAL 175 (177) T ss_pred --------------CCCHHHHHHHHHHHC T ss_conf --------------784899999999975 |
They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and 2 that point to different biological roles for these proteins. The main difference is the presence of about 7 |
>cd06143 PAN2_exo PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs | Back alignment and domain information |
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Probab=98.28 E-value=1.7e-06 Score=57.01 Aligned_cols=75 Identities=20% Similarity=-0.028 Sum_probs=49.9 Q ss_pred HCCCCCEEECCCCHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHH Q ss_conf 323640230100001688865420000-0004578988652110000008877765420024675200365654432368 Q gi|254780636|r 71 VDEKREKIFHYGRFDIAVLFYTFGVRV-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQ 149 (207) Q Consensus 71 ~d~~i~KV~Hn~~~D~~~L~~~~gi~~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Q 149 (207) T Consensus 99 i~~~~ILVGHsL~nDL~aL~l~---hP~~~i~DTs~l~~~--~~~r~~sLk~La~~~Lg~~IQ~g--------------- 158 (174) T cd06143 99 VDLGCIFVGHGLAKDFRVINIQ---VPKEQVIDTVELFHL--PGQRKLSLRFLAWYLLGEKIQSE--------------- 158 (174) T ss_pred CCCCCEEECCCCHHHHHHHCCC---CCCCCEEECHHHCCC--CCCCCCCHHHHHHHHCCCCCCCC--------------- T ss_conf 4799689789636679885066---998665777885268--99887089999999808104698--------------- Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999864599999999 Q gi|254780636|r 150 LQYAASDVVHLHALRL 165 (207) Q Consensus 150 i~YAA~Dv~~l~~L~~ 165 (207) T Consensus 159 ~HdSvEDArAam~LYr 174 (174) T cd06143 159 THDSIEDARTALKLYR 174 (174) T ss_pred CCCCHHHHHHHHHHHC T ss_conf 9593999999999629 |
PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. |
>KOG3657 consensus | Back alignment and domain information |
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Probab=97.69 E-value=0.00013 Score=46.09 Aligned_cols=98 Identities=17% Similarity=0.201 Sum_probs=66.4 Q ss_pred CCCEEECCCCHHHHHHHHHHHCCC-CC-HHHHHHHH----HHHHHH---------------------------------- Q ss_conf 640230100001688865420000-00-04578988----652110---------------------------------- Q gi|254780636|r 74 KREKIFHYGRFDIAVLFYTFGVRV-RP-VFCTKIAS----RLTRTY---------------------------------- 113 (207) Q Consensus 74 ~i~KV~Hn~~~D~~~L~~~~gi~~-~~-i~DT~ias----~l~~~~---------------------------------- 113 (207) T Consensus 241 e~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~-S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~ 319 (1075) T KOG3657 241 EQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMC-SRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGR 319 (1075) T ss_pred CCEEEECCCCCHHHHHHHHHHCCCCCEEEEECHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH T ss_conf 7568733554008999998702665406643112233332133-223316766313145565022487666643566421 Q ss_pred CCCHHHHHHHHHHHCCC-CCCCCEECCCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00000887776542002-467520036565443------2368999986459999999999999997 Q gi|254780636|r 114 TNQHGLKDNLKELLGIN-ISKAQQSSDWSADDL------SDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 114 ~~~~~L~~L~~~~lg~~-ldK~~q~SdW~~rpL------s~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) T Consensus 320 SS~NSL~dVhk~~c~~~~LdKt~Rd~-Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fle 385 (1075) T KOG3657 320 SSLNSLVDVHKFHCGIDALDKTPRDS-FVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLE 385 (1075) T ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 00577999999617997234463776-6408689999999999998732449999999998499998 |
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>cd05779 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon | Back alignment and domain information |
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Probab=97.55 E-value=0.00056 Score=42.38 Aligned_cols=88 Identities=23% Similarity=0.234 Sum_probs=51.5 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHH---HCCCCC-----------------H-HHHHHHHHHH-HH-H--CCCHHHHHHHH Q ss_conf 323640230100-00168886542---000000-----------------0-4578988652-11-0--00000887776 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTF---GVRVRP-----------------V-FCTKIASRLT-RT-Y--TNQHGLKDNLK 124 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~---gi~~~~-----------------i-~DT~ias~l~-~~-~--~~~~~L~~L~~ 124 (207) T Consensus 87 ~~pdii-~gyN~~~FD~pyl~~Ra~~~~~~~~~~~~~~~~~~~~~~~~~~vhiDly---~~v~rd~~l~~~sy~Ln~Vs~ 162 (204) T cd05779 87 VKPHII-VTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCF---RWVKRDSYLPQGSQGLKAVTK 162 (204) T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCHHHHCCCCCCCCCCEECCCCEEEECH---HHHHHHCCCCCCCCCHHHHHH T ss_conf 499999-8558767767999999999599825531800067772762672563007---765101217556877899999 Q ss_pred HHHCCCCCCC--CEECC-CCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 5420024675--20036-5654432368999986459999999 Q gi|254780636|r 125 ELLGINISKA--QQSSD-WSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 125 ~~lg~~ldK~--~q~Sd-W~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) T Consensus 163 ~~Lg~~K~dv~~~~m~~l~~~~~--~~la~Y~~~Da~~Ty~l~ 203 (204) T cd05779 163 AKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLY 203 (204) T ss_pred HHHCCCCCCCCHHHHHHHHCCCH--HHHHHCCHHHHHHHHHHH T ss_conf 99689975089999999982891--555524099999999976 |
DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is ort |
>cd05782 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
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Probab=97.01 E-value=0.011 Score=34.84 Aligned_cols=97 Identities=23% Similarity=0.287 Sum_probs=57.0 Q ss_pred HHHHHHHCCCCCEEECCC-CHHHHHHHHHH---HCCCCC------------------HHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 776777323640230100-00168886542---000000------------------04578988652110000008877 Q gi|254780636|r 65 NLVGMLVDEKREKIFHYG-RFDIAVLFYTF---GVRVRP------------------VFCTKIASRLTRTYTNQHGLKDN 122 (207) Q Consensus 65 ~L~~ll~d~~i~KV~Hn~-~~D~~~L~~~~---gi~~~~------------------i~DT~ias~l~~~~~~~~~L~~L 122 (207) T Consensus 84 ~F~~~i~~~~p~lv~~Ng~~FD~P~l~~Ral~~gi~~p~~~~~~~~~~~y~~r~~~~H~Dl~d~l~~~-~~~~~~sLd~l 162 (208) T cd05782 84 DFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFY-GARARASLDLL 162 (208) T ss_pred HHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHCC-CCCCCCCHHHH T ss_conf 99999986599799636875758999999999198975554048874112488876313299998554-87577889999 Q ss_pred HHHHHCCCCCCCC----EECC-CCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 7654200246752----0036-56544323689999864599999999 Q gi|254780636|r 123 LKELLGINISKAQ----QSSD-WSADDLSDEQLQYAASDVVHLHALRL 165 (207) Q Consensus 123 ~~~~lg~~ldK~~----q~Sd-W~~rpLs~~Qi~YAA~Dv~~l~~L~~ 165 (207) T Consensus 163 a-~llG~p-gK~~~~Gs~V~~~~~~g~l-~~I~~YCe~DVl~T~~v~l 207 (208) T cd05782 163 A-KLLGIP-GKMDVDGSQVWELYAEGKL-DEIAEYCETDVLNTYLLYL 207 (208) T ss_pred H-HHHCCC-CCCCCCHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHH T ss_conf 9-983899-7578888999999981998-8999999999999999980 |
This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. |
>KOG2248 consensus | Back alignment and domain information |
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Probab=96.74 E-value=0.0021 Score=39.00 Aligned_cols=83 Identities=18% Similarity=0.131 Sum_probs=51.5 Q ss_pred HHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCEECCCCCCC Q ss_conf 76777323640230100001688865420000000457898865211-00000088777654200246752003656544 Q gi|254780636|r 66 LVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRT-YTNQHGLKDNLKELLGINISKAQQSSDWSADD 144 (207) Q Consensus 66 L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~-~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rp 144 (207) T Consensus 287 l~~~~~~~TIL-VGHSLenDL~aLKl~----H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq-~----~~~~-- 354 (380) T KOG2248 287 LLELISKNTIL-VGHSLENDLKALKLD----HPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQ-E----GVGG-- 354 (380) T ss_pred HHHHCCCCCEE-EEECHHHHHHHHHHH----CCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHH-C----CCCC-- T ss_conf 99646867179-951003078897642----7742200588864889854259999999999889986-1----6778-- Q ss_pred CCHHHHHHHHHHHHHHHHHHHH Q ss_conf 3236899998645999999999 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQ 166 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~ 166 (207) T Consensus 355 ------HdS~eDA~acm~Lv~~ 370 (380) T KOG2248 355 ------HDSVEDALACMKLVKL 370 (380) T ss_pred ------CCCHHHHHHHHHHHHH T ss_conf ------7608889999999999 |
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>cd05777 DNA_polB_delta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta | Back alignment and domain information |
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Probab=96.70 E-value=0.0097 Score=35.17 Aligned_cols=104 Identities=13% Similarity=0.014 Sum_probs=59.6 Q ss_pred HHHHH--HCCCCCEEECCC-CHHHHHHHHHHH---CC----------------------------------CCC--HHHH Q ss_conf 76777--323640230100-001688865420---00----------------------------------000--0457 Q gi|254780636|r 66 LVGML--VDEKREKIFHYG-RFDIAVLFYTFG---VR----------------------------------VRP--VFCT 103 (207) Q Consensus 66 L~~ll--~d~~i~KV~Hn~-~~D~~~L~~~~g---i~----------------------------------~~~--i~DT 103 (207) T Consensus 78 F~~~i~~~dPDii-tGyN~~~FD~pYL~~Ra~~l~~~~~~~lgr~~~~~~~~~~~~~~s~~~g~~~~~~~~i~Gr~~lD~ 156 (230) T cd05777 78 WRDFVQEVDPDII-TGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDL 156 (230) T ss_pred HHHHHHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCCHHHHCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCEEHHHH T ss_conf 9999998099999-963666788789999999968861454176678763574165222312640026998758759999 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-C-CEECC-CCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 898865211000000887776542002467-5-20036-56544-323689999864599999999999999 Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISK-A-QQSSD-WSADD-LSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-~-~q~Sd-W~~rp-Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) T Consensus 157 ~~~~r~-~~~l~sY~L~~Va~~~Lg~~K~d~~~~~i~~~~~~~~~~~~~~~~Y~i~D~~L~~~L~~Kl~~~~ 227 (230) T cd05777 157 LQVIQR-DYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLV 227 (230) T ss_pred HHHHHH-HCCHHHCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCHHHHHHHHEECHHHHHHHHHHHHHHHHHH T ss_conf 999997-50163364999999983899887999999999947964645600642687799999999987774 |
DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polyme |
>cd05776 DNA_polB_alpha_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha | Back alignment and domain information |
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Probab=95.21 E-value=0.032 Score=32.20 Aligned_cols=95 Identities=17% Similarity=0.186 Sum_probs=58.7 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHH---CC----------------------------CCC-HHHHHHHHHHHHHHCCCH Q ss_conf 323640230100-001688865420---00----------------------------000-045789886521100000 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFG---VR----------------------------VRP-VFCTKIASRLTRTYTNQH 117 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~g---i~----------------------------~~~-i~DT~ias~l~~~~~~~~ 117 (207) T Consensus 96 ~DPDii-~Ghni~~fdl~~L~~R~~~lki~~wsriGRlkr~~~p~~~~~~~~~~~~~~~GRl~~D~~~~~ke~~-k~~sy 173 (234) T cd05776 96 IDPDVL-VGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLSAKELI-RCKSY 173 (234) T ss_pred CCCCEE-EEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCEEEEECHHHHHHHH-CCCCC T ss_conf 099899-8506377759999999998099853313550014376445656534420352358876099999874-66778 Q ss_pred HHHHHHHHHHCCCC---CCCCEECCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 08877765420024---675200365654-4323689999864599999999999 Q gi|254780636|r 118 GLKDNLKELLGINI---SKAQQSSDWSAD-DLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 118 ~L~~L~~~~lg~~l---dK~~q~SdW~~r-pLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) T Consensus 174 ~L~~v~~~~L~~~k~dv~~~~i~~~~~~~~~l-~~l~~~~~~Da~l~~~L~~~L~ 227 (234) T cd05776 174 DLTELSQQVLGIERQDIDPEEILNMYNDSESL-LKLLEHTEKDAYLILQLMFKLN 227 (234) T ss_pred CHHHHHHHHHCCCCCCCCHHHHHHHHHCHHHH-HHHHHHHHHHHHHHHHHHHHHC T ss_conf 88999999968676679999999998693999-9999999999999999999958 |
DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair r |
>smart00486 POLBc DNA polymerase type-B family | Back alignment and domain information |
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Probab=94.25 E-value=0.38 Score=25.90 Aligned_cols=95 Identities=18% Similarity=0.073 Sum_probs=52.8 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCCCC--------------------------------------CHHHHHHHHHHHH Q ss_conf 323640230100-0016888654200000--------------------------------------0045789886521 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVRVR--------------------------------------PVFCTKIASRLTR 111 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~~~--------------------------------------~i~DT~ias~l~~ 111 (207) T Consensus 83 ~dpdii-~g~N~~~FD~~yi~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~D~~~~~~~~~ 161 (471) T smart00486 83 YDPDII-YGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVIDLYNLYKNKL 161 (471) T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCEECCCCCCCCCCCEEEEEEEEEEEEEHHHHHHHHH T ss_conf 199999-9658878768999999998489647763735778764320332101256631489985599978899998860 Q ss_pred HHCCCHHHHHHHHHHHCCCCC---CCCEECCCCCC-CCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 100000088777654200246---75200365654-432368999986459999999999 Q gi|254780636|r 112 TYTNQHGLKDNLKELLGINIS---KAQQSSDWSAD-DLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 112 ~~~~~~~L~~L~~~~lg~~ld---K~~q~SdW~~r-pLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) T Consensus 162 -~l~sy~L~~v~~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~~ 220 (471) T smart00486 162 -KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471) T ss_pred -CCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -44668889999999577888899899999985393679999999999999999999986 |
DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases |
>PRK06722 exonuclease; Provisional | Back alignment and domain information |
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Probab=94.77 E-value=0.16 Score=28.11 Aligned_cols=46 Identities=11% Similarity=0.067 Sum_probs=29.1 Q ss_pred CCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHH---HCCCCC--HHHHH Q ss_conf 5778570677677732364023010000168886542---000000--04578 Q gi|254780636|r 57 AAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTF---GVRVRP--VFCTK 104 (207) Q Consensus 57 ~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~---gi~~~~--i~DT~ 104 (207) T Consensus 36 P~ieeVLp~FleFIGd~~L--VAHNAsFD~gFL~~~C~~hg~e~P~~~~~~~~ 86 (242) T PRK06722 36 EKFPQIIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHGVECPCMEKERRI 86 (242) T ss_pred CCHHHHHHHHHHHHCCCEE--EEECCHHHHHHHHHHHHHCCCCCCCCCCHHHH T ss_conf 9789999999998278838--97344022779997752428999998421088 |
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>cd06135 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides | Back alignment and domain information |
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Probab=92.78 E-value=0.28 Score=26.67 Aligned_cols=19 Identities=37% Similarity=0.623 Sum_probs=15.8 Q ss_pred CEEEECCCCCCCCCCCEEE Q ss_conf 2799717778985445079 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLC 40 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~ 40 (207) T Consensus 1 lvWiDlEmTGLd~~~d~Ii 19 (173) T cd06135 1 LVWIDLEMTGLDPEKDRIL 19 (173) T ss_pred CEEEECCCCCCCCCCCEEE T ss_conf 9599330368888886489 |
It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for E.coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling. |
Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch
Homologous Structures Detected by PSI-BLAST against Nonredundant Database
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | ||
1yt3_A | 375 | Crystal Structure Of Escherichia Coli Rnase D, An E | 2e-22 | |
1dpi_A | 605 | Structure Of Large Fragment Of Escherichia Coli Dna | 2e-18 | |
1kfs_A | 605 | Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta | 2e-18 | |
2hbj_A | 410 | Structure Of The Yeast Nuclear Exosome Component, R | 3e-18 | |
1kln_A | 605 | Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta | 1e-16 | |
1d8y_A | 605 | Crystal Structure Of The Complex Of Dna Polymerase | 9e-15 | |
3cym_A | 440 | Crystal Structure Of Protein Bad_0989 From Bifidoba | 2e-10 | |
2e6l_A | 208 | Structure Of Mouse Wrn Exonuclease Domain Length = | 3e-08 | |
2fbt_A | 205 | Wrn Exonuclease Length = 205 | 7e-08 |
gi|75765643|pdb|1YT3|A Chain A, Crystal Structure Of Escherichia Coli Rnase D, An Exoribonuclease Involved In Structured Rna Processing Length = 375 | Back alignment and structure |
Score = 109 bits (272), Expect = 2e-22, Method: Composition-based stats. Identities = 48/192 (25%), Positives = 83/192 (43%), Gaps = 6/192 (3%) Query: 2 TTIRVHEGD--IPAECAA-RYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA 58 ++ D + + C A R AIA+DTE + +L ++QL G+ I + Sbjct: 1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPL-- 58 Query: 59 GQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHG 118 G + L +L D K H G D+ V FG +P+ T+I + G Sbjct: 59 GITDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPM-SWG 117 Query: 119 LKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSD 178 ++E G+ + K++ +DW A L++ Q +YAA+DV +L + + + + G Sbjct: 118 FASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLP 177 Query: 179 LATSCCNFLMDR 190 A C + R Sbjct: 178 AALDECRLMQMR 189 |
>gi|157830862|pdb|1DPI|A Chain A, Structure Of Large Fragment Of Escherichia Coli Dna Polymerase I Complexed With DTMP Length = 605 | Back alignment and structure |
Score = 96.7 bits (239), Expect = 2e-18, Method: Composition-based stats. Identities = 37/201 (18%), Positives = 70/201 (34%), Gaps = 18/201 (8%) Query: 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN----------L 66 A DTET L L + + G I +A +AP+ L Sbjct: 23 LEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELL 82 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L DEK K+ ++D +L F T + S + + +H + + Sbjct: 83 KPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERW 142 Query: 127 LGINISKAQQSSDWSADDLSDEQL------QYAASDVVHLHALRLQFTEKLQRL-GRSDL 179 L ++ + + L+ Q+ +YAA D L L+ LQ+ G ++ Sbjct: 143 LKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNV 202 Query: 180 ATS-CCNFLMDRAELDLLGWE 199 + + + ++ G + Sbjct: 203 FENIEMPLVPVLSRIERNGVK 223 |
gi|2982102|pdb|1KFS|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 | Back alignment and structure |
Score = 96.7 bits (239), Expect = 2e-18, Method: Composition-based stats. Identities = 37/201 (18%), Positives = 70/201 (34%), Gaps = 18/201 (8%) Query: 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN----------L 66 A DTET L L + + G I +A +AP+ L Sbjct: 23 LEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELL 82 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L DEK K+ ++D +L F T + S + + +H + + Sbjct: 83 KPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERW 142 Query: 127 LGINISKAQQSSDWSADDLSDEQL------QYAASDVVHLHALRLQFTEKLQRL-GRSDL 179 L ++ + + L+ Q+ +YAA D L L+ LQ+ G ++ Sbjct: 143 LKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNV 202 Query: 180 ATS-CCNFLMDRAELDLLGWE 199 + + + ++ G + Sbjct: 203 FENIEMPLVPVLSRIERNGVK 223 |
>gi|112491261|pdb|2HBJ|A Chain A, Structure Of The Yeast Nuclear Exosome Component, Rrp6p, Reveals An Interplay Between The Active Site And The Hrdc Domain Length = 410 | Back alignment and structure |
Score = 95.9 bits (237), Expect = 3e-18, Method: Composition-based stats. Identities = 38/162 (23%), Positives = 60/162 (37%), Gaps = 3/162 (1%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKR 75 + IAVD E +C++Q+S + ++ ++N L + + Sbjct: 102 DLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERD-YLVDTLKLRENLHILNEVFTNPSI 160 Query: 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQ 135 K+FH DI L G+ V +F T AS+ +H L L+ SK Sbjct: 161 VKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIG--LPRHSLAYLLENFANFKTSKKY 218 Query: 136 QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRS 177 Q +DW LS A +D L + Q KL + Sbjct: 219 QLADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKL 260 |
>gi|809180|pdb|1KLN|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 | Back alignment and structure |
Score = 90.5 bits (223), Expect = 1e-16, Method: Composition-based stats. Identities = 36/201 (17%), Positives = 69/201 (34%), Gaps = 18/201 (8%) Query: 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN----------L 66 A TET L L + + G I +A +AP+ L Sbjct: 23 LEKAPVFAFATETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELL 82 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L DEK K+ ++D +L F T + S + + +H + + Sbjct: 83 KPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERW 142 Query: 127 LGINISKAQQSSDWSADDLSDEQL------QYAASDVVHLHALRLQFTEKLQRL-GRSDL 179 L ++ + + L+ Q+ +YAA D L L+ LQ+ G ++ Sbjct: 143 LKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNV 202 Query: 180 ATS-CCNFLMDRAELDLLGWE 199 + + + ++ G + Sbjct: 203 FENIEMPLVPVLSRIERNGVK 223 |
>gi|6730276|pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I Klenow Fragment With Dna Length = 605 | Back alignment and structure |
Score = 84.4 bits (207), Expect = 9e-15, Method: Composition-based stats. Identities = 35/201 (17%), Positives = 68/201 (33%), Gaps = 18/201 (8%) Query: 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN----------L 66 A T T L L + + G I +A +AP+ L Sbjct: 23 LEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELL 82 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L DEK K+ ++D +L F T + S + + +H + + Sbjct: 83 KPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERW 142 Query: 127 LGINISKAQQSSDWSADDLSDEQL------QYAASDVVHLHALRLQFTEKLQRL-GRSDL 179 L ++ + + L+ Q+ +YAA D L L+ LQ+ G ++ Sbjct: 143 LKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNV 202 Query: 180 ATS-CCNFLMDRAELDLLGWE 199 + + + ++ G + Sbjct: 203 FENIEMPLVPVLSRIERNGVK 223 |
>gi|189096244|pdb|3CYM|A Chain A, Crystal Structure Of Protein Bad_0989 From Bifidobacterium Adolescentis Length = 440 | Back alignment and structure |
Score = 70.1 bits (170), Expect = 2e-10, Method: Composition-based stats. Identities = 40/172 (23%), Positives = 65/172 (37%), Gaps = 4/172 (2%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQL-SPGDGTVDIIRIAAGQKNAPNLVGMLVDEK 74 A ++A D E +VQ G G + A A Sbjct: 34 LASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGD 93 Query: 75 REKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134 I H D+ G+ + +F T+IA+RL + GL + LG+ ++K Sbjct: 94 AVWILHDSLQDLPGFD-ELGMEPQRLFDTEIAARLLGLK--RFGLAAVTEHFLGLTLAKE 150 Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNF 186 ++DWS L + YAA DV L L + +L+R G+ + A ++ Sbjct: 151 HSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQGKMEWAQEEFDY 202 |
>gi|126030364|pdb|2E6L|A Chain A, Structure Of Mouse Wrn Exonuclease Domain Length = 208 | Back alignment and structure |
Score = 62.8 bits (151), Expect = 3e-08, Method: Composition-based stats. Identities = 29/163 (17%), Positives = 60/163 (36%), Gaps = 6/163 (3%) Query: 11 IPAECA--ARYVDAIAVDTETLGLMP--RRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNL 66 + + + D + D E + +R R+ ++QL + + I++ L Sbjct: 29 LSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISSMSVFPQGL 88 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L ++ +K D L F V++ + L +K + Sbjct: 89 KMLLENKSIKKAGVGIEGDQWKLLRDFDVKLESFVELTDVANEKLKCAETWSLNGLVKHV 148 Query: 127 LGIN--ISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 LG K+ + S+WS L+++Q YAA+D + + Sbjct: 149 LGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKL 191 |
>gi|99032230|pdb|2FBT|A Chain A, Wrn Exonuclease Length = 205 | Back alignment and structure |
Score = 61.2 bits (147), Expect = 7e-08, Method: Composition-based stats. Identities = 28/164 (17%), Positives = 60/164 (36%), Gaps = 6/164 (3%) Query: 11 IPAECA--ARYVDAIAVDTETLGL--MPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNL 66 + + + D + D E L + ++ ++QL + + +++ L Sbjct: 34 LSEDISMSLSDGDVVGFDMEWPPLYNRGKLGKVALIQLCVSESKCYLFHVSSMSVFPQGL 93 Query: 67 VGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKEL 126 +L ++ +K D L F ++++ + T L +K L Sbjct: 94 KMLLENKAVKKAGVGIEGDQWKLLRDFDIKLKNFVELTDVANKKLKCTETWSLNSLVKHL 153 Query: 127 LGIN--ISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 LG K+ + S+WS L+++Q YAA+D + Sbjct: 154 LGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYAGFIIYRNLE 197 |
Homologous Structures in PDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | ||
3cym_A | 440 | Uncharacterized protein BAD_0989; structural genomics, | 2e-32 | |
2e6m_A | 208 | Werner syndrome ATP-dependent helicase homolog; APO for | 6e-20 | |
1vk0_A | 206 | Hypothetical protein; homohexamer, AT5G06450, structura | 3e-19 | |
1yt3_A | 375 | Ribonuclease D, RNAse D; exoribonuclease, exonuclease, | 2e-18 | |
2hbj_A | 410 | Exosome complex exonuclease RRP6; RNA metabolism, RNA s | 5e-17 | |
1x9m_A | 698 | DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene | 4e-07 | |
3m8r_A | 540 | DNA polymerase I, thermostable; DNA polymerase, DNA rep | 8e-06 | |
2hhv_A | 580 | DNA polymerase I; DNA replication, klenow fragment, pro | 2e-16 | |
2kfn_A | 605 | Klenow fragment of DNA polymerase I; complex (polymeras | 7e-12 |
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} Length = 440 | Back alignment and structure |
---|
Score = 134 bits (338), Expect = 2e-32 Identities = 37/175 (21%), Positives = 66/175 (37%), Gaps = 4/175 (2%) Query: 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGML-VDEKR 75 A ++A D E +VQ + ++ A + Sbjct: 35 ASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGDA 94 Query: 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQ 135 I H D+ G+ + +F T+IA+RL + GL + LG+ ++K Sbjct: 95 VWILHDSLQDLPGF-DELGMEPQRLFDTEIAARLL--GLKRFGLAAVTEHFLGLTLAKEH 151 Query: 136 QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 ++DWS L + YAA DV L L + +L+R G+ + A ++ + Sbjct: 152 SAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQGKMEWAQEEFDYALKE 206 |
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* Length = 208 | Back alignment and structure |
---|
Score = 92.7 bits (229), Expect = 6e-20 Identities = 30/164 (18%), Positives = 60/164 (36%), Gaps = 4/164 (2%) Query: 21 DAIAVDTETLGL--MPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKI 78 D + D E + +R R+ ++QL + + I++ L +L ++ +K Sbjct: 41 DVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKA 100 Query: 79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK--AQQ 136 D L F V++ + L +K +LG + K + + Sbjct: 101 GVGIEGDQWKLLRDFDVKLESFVELTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIR 160 Query: 137 SSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 S+WS L+++Q YAA+D + + + L Sbjct: 161 CSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGDTVQVFALN 204 |
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, structural genomics, protein structure initiative, center for eukaryotic structural genomics; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A Length = 206 | Back alignment and structure |
---|
Score = 90.1 bits (223), Expect = 3e-19 Identities = 24/169 (14%), Positives = 54/169 (31%), Gaps = 14/169 (8%) Query: 14 ECAARYVDAIAVDTETLGLMPRRD--------RLCIVQLSPGDGTVDIIRI-AAGQKNAP 64 + A+ D P + L V+LS + + +R+ N Sbjct: 40 DSILNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCL-FLRLPKPFHDNLK 98 Query: 65 NLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCT--KIASRLTRTYTNQHGLKDN 122 +L + + D+ +L G+ +R A G ++ Sbjct: 99 DLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTREL 158 Query: 123 LKELLGINISK-AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 +L ++ + + W +EQL+ AA + + + Q +++ Sbjct: 159 AHRVLWSDLGQLDSIEAKWEKA-GPEEQLEAAAIEGWLIVNVWDQLSDE 206 |
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Length = 375 | Back alignment and structure |
---|
Score = 87.7 bits (216), Expect = 2e-18 Identities = 43/171 (25%), Positives = 74/171 (43%), Gaps = 3/171 (1%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 AIA+DTE + +L ++QL G+ I + + L +L D K H Sbjct: 23 PAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLG--ITDWSPLKAILRDPSITKFLH 80 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 G D+ V FG +P+ T+I + G ++E G+ + K++ +DW Sbjct: 81 AGSEDLEVFLNVFGELPQPLIDTQILAAFCG-RPMSWGFASMVEEYSGVTLDKSESRTDW 139 Query: 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDRA 191 A L++ Q +YAA+DV +L + + + + G A C + R Sbjct: 140 LARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAALDECRLMQMRR 190 |
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* Length = 410 | Back alignment and structure |
---|
Score = 83.0 bits (204), Expect = 5e-17 Identities = 39/170 (22%), Positives = 61/170 (35%), Gaps = 3/170 (1%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 IAVD E +C++Q+S + ++ ++N L + + K+FH Sbjct: 107 KEIAVDLEHHDYRSYYGIVCLMQISTRERDY-LVDTLKLRENLHILNEVFTNPSIVKVFH 165 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 DI L G+ V +F T AS+ +H L L+ SK Q +DW Sbjct: 166 GAFMDIIWLQRDLGLYVVGLFDTYHASKAIG--LPRHSLAYLLENFANFKTSKKYQLADW 223 Query: 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 LS A +D L + Q KL + + R Sbjct: 224 RIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKR 273 |
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A* Length = 698 | Back alignment and structure |
---|
Score = 50.1 bits (118), Expect = 4e-07 Identities = 34/214 (15%), Positives = 58/214 (27%), Gaps = 39/214 (18%) Query: 23 IAVDTETLGLMPRRDRL-CIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHY 81 I D E L+ + C V R + L + +FH Sbjct: 2 IVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGG-LIVFHN 60 Query: 82 G-RFDIAVLFYTFGVRVRP--------VFCTKIASRL------------TRTYTNQHGL- 119 G ++D+ L +++ T + SRL R+ L Sbjct: 61 GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALE 120 Query: 120 -------------KDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQ 166 KD+ K +L + +W ++E + Y DVV AL + Sbjct: 121 AWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWN--FNEEMMDYNVQDVVVTKALLEK 178 Query: 167 FTEKLQRLGRSDLATSCCNFLMDRAELDLLGWEN 200 T L+ + E+ Sbjct: 179 LLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEH 212 |
>3m8r_A DNA polymerase I, thermostable; DNA polymerase, DNA replication, nucleotides, modified nucleotide, artificial nucleotide; HET: DNA DOC HXZ 15P; 2.00A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 1ktq_A* 5ktq_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* Length = 540 | Back alignment and structure |
---|
Score = 45.5 bits (107), Expect = 8e-06 Identities = 18/148 (12%), Positives = 37/148 (25%), Gaps = 24/148 (16%) Query: 28 ETLGLMPRRDRLCIVQLS-PGDGTVDIIRIAAGQKNAPN--LVGMLVDEKREKIFHYGRF 84 E P LS D++ +AA + + ++ Sbjct: 3 EEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAK 62 Query: 85 DIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADD 144 D++VL G+ + P + + L + + + G Sbjct: 63 DLSVLALREGLGLPPGDDPMLLAYLLD--PSNTTPEGVARRYGG---------------- 104 Query: 145 LSDEQLQYAASDVVHLHALRLQFTEKLQ 172 E + A L +L+ Sbjct: 105 ---EWTEEAGERAALSERLFANLWGRLE 129 |
>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... Length = 580 | Back alignment and structure |
---|
Score = 80.8 bits (198), Expect = 2e-16 Identities = 18/130 (13%), Positives = 37/130 (28%), Gaps = 4/130 (3%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 D A+ E + + + + G + A P V L DE ++K Sbjct: 18 DKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETA--LADPQFVAWLGDETKKKSMF 75 Query: 81 YGRFDIAVLFYTFGVRVR-PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139 + L + G+ + F +A+ L + K + + Sbjct: 76 DSKRAAVALKW-KGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYG 134 Query: 140 WSADDLSDEQ 149 A ++ Sbjct: 135 KGAKRAVPDE 144 |
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Length = 605 | Back alignment and structure |
---|
Score = 65.6 bits (159), Expect = 7e-12 Identities = 29/141 (20%), Positives = 54/141 (38%), Gaps = 12/141 (8%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPN----------LVGML 70 A DTET L L + + G I +A +AP+ L +L Sbjct: 27 PVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLL 86 Query: 71 VDEKREKIFHYGRFDIAVLFYTFGVRVR-PVFCTKIASRLTRTYTNQHGLKDNLKELLGI 129 DEK K+ ++D +L +G+ +R F T + S + + +H + + L Sbjct: 87 EDEKALKVGQNLKYDRGIL-ANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKH 145 Query: 130 NISKAQQSSDWSADDLSDEQL 150 ++ + + L+ Q+ Sbjct: 146 KTITFEEIAGKGKNQLTFNQI 166 |
Homologous Structures in PDB70 Database Detected by HHsearch
Original result of HHsearch against PDB70 database
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | ||
1yt3_A | 375 | Ribonuclease D, RNAse D; exoribonuclease, exonuclease, | 100.0 | |
2hbj_A | 410 | Exosome complex exonuclease RRP6; RNA metabolism, RNA s | 100.0 | |
3cym_A | 440 | Uncharacterized protein BAD_0989; structural genomics, | 100.0 | |
2e6m_A | 208 | Werner syndrome ATP-dependent helicase homolog; APO for | 100.0 | |
2hhv_A | 580 | DNA polymerase I; DNA replication, klenow fragment, pro | 100.0 | |
1vk0_A | 206 | Hypothetical protein; homohexamer, AT5G06450, structura | 100.0 | |
2kfn_A | 605 | Klenow fragment of DNA polymerase I; complex (polymeras | 99.97 | |
1x9m_A | 698 | DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene | 99.93 | |
3m8r_A | 540 | DNA polymerase I, thermostable; DNA polymerase, DNA rep | 99.9 | |
1bgx_T | 832 | TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibitio | 99.73 | |
1wlj_A | 189 | Interferon stimulated gene 20KDA; exoribonuclease, hydr | 99.38 | |
2p1j_A | 186 | POLIII, DNA polymerase III POLC-type; structural genomi | 99.05 | |
2is3_A | 215 | Ribonuclease T; RNAse, exoribonuclease, exonuclease, hy | 99.01 | |
2ioc_B | 242 | Three prime repair exonuclease 1; proline helix, nucleo | 98.73 | |
2qxf_A | 482 | Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfa | 98.39 | |
2gui_A | 194 | DNA polymerase III epsilon subunit; DNA polymerase proo | 97.89 | |
2d5r_A | 252 | CCR4-NOT transcription complex subunit 7; poly(A) deade | 97.58 | |
2xri_A | 224 | ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A | 97.57 | |
1qht_A | 775 | Protein (DNA polymerase); archaea, hyperthermostable, f | 97.56 | |
1uoc_A | 289 | POP2; hydrolase, DEDD nuclease, mRNA degradation, poly( | 97.5 | |
1s5j_A | 847 | DNA polymerase I; replication, disulfide bonds, transfe | 97.45 | |
2py5_A | 575 | DNA polymerase; protein-DNA complex, replication, trans | 97.34 | |
2p51_A | 333 | SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene | 97.31 | |
3k59_A | 786 | POL II, DNA polymerase II; protein-DNA complex, DNA dam | 95.83 | |
3cg7_A | 308 | CRN-4, cell death-related nuclease 4; hydrolase, apopto | 94.39 | |
1y97_A | 238 | Three prime repair exonuclease 2; TREX2, hydrolase; 2.5 | 98.58 | |
2f96_A | 224 | Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SA | 98.58 | |
3ikm_A | 1172 | DNA polymerase subunit gamma-1; human mitochondrial DNA | 98.19 | |
3nae_A | 903 | DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 | 96.79 | |
2gv9_A | 1193 | DNA polymerase; polymerase alpha fold, transferase; HET | 96.73 | |
3iay_A | 919 | DNA polymerase delta catalytic subunit; protein-DNA com | 96.52 | |
1w0h_A | 204 | 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET | 95.45 | |
3d45_A | 507 | Poly(A)-specific ribonuclease PARN; CAP analogue, cytop | 95.39 | |
1noy_A | 388 | Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DN | 95.14 | |
2a1r_A | 430 | Poly(A)-specific ribonuclease PARN; DEDD, nuclease doma | 92.85 | |
2gbz_A | 194 | Oligoribonuclease; ORN, deddh, structural genomics, X-R | 96.14 | |
2igi_A | 180 | Oligoribonuclease; RNAse, exoribonuclease, exonuclease, | 96.01 |
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 | Back alignment and structure |
---|
Probab=100.00 E-value=0 Score=307.87 Aligned_cols=188 Identities=24% Similarity=0.361 Sum_probs=167.5 Q ss_pred CCEEECCC--CCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEE Q ss_conf 72153257--888578-424898279971777898544507999984189428997465778570677677732364023 Q gi|254780636|r 2 TTIRVHEG--DIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKI 78 (207) Q Consensus 2 ~~~~~~~~--dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV 78 (207) |||+++.. +|.+.+ .++.+++|||||||+++++|++++||||||++++ +|++++.... ....|+++|+|++|+|| T Consensus 1 m~y~~I~t~~~L~~~~~~l~~~~~ia~DtE~~~~~ty~~~l~LiQi~~~~~-~~liD~l~~~-~~~~L~~ll~~~~i~kv 78 (375) T 1yt3_A 1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEH-LALIDPLGIT-DWSPLKAILRDPSITKF 78 (375) T ss_dssp CCCEEECSHHHHHHHHHHHTTSSEEEEEEEEECCSCSSCEEEEEEEECSSC-EEEECGGGCS-CCHHHHHHHHCTTSEEE T ss_pred CCEEEECCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEEEECCE-EEEEECCCCC-CHHHHHHHHHCCCCEEE T ss_conf 927998989999999999847990899798489888888789999876892-7999658987-78999999819886199 Q ss_pred ECCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHH Q ss_conf 01000016888654200000004578988652110000008877765420024675200365654432368999986459 Q gi|254780636|r 79 FHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVV 158 (207) Q Consensus 79 ~Hn~~~D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~ 158 (207) |||+++|+.+|.+++|+.+.|+||||+|+.+++ ++.++||+.+++++||++++|+.|+|||+.||||++|+.|||.||+ T Consensus 79 ~h~~~~D~~~L~~~~~~~~~~~fDt~ia~~~~~-~~~~~~l~~l~~~~l~~~l~K~~~~sdW~~rPLs~~ql~YAa~Dv~ 157 (375) T 1yt3_A 79 LHAGSEDLEVFLNVFGELPQPLIDTQILAAFCG-RPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVW 157 (375) T ss_dssp ESSCHHHHHHHHHHHSSCCSSEEEHHHHHHHTT-CCTTCCHHHHHHHHHCCCCCCTTTTSCTTSSSCCHHHHHHHHHHHH T ss_pred EECHHHHHHHHHHHCCCCCCCEEECHHHHHHHC-CCCHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHCCCE T ss_conf 725586799999964988887166388898838-7506788899999864503305545222566687899999840732 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 9999999999999974918999999964006899 Q gi|254780636|r 159 HLHALRLQFTEKLQRLGRSDLATSCCNFLMDRAE 192 (207) Q Consensus 159 ~l~~L~~~l~~~L~~~~~~~~~~~e~~~l~~~~~ 192 (207) ||++||+.|.++|.+.|+.+|+.+||+.+..... T Consensus 158 ~l~~l~~~l~~~L~~~~~~~~~~ee~~~l~~~~~ 191 (375) T 1yt3_A 158 YLLPITAKLMVETEASGWLPAALDECRLMQMRRQ 191 (375) T ss_dssp THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH T ss_pred EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 3799999999877630004678999999874431 |
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance, RNA processing, hydrolase, gene regulation; 2.10A {Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB: 2hbk_A 2hbl_A* 2hbm_A* | Back alignment and structure |
---|
Probab=100.00 E-value=0 Score=295.35 Aligned_cols=176 Identities=22% Similarity=0.204 Sum_probs=159.0 Q ss_pred CCCHHH-HCCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHH Q ss_conf 888578-4248982799717778985445079999841894289974657785706776777323640230100001688 Q gi|254780636|r 10 DIPAEC-AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAV 88 (207) Q Consensus 10 dl~~~~-~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~ 88 (207) +|.+.+ .++.++.|||||||++.+++++++||||+|++++ +|++++.........|+++|+|++|+|||||+++|+.+ T Consensus 95 ~L~~~~~~L~~~~~iavDtE~~~~~t~~~~l~LiQi~t~~~-~~liD~l~l~~~l~~L~~ll~d~~I~KV~H~~~~Dl~~ 173 (410) T 2hbj_A 95 ELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRER-DYLVDTLKLRENLHILNEVFTNPSIVKVFHGAFMDIIW 173 (410) T ss_dssp HHHHHHHHHTTCSEEEEEEEEECSSSSSCEEEEEEEECSSC-EEEEETTTTTTTGGGGHHHHTCTTSEEEESSCHHHHHH T ss_pred HHHHHHHHHHCCCEEEEEEEECCCCCCCCCEEEEEEEECCC-CEEEEECCCCCCHHHHHHHHCCCCCEEEEECHHHHHHH T ss_conf 99999999845991999704778851677068999981897-78985014533589999997499942999557877999 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 86542000000045789886521100000088777654200246752003656544323689999864599999999999 Q gi|254780636|r 89 LFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 89 L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) |.+++|+.+.|+||||+|+++++. .++||+.|+++|||++++|+.|+|||++||||++|+.|||.||+||++||+.|. T Consensus 174 L~~~~g~~~~~~fDT~ia~~~l~~--~~~sL~~L~~~~l~~~l~K~~q~sDW~~RPL~~~qi~YAa~Dv~~Ll~ly~~L~ 251 (410) T 2hbj_A 174 LQRDLGLYVVGLFDTYHASKAIGL--PRHSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLR 251 (410) T ss_dssp HHHHHCCCCSSEEEHHHHHHHHTC--SCCSHHHHHHHHSCCCCCCTTTTSCTTCSSCCHHHHHHHHHHHHTHHHHHHHHH T ss_pred HHHHCCCCCCCCCCHHHHHHHCCC--CCCCHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 998457567872026999998098--875699999987366656413342004555879999999853788999999999 Q ss_pred HHHHHCCCHHHHHHHHHHHH Q ss_conf 99997491899999996400 Q gi|254780636|r 169 EKLQRLGRSDLATSCCNFLM 188 (207) Q Consensus 169 ~~L~~~~~~~~~~~e~~~l~ 188 (207) ++|.+.|+++|+.+||+.+. T Consensus 252 ~~L~~~~~l~~~~ee~~~~~ 271 (410) T 2hbj_A 252 NKLIESNKLAGVLYESRNVA 271 (410) T ss_dssp HHHHHTTCHHHHHHHHHHHH T ss_pred HHHHHCCCHHHHHHHHHHHH T ss_conf 99997666589999999999 |
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown function, ribonuclease D, exonuclease; 2.10A {Bifidobacterium adolescentis ATCC15703} | Back alignment and structure |
---|
Probab=100.00 E-value=0 Score=288.94 Aligned_cols=175 Identities=21% Similarity=0.307 Sum_probs=149.8 Q ss_pred CCCHHHH-C-CCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCC---CCCCCHHHHHHHHCCCCCEEECCCCH Q ss_conf 8885784-2-48982799717778985445079999841894289974657---78570677677732364023010000 Q gi|254780636|r 10 DIPAECA-A-RYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAA---GQKNAPNLVGMLVDEKREKIFHYGRF 84 (207) Q Consensus 10 dl~~~~~-l-~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~---~~~~~~~L~~ll~d~~i~KV~Hn~~~ 84 (207) +|.+.+. + +..++|||||||+++++|++++|||||++.++.+|+|++.. .......|++++. +|+|||||+++ T Consensus 26 ~l~~~~~~L~~~~~~iavDtE~~~~~~y~~~~~LvQi~~~g~~~~liDp~~~~~~~~~~~~L~~~l~--~i~kv~H~~~~ 103 (440) T 3cym_A 26 AFRDYCSELASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVG--DAVWILHDSLQ 103 (440) T ss_dssp HHHHHHHHHHSCEEEEEEEEEECTTTSSSCCEEEEEEEEETTEEEEECHHHHHHTTCCHHHHHHHHT--TCEEEESSHHH T ss_pred HHHHHHHHHHHCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCCCHHHHHHHHHC--CCEEEEECCHH T ss_conf 9999999997179918997986788806874789998678988799805555655531799999867--98199977478 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 16888654200000004578988652110000008877765420024675200365654432368999986459999999 Q gi|254780636|r 85 DIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 85 D~~~L~~~~gi~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) |+.+|.+ +|+.|.|+||||+|+++++ . .++||+.|++++||++++|+.|+|||++||||++|+.|||.||.||++|| T Consensus 104 Dl~~l~~-~g~~~~~~fDTqiAa~~lg-~-~~~gl~~l~~~~lg~~l~K~~~~sdW~~rPLs~~q~~YAa~Dv~~L~~l~ 180 (440) T 3cym_A 104 DLPGFDE-LGMEPQRLFDTEIAARLLG-L-KRFGLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELE 180 (440) T ss_dssp HHHHHHH-HTCCCCEEEEHHHHHHHTT-C-SSCSHHHHHHHHHCEECCCCCTTCCTTCSSCCHHHHHHHHHHHHTHHHHH T ss_pred HHHHHHH-CCCCCCCCHHHHHHHHHCC-C-CCCCHHHHHHHHHCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999998-7881288122999998728-8-87779999999947665638888761787788899999986067789999 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9999999974918999999964006 Q gi|254780636|r 165 LQFTEKLQRLGRSDLATSCCNFLMD 189 (207) Q Consensus 165 ~~l~~~L~~~~~~~~~~~e~~~l~~ 189 (207) +.|.++|.+.++.+|+++||..+-. T Consensus 181 ~~l~~~L~~~~~~~~~~ee~~~~~~ 205 (440) T 3cym_A 181 TKMRAELKRQGKMEWAQEEFDYALK 205 (440) T ss_dssp HHHHHHHHHHTCHHHHHHHHHHHHH T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHH T ss_conf 9999999871217889999999985 |
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form, hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A 2fbv_A 2fbx_A 2fbt_A 2fc0_A* | Back alignment and structure |
---|
Probab=100.00 E-value=1.1e-37 Score=237.01 Aligned_cols=167 Identities=18% Similarity=0.142 Sum_probs=144.5 Q ss_pred CCCCCCEEEECCCC--CCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHH Q ss_conf 24898279971777--8985445079999841894289974657785706776777323640230100001688865420 Q gi|254780636|r 17 ARYVDAIAVDTETL--GLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFG 94 (207) Q Consensus 17 l~~~~~iaiDtEt~--~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g 94 (207) +...++|||||||+ ......+++|+||+|++++.|+++++......++.|+++|+|++|.|||||+++|+..|.+++| T Consensus 37 l~~~~vig~D~E~~~~~~~~~~~~v~liQla~~~~~~~i~~~~~~~~~~~~L~~lL~~~~i~Kvg~~~~~D~~~L~~~~~ 116 (208) T 2e6m_A 37 LSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFD 116 (208) T ss_dssp CCTTCEEEEEEECCC---CCSCCCCCEEEEECSSSEEEEECGGGCSSCCHHHHHHHTCTTSEEEESSHHHHHHHHHHHHC T ss_pred HCCCCEEEEECEECCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCC T ss_conf 54899899977017887888548678999986898789993676663439999997699823034337518999843022 Q ss_pred CCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC--CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000000457898865211000000887776542002467--520036565443236899998645999999999999999 Q gi|254780636|r 95 VRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK--AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ 172 (207) Q Consensus 95 i~~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK--~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~ 172 (207) +.+.|++|++.++........++||+.+++++||.+++| +.|+|||++||||++|+.|||.||++++.||++|.+..+ T Consensus 117 ~~~~~~~d~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~k~k~~q~s~W~~rpLt~~qi~YAA~Da~~~~~l~~~L~~~~~ 196 (208) T 2e6m_A 117 VKLESFVELTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLGNLGD 196 (208) T ss_dssp CCCCSEEEHHHHHHHHTTCCCCCCHHHHHHHHHSCBCCCCHHHHTSCTTSSSCCHHHHHHHHHHHHHHHHHHHHHHTCC- T ss_pred CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHCCEECCCHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 34573121538999981587653599999998293214207553477765889999999999999999999999986115 Q ss_pred HCCCHHHHHHH Q ss_conf 74918999999 Q gi|254780636|r 173 RLGRSDLATSC 183 (207) Q Consensus 173 ~~~~~~~~~~e 183 (207) +....+++++| T Consensus 197 ~~~~~~~~~~~ 207 (208) T 2e6m_A 197 TVQVFALNKAE 207 (208) T ss_dssp ----------- T ss_pred HHHHHHHHHHC T ss_conf 18899988741 |
>2hhv_A DNA polymerase I; DNA replication, klenow fragment, protein- DNA complex, O6-methyl-guanine, transferase/DNA complex; HET: DNA 6OG SUC; 1.55A {Geobacillus stearothermophilus} SCOP: c.55.3.5 e.8.1.1 PDB: 2hhs_A* 2hht_A* 2hhu_A* 2hhq_A* 2hhx_A* 2hw3_A* 1nk4_A* 1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* 1njw_A* 1l3s_A* 1njy_A* 1njz_A* 1nk0_A* 1njx_A* 1nk5_A* 1nk6_A* 1nk7_A* ... | Back alignment and structure |
---|
Probab=100.00 E-value=1.2e-34 Score=219.40 Aligned_cols=180 Identities=16% Similarity=0.100 Sum_probs=153.0 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCC Q ss_conf 98279971777898544507999984189428997465778570677677732364023010000168886542000000 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRP 99 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~ 99 (207) ++.+||||||+|++++.+++++|++|.+++.+|+++.... ..+.|+++|+|+++.||+||++||+.+|.++ |+.+++ T Consensus 17 ~~~~a~~~e~~~~~~~~~~ivGis~~~~~~~~~y~p~~~~--~~~~l~~~l~d~~~~ki~hN~k~D~~~L~~~-Gi~l~g 93 (580) T 2hhv_A 17 ADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETAL--ADPQFVAWLGDETKKKSMFDSKRAAVALKWK-GIELCG 93 (580) T ss_dssp CSEEEEEEECCSSSCTTCCCCEEEEEETTEEEEECHHHHT--TCHHHHHHHHCTTSEEEESSHHHHHHHHHTT-TCCCCC T ss_pred CCCCEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCC--CHHHHHHHHCCCCCCEEEEEHHHHHHHHHHC-CCCCCC T ss_conf 7884799976999735072899999966977999453546--6489999966999865885279999999978-882799 Q ss_pred H-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECC---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0-457898865211000000887776542002467520036---565443236899998645999999999999999749 Q gi|254780636|r 100 V-FCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD---WSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 100 i-~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~Sd---W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) + ||||||++++++....++|+.+++++++..+.+...... +...|-.+....|||.||.++++||+.|.++|.+.+ T Consensus 94 ~~~DTmiaa~ll~~~~~~~~L~~l~~~~~~~~~~~~~~~~gk~~~~~~~~~~~~~~Ya~~Da~~t~~L~~~l~~~l~~~~ 173 (580) T 2hhv_A 94 VSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNE 173 (580) T ss_dssp EEEEHHHHHHHHCGGGCCCSHHHHHHTTTCCSSCCHHHHHCSGGGCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT T ss_pred CEEHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 73289999997599999888999999867998784887518771002632799999999999999999999999975434 Q ss_pred CHHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 189999-9996400689998667988884 Q gi|254780636|r 176 RSDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 176 ~~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) +..+|. .|++++|++++||.+|++ +|. T Consensus 174 l~~~~~~iE~pl~~vL~~ME~~Gi~-vD~ 201 (580) T 2hhv_A 174 QDRLLVELEQPLSSILAEMEFAGVK-VDT 201 (580) T ss_dssp CHHHHHTTHHHHHHHHHHHHHHCEE-ECH T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEE-EEH T ss_conf 3314888997789999999745988-708 |
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, structural genomics, protein structure initiative, center for eukaryotic structural genomics; 2.10A {Arabidopsis thaliana} SCOP: c.55.3.5 PDB: 2q3s_A | Back alignment and structure |
---|
Probab=100.00 E-value=8.3e-34 Score=214.46 Aligned_cols=151 Identities=15% Similarity=0.074 Sum_probs=124.9 Q ss_pred CCCCCCEEEECCCCCC--------CCCCCEEEEEEEEECCCCEEEECCCC-CCCCCHHHHHHHHCCCCCEEECCCCHHHH Q ss_conf 2489827997177789--------85445079999841894289974657-78570677677732364023010000168 Q gi|254780636|r 17 ARYVDAIAVDTETLGL--------MPRRDRLCIVQLSPGDGTVDIIRIAA-GQKNAPNLVGMLVDEKREKIFHYGRFDIA 87 (207) Q Consensus 17 l~~~~~iaiDtEt~~l--------~~~~~~l~LiQl~~~~~~~~l~~~~~-~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~ 87 (207) +....+|||||||... .....++|+||||+++ .|+++++.+ ....++.|+++|+|++|+||||++++|+. T Consensus 43 ~~~~~~ig~D~EW~~~~~~~~~~~~~~~~~valiQl~t~~-~~~li~l~~~~~~~~~~L~~~L~~~~i~KVG~~i~~D~~ 121 (206) T 1vk0_A 43 LNGNRAVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRN-LCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLD 121 (206) T ss_dssp HHSTTEEEEEEEEECCC------CGGGGCEEEEEEEECSS-EEEEEECCSSCCGGGHHHHHHHTCSSSEEEESSCHHHHH T ss_pred HCCCCEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECC-CEEEEECCCCCCHHHHHHHHHHCCCCEEEEEECHHHHHH T ss_conf 2379669998004787766776553357615999998689-389998882111107999999659981599962698899 Q ss_pred HHHHHHHCCCCCHHHHHHHH-HHHH-HHCCCHHHHHHHHHHHCCCCCCCCE-ECCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 88654200000004578988-6521-1000000887776542002467520-0365654432368999986459999999 Q gi|254780636|r 88 VLFYTFGVRVRPVFCTKIAS-RLTR-TYTNQHGLKDNLKELLGINISKAQQ-SSDWSADDLSDEQLQYAASDVVHLHALR 164 (207) Q Consensus 88 ~L~~~~gi~~~~i~DT~ias-~l~~-~~~~~~~L~~L~~~~lg~~ldK~~q-~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~ 164 (207) .|.+++|+.+++++|++..+ .... +...++||+.|++++||+.++|..+ +|+|. ||||++|+.|||.||+++++|| T Consensus 122 ~L~~~~gi~~~~~vDl~~~a~~~~~~~~~~~~~l~~L~~~~lg~~l~K~~~~~s~W~-~pLs~~Qi~YAA~DA~~~~~iy 200 (206) T 1vk0_A 122 LLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWE-KAGPEEQLEAAAIEGWLIVNVW 200 (206) T ss_dssp HHHHHHCCCCSSEEEHHHHHHHHHTCGGGGGCCHHHHHHHHHCCCCHHHHHHHHTGG-GSCHHHHHHHHHHHHHHHHHHH T ss_pred HHHHHCCCCCCCEEECHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCEECCCCC-CCCCHHHHHHHHHHHHHHHHHH T ss_conf 985124976553552569999873254413100999999976986786765214876-8899999999999899999999 Q ss_pred HHHHH Q ss_conf 99999 Q gi|254780636|r 165 LQFTE 169 (207) Q Consensus 165 ~~l~~ 169 (207) ++|.+ T Consensus 201 ~~L~~ 205 (206) T 1vk0_A 201 DQLSD 205 (206) T ss_dssp HHHHH T ss_pred HHHHC T ss_conf 99852 |
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* | Back alignment and structure |
---|
Probab=99.97 E-value=2e-31 Score=200.64 Aligned_cols=199 Identities=20% Similarity=0.167 Sum_probs=156.8 Q ss_pred CEEECCC--CCCHHHH-CCCCCCEEEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCC----------CHHHHHH Q ss_conf 2153257--8885784-2489827997177789854450799998418942899746577857----------0677677 Q gi|254780636|r 3 TIRVHEG--DIPAECA-ARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKN----------APNLVGM 69 (207) Q Consensus 3 ~~~~~~~--dl~~~~~-l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~----------~~~L~~l 69 (207) ||+.+.+ +|...+. +...+.+||||||+|++++.+++++||+|..++.++++|+.+.... ...|+++ T Consensus 6 ~y~~i~~~~~l~~~~~~l~~~~~~a~D~ETt~ld~~~~~ivgis~s~~~~~~~yipi~h~~~~~~~~~~~~~vl~~Lk~~ 85 (605) T 2kfn_A 6 NYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPL 85 (605) T ss_dssp SSEECCSHHHHHHHHHHHHTSSSEEEEEEESCSCTTTCCEEEEEEEEETTEEEEEECCCCSTTCCCCCCHHHHHHHHHHH T ss_pred CCEEECCHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCEEEEEEEECCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHH T ss_conf 65288989999999999852994999831799983657499999982498599998226667775558999999999999 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCC-- Q ss_conf 732364023010000168886542000000-04578988652110000008877765420024675200365654432-- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTFGVRVRP-VFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLS-- 146 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~-i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs-- 146 (207) |+|+++.||+||++||+.+|.++ |+.+.+ ++|||+|+++++.....+++..+++++++..+++.....+|++..++ T Consensus 86 l~~~~i~kV~HNakFD~~~L~~~-Gi~l~~~~~DTmiaa~ll~~~~~~~~l~~~~~~~l~~~~~~~~~~~g~~k~~~~~~ 164 (605) T 2kfn_A 86 LEDEKALKVGQNLKYDRGILANY-GIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFN 164 (605) T ss_dssp HTCTTSCEEESSHHHHHHHHHTT-TCCCCCEEEEHHHHHHHHCTTSSCCSHHHHHHHHSCCCCCCHHHHHCSSTTCCCGG T ss_pred HHCCCCCEEEECHHHHHHHHHHC-CCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHCCCCCCCCHH T ss_conf 81899979997269999999977-99889840207778777256555565899999863877675898705774438801 Q ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHH-HHHHHHHHHHHHHHCCCCCCCC Q ss_conf ----368999986459999999999999997491-89999-9996400689998667988884 Q gi|254780636|r 147 ----DEQLQYAASDVVHLHALRLQFTEKLQRLGR-SDLAT-SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 147 ----~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~-~~~~~-~e~~~l~~~~~me~~g~~~~~~ 203 (207) .....|++.|+..+..++..+...+.+... ..++. .|+++.+++++|+..|+. +|. T Consensus 165 ~~~~~~~~~y~~~d~~~~~~~~~~l~~~~~~~~~~~~~~~~lE~pl~~vla~Me~~Gi~-vD~ 226 (605) T 2kfn_A 165 QIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVK-IDP 226 (605) T ss_dssp GSCHHHHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHTHHHHHHHHHHHHHHCBC-BCH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-HHH T ss_conf 22377899999999999999999999999986899999999981738999988440176-529 |
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A* | Back alignment and structure |
---|
Probab=99.93 E-value=1e-25 Score=167.38 Aligned_cols=177 Identities=16% Similarity=0.127 Sum_probs=130.7 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCC-CEEEECCCCCCCCCHHHHHHHHCCCCCEEECCC-CHHHHHHHHHHHCCC-- Q ss_conf 2799717778985445079999841894-289974657785706776777323640230100-001688865420000-- Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSPGDG-TVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYG-RFDIAVLFYTFGVRV-- 97 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~~~~-~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~-~~D~~~L~~~~gi~~-- 97 (207) +|+||+||+||.+..+++..|.+...+. .++.+.........+.++.++++.+.+ ||||+ +||+.+|.+.+|+.+ T Consensus 1 ~~v~DiET~gL~~~~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~l-VgHN~~~FD~~~L~k~~g~~~~~ 79 (698) T 1x9m_A 1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLI-VFHNGHKYDVPALTKLAKLQLNR 79 (698) T ss_dssp CEEEEEEESSCGGGCCCEEEEEEEETTTTEEEEECGGGHHHHHHHHHHHHHTTCCE-EESSTTTTHHHHHHHHHHHHHCC T ss_pred CEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEECCCCHHHHHHHHHHHHHCCCEE-EECCCHHCCHHHHHHHHCCCCCC T ss_conf 98999168997756787999999978997289847654057999999998559969-97572320899998873874233 Q ss_pred ------CCHHHHHHHHHHHHHH------------CCCHHHHHHHHHHHCCC---------------CCCCCEECCCCCCC Q ss_conf ------0004578988652110------------00000887776542002---------------46752003656544 Q gi|254780636|r 98 ------RPVFCTKIASRLTRTY------------TNQHGLKDNLKELLGIN---------------ISKAQQSSDWSADD 144 (207) Q Consensus 98 ------~~i~DT~ias~l~~~~------------~~~~~L~~L~~~~lg~~---------------ldK~~q~SdW~~rp 144 (207) ..++||||+|+++++. ...|||+++..+ ||.. ..+....++|.. T Consensus 80 ~~~~~~~~v~DTmi~s~ll~p~~~~~~~~~~~~~~~~hsL~a~g~r-lg~~K~~~~~~~~~~~~~~~~~~~~~~~~~~-- 156 (698) T 1x9m_A 80 EFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALEAWGYR-LGEMKGEYKDDFKRMLEEQGEEYVDGMEWWN-- 156 (698) T ss_dssp CCCCCGGGEEEHHHHHHHHTTTSCCCTTTTSCGGGSCSCCCHHHHH-HHHHHHHHHHHHHHHHHHTTCCCCTTGGGTS-- T ss_pred CCCCCCCCEEEHHHHHHHHCCCCCCCCCHHHHCCCCCCCHHHHHHH-HCCCCCCHHHHHHHHHHHCCCCCCCHHHHHH-- T ss_conf 4566778750277887663998644431122026678788999998-5865431377764322210223344133433-- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH----------------HHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 323689999864599999999999999974918----------------99999996400689998667988884 Q gi|254780636|r 145 LSDEQLQYAASDVVHLHALRLQFTEKLQRLGRS----------------DLATSCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 145 Ls~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~----------------~~~~~e~~~l~~~~~me~~g~~~~~~ 203 (207) +|++|+.||+.||.++++||+.|.+.+...+.. +....|+++.+++++||.+||+ +|+ T Consensus 157 ~s~em~~Ya~~Dv~iT~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lE~~~~~~l~~mE~nG~~-vD~ 230 (698) T 1x9m_A 157 FNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFP-FDT 230 (698) T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHTCTTTSCTTSCTTSSCHHHHHHHSCHHHHHHHHHHHHHHHHHHHCEE-BCH T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCEE-ECH T ss_conf 48999999998999999999999998643010012333210001012478999988999999998853989-729 |
>3m8r_A DNA polymerase I, thermostable; DNA polymerase, DNA replication, nucleotides, modified nucleotide, artificial nucleotide; HET: DNA DOC HXZ 15P; 2.00A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 1ktq_A* 5ktq_A* 4ktq_A* 1qtm_A* 2ktq_A* 1qss_A* 1qsy_A* | Back alignment and structure |
---|
Probab=99.90 E-value=5e-24 Score=157.65 Aligned_cols=155 Identities=14% Similarity=-0.002 Sum_probs=121.8 Q ss_pred CCCCCCCCCCCEEEEEEEEECC-CCEEEECCCCC--CCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHH Q ss_conf 1777898544507999984189-42899746577--85706776777323640230100001688865420000000457 Q gi|254780636|r 27 TETLGLMPRRDRLCIVQLSPGD-GTVDIIRIAAG--QKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCT 103 (207) Q Consensus 27 tEt~~l~~~~~~l~LiQl~~~~-~~~~l~~~~~~--~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT 103 (207) .||+++.|..+.++++.+|.++ ..++++++... .........+.....+.|++||.++|+.+|..+.||.+.++||| T Consensus 2 ~e~~~~~p~~~~~vG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~l~~~~Gi~~~~~~Dt 81 (540) T 3m8r_A 2 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDP 81 (540) T ss_dssp CEEECSSCCTTCEEEEEESSSCTTTCCEEEEEEEETTEEEECSSHHHHGGGCSCBCSTTHHHHHHHHHHTTCCCCBCCCH T ss_pred CCCCCCCCCCCEEEEEEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH T ss_conf 88789998884189999985588737864012234453222257998634346777568887999999679988997718 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHH- Q ss_conf 89886521100000088777654200246752003656544323689999864599999999999999974-9189999- Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL-GRSDLAT- 181 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~- 181 (207) ||||+++++ .+|||..++++|+|.. ..|||.||.++++||+.|.++|.++ ++.++|. T Consensus 82 mlaa~ll~~--~~~~l~~la~~~l~~~-------------------~~YA~~Da~~t~~L~~~l~~~L~~~~~l~~ly~~ 140 (540) T 3m8r_A 82 MLLAYLLDP--SNTTPEGVARRYGGEW-------------------TEEAGERAALSERLFANLWGRLEGEERLLWLYRE 140 (540) T ss_dssp HHHHHHHCT--TCCCHHHHHHHHTCCC-------------------CSCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHH T ss_pred HHHHHHHCC--CCCCHHHHHHHHCCCC-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998399--8998699999977521-------------------5889999999999999999998602558999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 9996400689998667988884 Q gi|254780636|r 182 SCCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 182 ~e~~~l~~~~~me~~g~~~~~~ 203 (207) .|++++|++++||.+|++ +|. T Consensus 141 iE~pl~~vLa~ME~~Gi~-vD~ 161 (540) T 3m8r_A 141 VERPLSAVLAHMEATGVR-LDV 161 (540) T ss_dssp THHHHHHHHHHHHHHCBE-ECH T ss_pred HHHHHHHHHHHHHHCCEE-EEH T ss_conf 986899999999974999-829 |
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* | Back alignment and structure |
---|
Probab=99.73 E-value=6.3e-18 Score=122.19 Aligned_cols=146 Identities=14% Similarity=0.013 Sum_probs=114.5 Q ss_pred EEECCCCCCCCCCCEEEEEEEEECCCCEEEECCCCCCCCCHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHCCCCCHHHH Q ss_conf 99717778985445079999841894289974657785706776777323640230100001688865420000000457 Q gi|254780636|r 24 AVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCT 103 (207) Q Consensus 24 aiDtEt~~l~~~~~~l~LiQl~~~~~~~~l~~~~~~~~~~~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~gi~~~~i~DT 103 (207) .+++++.+.++....+..+.++.+ +.++.++.. ++. + .++.|+.|+.++|+.+|..+.|+...++||| T Consensus 306 ~~~~~~~~~~~~~a~~vg~~~~~~-~~~~~~p~~--------~~~-l--~~l~k~~~~lk~d~~vl~~~~gi~~~~~~Dt 373 (832) T 1bgx_T 306 FVGFVLSRKEPMWADLLALAAARG-GRVHRAPEP--------YKA-L--RDLKEARGLLAKDLSVLALREGLGLPPGDDP 373 (832) T ss_dssp CBEEECSSSCTTTCCCCEEECBSS-SEEECCSCH--------HHH-H--HHCSSBCBTTHHHHHHHHHHHTCCCCBCCCH T ss_pred EEEEEECCCCCCHHHHHHHHHCCC-CEEEECCHH--------HHH-H--HHHHHHHCCCCCCHHHHHHHHHHCCCHHHHH T ss_conf 578885267641215776654048-848975404--------666-6--7688862443003999864101124400259 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHH Q ss_conf 89886521100000088777654200246752003656544323689999864599999999999999974-91899999 Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL-GRSDLATS 182 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~-~~~~~~~~ 182 (207) |+|++++++ .++++..+++++++.. ..||+.||.++++||..|.++|.++ ++..+|.. T Consensus 374 miaayLl~p--~~~~~~~l~~~~~~e~-------------------~eYa~~Da~~t~~L~~~L~~~L~~e~~l~~l~~~ 432 (832) T 1bgx_T 374 MLLAYLLDP--SNTTPEGVARRYGGEW-------------------TEEAGERAALSERLFANLWGRLEGEERLLWLYRE 432 (832) T ss_dssp HHHHHHHCT--TCCSTTHHHHHHSCCC-------------------CSSHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHT T ss_pred HHHHHHHCC--CCCCHHHHHHHHCCCC-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999998647--7868067777625441-------------------5779999999999999999998877889999999 Q ss_pred -HHHHHHHHHHHHHCCCCCCCC Q ss_conf -996400689998667988884 Q gi|254780636|r 183 -CCNFLMDRAELDLLGWENVDI 203 (207) Q Consensus 183 -e~~~l~~~~~me~~g~~~~~~ 203 (207) |+++++++++||.+|++ +|. T Consensus 433 IE~pl~~vLa~ME~~Gi~-vD~ 453 (832) T 1bgx_T 433 VERPLSAVLAHMEATGVR-LDV 453 (832) T ss_dssp THHHHHHHHHHHHHHCBC-BCT T ss_pred HHHHHHHHHHHHHHCCCC-CCH T ss_conf 987887888999871554-329 |
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 | Back alignment and structure |
---|
Probab=99.38 E-value=1.1e-12 Score=91.72 Aligned_cols=143 Identities=17% Similarity=0.103 Sum_probs=91.6 Q ss_pred CCCCCEEEECCCCCCCCCCCE-EEEEEEEECCCCEEE---ECCCC-CCCC---------------------CHHHHHHHH Q ss_conf 489827997177789854450-799998418942899---74657-7857---------------------067767773 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDR-LCIVQLSPGDGTVDI---IRIAA-GQKN---------------------APNLVGMLV 71 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~-l~LiQl~~~~~~~~l---~~~~~-~~~~---------------------~~~L~~ll~ 71 (207) ...++|++||||+|+++.++. ++.+.+...++...+ +.+.. .... .+.+.+++. T Consensus 3 ~~~~~V~iD~ETtGl~~~~~~~i~~~aiv~~~g~~v~~~~v~p~~~i~~~~~~i~GIt~e~l~~~~~~~~v~~~~~~~~~ 82 (189) T 1wlj_A 3 GSREVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMVGATPFAVARLEILQLLK 82 (189) T ss_dssp ---CEEEEEEEEEEETTTTEEEEEEEEEECTTCCEEEEEEEECSSCEEECCHHHHCCCHHHHTTCEEHHHHHHHHHHHHT T ss_pred CCCCEEEEEEECCCCCCCCCCEEEEEEEEEECCCEEEEEEECCCCCCCHHHCCCCCCCHHHHHCCCCHHHHHHHHHHHHC T ss_conf 99989999768088899998679999999837959999986699989830024889997896227847888999987631 Q ss_pred CCCCCEEECCCCHHHHHHHHHHHC-CC-CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHH Q ss_conf 236402301000016888654200-00-0004578988652110000008877765420024675200365654432368 Q gi|254780636|r 72 DEKREKIFHYGRFDIAVLFYTFGV-RV-RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQ 149 (207) Q Consensus 72 d~~i~KV~Hn~~~D~~~L~~~~gi-~~-~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Q 149 (207) +...|+||++||..+|...+.- .. .+..||+..++...+...++||..|++.++|..+....+ T Consensus 83 --~~~lV~hn~~fD~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~~l~~~i~~~~~------------- 147 (189) T 1wlj_A 83 --GKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHCRRVSLRVLSERLLHKSIQNSLL------------- 147 (189) T ss_dssp --TSEEEESSHHHHHHHTTCCCTTCEEEEGGGCHHHHHHHTC-----CCHHHHHHHHTCCCCSCCTT------------- T ss_pred --CCEEEEECHHHHHHHHHHHCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCC------------- T ss_conf --34589735687899999867032665841216999998736677889999999980987789998------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 99998645999999999999999749 Q gi|254780636|r 150 LQYAASDVVHLHALRLQFTEKLQRLG 175 (207) Q Consensus 150 i~YAA~Dv~~l~~L~~~l~~~L~~~~ 175 (207) -.-|..||..+.+||..+.+.-.+.+ T Consensus 148 ~H~Al~DA~at~~l~~~~~~~~~~~~ 173 (189) T 1wlj_A 148 GHSSVEDARATMELYQISQRIRARRG 173 (189) T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHTT T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 88819999999999999999997469 |
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} | Back alignment and structure |
---|
Probab=99.05 E-value=3.1e-10 Score=77.45 Aligned_cols=142 Identities=20% Similarity=0.300 Sum_probs=87.5 Q ss_pred HHHCCCCCCEEEECCCCCCCCCCCEEEEEEEEE---CCCC----E-EEECCCCCCCC----------------------C Q ss_conf 784248982799717778985445079999841---8942----8-99746577857----------------------0 Q gi|254780636|r 14 ECAARYVDAIAVDTETLGLMPRRDRLCIVQLSP---GDGT----V-DIIRIAAGQKN----------------------A 63 (207) Q Consensus 14 ~~~l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~---~~~~----~-~l~~~~~~~~~----------------------~ 63 (207) +--+.....|.+|+||||++|.++++ ||++. .++. + .++........ . T Consensus 6 ~~~~~~~~yvviD~ETTGl~~~~~~I--ieig~v~~~~~~i~~~~~~~v~p~~~~~~~~~~i~gi~~~~~~~~~~~~~~~ 83 (186) T 2p1j_A 6 DSTFGDATFVVLDFETTGLDPQVDEI--IEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVL 83 (186) T ss_dssp -------CEEEEEEEESCSCTTTCCE--EEEEEEEEETTEEEEEEEEECBCSSCCCHHHHHHHCCCHHHHTTCCBHHHHH T ss_pred CCCCCCCCEEEEEEECCCCCCCCCEE--EEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHCCCCHHHCCCCCHHHHHH T ss_conf 98178884999998728999999868--9999999989968778899866887689899987098756500212199999 Q ss_pred HHHHHHHHCCCCCEEECCCCHHHHHHHHHHH----CC-CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 6776777323640230100001688865420----00-000045789886521100000088777654200246752003 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTFG----VR-VRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSS 138 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g----i~-~~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~S 138 (207) +.+.+++.+ ..-|+||+.||..+|.+.+. .. +.+++||+-.++.... ..+++|.+++++ +|+...+. T Consensus 84 ~~~~~~~~~--~~~v~hn~~fD~~~L~~~~~~~~~~~~~~~~id~~~~~~~~~~-~~~~~L~~l~~~-~gi~~~~~---- 155 (186) T 2p1j_A 84 PEFLGFLED--SIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLK-LRSYSLDSVVEK-LGLGPFRH---- 155 (186) T ss_dssp HHHHHHSSS--CEEEETTHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHTC-CSCCSHHHHHHH-TTCCSTTC---- T ss_pred HHHHHHCCC--CEEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCCC---- T ss_conf 999974699--9899977898799999999984498766762020999998656-789889999998-69998989---- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 656544323689999864599999999999999974918 Q gi|254780636|r 139 DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRS 177 (207) Q Consensus 139 dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~ 177 (207) .=|..||..+.++|.++.++++++|.. T Consensus 156 ------------H~Al~Da~~t~~l~~~l~~~~k~~G~~ 182 (186) T 2p1j_A 156 ------------HRALDDARVTAQVFLRFVEMMKKEGHH 182 (186) T ss_dssp ------------CHHHHHHHHHHHHHHHHTTCC------ T ss_pred ------------CCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf ------------788999999999999999999824997 |
>2is3_A Ribonuclease T; RNAse, exoribonuclease, exonuclease, hydrolase, stable RNA maturation, tRNA END-turnover; 3.10A {Escherichia coli K12} | Back alignment and structure |
---|
Probab=99.01 E-value=9.9e-10 Score=74.53 Aligned_cols=142 Identities=18% Similarity=0.242 Sum_probs=85.1 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE------CCCC-----E---EEECCCCCCC---------------------C Q ss_conf 48982799717778985445079999841------8942-----8---9974657785---------------------7 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP------GDGT-----V---DIIRIAAGQK---------------------N 62 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~------~~~~-----~---~l~~~~~~~~---------------------~ 62 (207) ++..+|.||+||||++|.++++ ||+|. +++. . ++.+...... . T Consensus 15 ~~~~~Vv~D~ETTGl~p~~d~I--IeIgav~i~~~~~~~~~~~~~~~~~~~p~~~~~i~~~~~~i~gi~~~~~~~~~~~~ 92 (215) T 2is3_A 15 RGFYPVVIDVETAGFNAKTDAL--LEIAAITLKMDEQGWLMPDTTLHFHVEPFVGANLQPEALAFNGIDPNDPDRGAVSE 92 (215) T ss_dssp TTEEEEEEEEEESSSCTTTSCE--EEEEEEEEEECTTSCEEEEEEEEEEBCCCTTCCCCHHHHHHHCCCTTCSTTCCBCH T ss_pred CCCCEEEEEEECCCCCCCCCCC--EEEEEEEEEECCCCCEECCCEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCH T ss_conf 2898599983799999999832--89999998956888683353599985268899988568760252138787079861 Q ss_pred CHHHHHHHHC----------CCCCEEECCCCHHHHHHHHHHH---CC-----CCCHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 0677677732----------3640230100001688865420---00-----0000457898865211000000887776 Q gi|254780636|r 63 APNLVGMLVD----------EKREKIFHYGRFDIAVLFYTFG---VR-----VRPVFCTKIASRLTRTYTNQHGLKDNLK 124 (207) Q Consensus 63 ~~~L~~ll~d----------~~i~KV~Hn~~~D~~~L~~~~g---i~-----~~~i~DT~ias~l~~~~~~~~~L~~L~~ 124 (207) .+.+.++++- .....|+||++||..+|.+.+. +. +...+||+..++.. .++++|..++. T Consensus 93 ~~~~~~~~~~i~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~l~~~~~~~~~~iDt~~~~~~~---~~~~~L~~l~~ 169 (215) T 2is3_A 93 YEALHEIFKVVRKGIKASGCNRAIMVAHNANFDHSFMMAAAERASLKRNPFHPFATFDTAALAGLA---LGQTVLSKACQ 169 (215) T ss_dssp HHHHHHHHHHHHHHHHHHTCSEEEEEETTHHHHHHHHHHHHHHHTCTTCCEEEEEEEEHHHHHHHH---HSCCSHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH---HCCCCHHHHHH T ss_conf 253599999999998763146550100376876999999999839998865330167799999887---36324999999 Q ss_pred HHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 5420024675200365654432368999986459999999999999997491899 Q gi|254780636|r 125 ELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDL 179 (207) Q Consensus 125 ~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~~~~~~ 179 (207) + +|++++ ..+-+=|..||..+.+||.++.+++++.+.+.+ T Consensus 170 ~-~~i~~~--------------~~~~H~Al~Da~~ta~lf~~l~~~~~~~g~~~~ 209 (215) T 2is3_A 170 T-AGMDFD--------------STQAHSALYDTERTAVLFCEIVNRWKRLGGWPL 209 (215) T ss_dssp H-TTCCCC--------------TTTTTCHHHHHHHHHHHHHHHHHHHHHTTCSCC T ss_pred H-CCCCCC--------------CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 8-599999--------------997678699999999999999999997589999 |
>2ioc_B Three prime repair exonuclease 1; proline helix, nucleotide complex, DNAQ family, hydrolase; HET: D5M; 2.10A {Mus musculus} SCOP: c.55.3.5 PDB: 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A | Back alignment and structure |
---|
Probab=98.73 E-value=4.4e-08 Score=64.96 Aligned_cols=134 Identities=18% Similarity=0.101 Sum_probs=79.4 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEEC----C-----------------------CCEEEECCCCC------------- Q ss_conf 9827997177789854450799998418----9-----------------------42899746577------------- Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPG----D-----------------------GTVDIIRIAAG------------- 59 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~----~-----------------------~~~~l~~~~~~------------- 59 (207) ...|.+||||||+++.++++ ||++.- + .-..++..... T Consensus 12 ~t~v~~D~ETTGl~~~~~~I--ieia~v~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~lv~P~~~I~~~a~~ihGIt~ 89 (242) T 2ioc_B 12 QTLIFLDLEATGLPSSRPEV--TELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSK 89 (242) T ss_dssp SEEEEEEEEESSCGGGCCCE--EEEEEEEEEHHHHHTSCCCCSSSCCCCCCCSSCEEEEEECCCSSCCCHHHHHHHCCCH T ss_pred CEEEEEEEECCCCCCCCCCE--EEEEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHEECCCCCCCHHHHHHCCCCH T ss_conf 85999998889969999876--8999999876753465222111113566541101233012889979988998629999 Q ss_pred ------C--C----CCHHHHHHHHC--CCCCEEECCC-CHHHHHHHHHH---HCCC--CC--HHHHHHHHHHHHH----- Q ss_conf ------8--5----70677677732--3640230100-00168886542---0000--00--0457898865211----- Q gi|254780636|r 60 ------Q--K----NAPNLVGMLVD--EKREKIFHYG-RFDIAVLFYTF---GVRV--RP--VFCTKIASRLTRT----- 112 (207) Q Consensus 60 ------~--~----~~~~L~~ll~d--~~i~KV~Hn~-~~D~~~L~~~~---gi~~--~~--i~DT~ias~l~~~----- 112 (207) . . ..+.++.+++. ....-|+||+ .||..+|.+.+ |+.. .+ ..||+-+++-+.. T Consensus 90 ~~l~~~~~~~~~~~~~~~~~~f~~~~~~~~~lVahN~~~FD~~~L~~~~~r~~~~~~~~~~~~iDtl~~~~~~~~~~~~~ 169 (242) T 2ioc_B 90 AELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPS 169 (242) T ss_dssp HHHHHTTCCCSCHHHHHHHHHHHHTSCSSEEEEETTTTTTHHHHHHHHHHTSSSCCTTTTCEEEEHHHHHHHHHHTC--- T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHCCCCC T ss_conf 99972015505689999899999741688559983547889999999999859988877886877899999970324222 Q ss_pred ---HCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---00000088777654200246752003656544323689999864599999999999999 Q gi|254780636|r 113 ---YTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 113 ---~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) ...+++|.+|+++++|..... -+=|..||..+.+++.++.+.+ T Consensus 170 ~~~~~~~~~L~~l~~~~~g~~~~~----------------aH~Al~Da~~t~~l~~~~~~~~ 215 (242) T 2ioc_B 170 GNGSRKSYSLGSIYTRLYWQAPTD----------------SHTAEGDVLTLLSICQWKPQAL 215 (242) T ss_dssp ----CCCCCHHHHHHHHHSSCCSS----------------TTSHHHHHHHHHHHHTSSHHHH T ss_pred CCCCCCCCCHHHHHHHHCCCCCCC----------------CCCHHHHHHHHHHHHHHHHHHH T ss_conf 467766856899999974999987----------------8388999999999999999999 |
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, product bound structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A* | Back alignment and structure |
---|
Probab=98.39 E-value=3.6e-06 Score=53.86 Aligned_cols=134 Identities=19% Similarity=0.070 Sum_probs=75.6 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE----CCC----C--EEEECCCCCCCCC------------------------ Q ss_conf 48982799717778985445079999841----894----2--8997465778570------------------------ Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP----GDG----T--VDIIRIAAGQKNA------------------------ 63 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~----~~~----~--~~l~~~~~~~~~~------------------------ 63 (207) .....|.+|+||||++|.++++ ||+|. .+. . .+...+....... T Consensus 7 ~~~~~v~~D~ETTGl~~~~d~i--iq~~ai~~d~~~~~~~~~~~~~~~~~~~~~p~~~a~~v~gi~~~~~~~~~~~~~e~ 84 (482) T 2qxf_A 7 QQSTFLFHDYETFGTHPALDRP--AQFAAIRTDSEFNVIGEPEVFYCKPADDYLPQPGAVLITGITPQEARAKGENEAAF 84 (482) T ss_dssp CCCEEEEEEEEESSSCTTTSCE--EEEEEEEECTTSCBCSCCEEEEBCCCTTCCCCHHHHHHHCCCHHHHHHHCBCHHHH T ss_pred CCCCEEEEEEECCCCCCCCCCE--EEEEEEEECCCCCEEEEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHCCCCCHHHH T ss_conf 6897899998878979999822--89999999899858514567763479999988789688494999997399999999 Q ss_pred -HHHHHHHHCCCCCEEECC-CCHHHHHHHHHHH---CCC--------CCHHHHHHHHHHHHH-------------HCCCH Q ss_conf -677677732364023010-0001688865420---000--------000457898865211-------------00000 Q gi|254780636|r 64 -PNLVGMLVDEKREKIFHY-GRFDIAVLFYTFG---VRV--------RPVFCTKIASRLTRT-------------YTNQH 117 (207) Q Consensus 64 -~~L~~ll~d~~i~KV~Hn-~~~D~~~L~~~~g---i~~--------~~i~DT~ias~l~~~-------------~~~~~ 117 (207) ..+.++++.+...-|||| +.||..+|...+- ..| ....||......+.. ...++ T Consensus 85 ~~~i~~~~~~~~~~~vg~N~~~FD~~~l~~~~~r~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (482) T 2qxf_A 85 AARIHSLFTVPKTCILGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPENDDGLPSF 164 (482) T ss_dssp HHHHHHHHTSTTEEEEESSTTTTHHHHHHHHHHHTTSCSSGGGTGGGCEEEEHHHHHHHHHHHCCTTSCCCBCTTSSBCC T ss_pred HHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 99999998448976999676334799999998874478501220268750256888888864044221243234686646 Q ss_pred HHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 08877765420024675200365654432368999986459999999999999 Q gi|254780636|r 118 GLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 118 ~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) .|..++.. .|+. ...-+=|..||.+|.+|...+.+. T Consensus 165 kL~~l~~~-~~i~----------------~~~aHdA~~D~~~t~~l~~~l~~~ 200 (482) T 2qxf_A 165 RLEHLTKA-NGIE----------------HSNAHDAMADVYATIAMAKLVKTR 200 (482) T ss_dssp CHHHHHHH-TTCC----------------CC---CTTHHHHHHHHHHHHHHHH T ss_pred CHHHHHHH-CCCC----------------CCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 69999998-1998----------------778866355179999999999874 |
>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* | Back alignment and structure |
---|
Probab=97.89 E-value=3.5e-05 Score=48.14 Aligned_cols=133 Identities=20% Similarity=0.208 Sum_probs=75.1 Q ss_pred CCCCCEEEECCCCCCCCCCCE---EEEEEEEEC---C-----CCE-EEECCCCCC-CC---------------------C Q ss_conf 489827997177789854450---799998418---9-----428-997465778-57---------------------0 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDR---LCIVQLSPG---D-----GTV-DIIRIAAGQ-KN---------------------A 63 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~---l~LiQl~~~---~-----~~~-~l~~~~~~~-~~---------------------~ 63 (207) +....|.|||||||+++.... =.+||++.- + ..+ .++...... .. . T Consensus 7 ~~~r~vv~D~ETTGl~~~~~~~~~drIieigav~~~~~~~~~~~~~~~v~P~~~~~~~~~~i~gi~~e~~~~~~~~~~v~ 86 (194) T 2gui_A 7 AITRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVA 86 (194) T ss_dssp -CCEEEEEEEEESCCCSSSSTTTTCCEEEEEEEEEETTEECSCCEEEECCCSSCCCHHHHHHHCCCHHHHTTSCCHHHHH T ss_pred CCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECCEEECEEEEEEECCCCCCCHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 88837999973799987645678954999999999999997407899989998655778987075576643345589988 Q ss_pred HHHHHHHHCCCCCEEECCCCHHHHHHHHHHH---CC--CC----CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCC Q ss_conf 6776777323640230100001688865420---00--00----004578988652110000008877765420024675 Q gi|254780636|r 64 PNLVGMLVDEKREKIFHYGRFDIAVLFYTFG---VR--VR----PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKA 134 (207) Q Consensus 64 ~~L~~ll~d~~i~KV~Hn~~~D~~~L~~~~g---i~--~~----~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~ 134 (207) ..+.+++.+. ..|+||..+|..++...+. .. .. .+.||...++-... ..+++|..+++. +|+..++ T Consensus 87 ~~~~~~l~~~--~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~p-~~~~~L~~l~~~-~~i~~~~- 161 (194) T 2gui_A 87 DEFMDYIRGA--ELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFP-GKRNSLDALCAR-YEIDNSK- 161 (194) T ss_dssp HHHHHHHTTS--EEEETTHHHHHHHHHHHHHHTCSCCCCGGGTSEEEEHHHHHHHHST-TSCCSHHHHHHH-TTCCCTT- T ss_pred HHHHHHHCCC--EEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCC- T ss_conf 9999870897--3899785131999999999809997655544200019999999748-987889999998-5999899- Q ss_pred CEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2003656544323689999864599999999999 Q gi|254780636|r 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 135 ~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) .+.+=|..||..+.+||.+|. T Consensus 162 -------------~~~H~Al~Da~~t~~l~~~m~ 182 (194) T 2gui_A 162 -------------RTLHGALLDAQILAEVYLAMT 182 (194) T ss_dssp -------------CSSCCHHHHHHHHHHHHHHHT T ss_pred -------------CCCCCHHHHHHHHHHHHHHHH T ss_conf -------------987488999999999999997 |
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 | Back alignment and structure |
---|
Probab=97.58 E-value=0.00033 Score=42.41 Aligned_cols=141 Identities=17% Similarity=0.174 Sum_probs=84.9 Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECCC------CEEEECC--C--CCCCC Q ss_conf 424898279971777898544-------------------507999984----1894------2899746--5--77857 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGDG------TVDIIRI--A--AGQKN 62 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~~------~~~l~~~--~--~~~~~ 62 (207) ..+..+.||+|||++|+.... +.+.+||++ ..++ .++-+.+ . ..... T Consensus 20 ~i~~~~fvAiDtEfpGl~~~~~~~~~~~~~~~Y~~lr~nv~~~~iiQlGlt~~~~~g~~~~~~~~w~FNf~f~~~~d~~~ 99 (252) T 2d5r_A 20 VIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYA 99 (252) T ss_dssp HHHHCCEEEEEEECCCCCCCCCSCCSSHHHHHHHHHHHHHTTCCCCEEEEEEECTTSCCCSSCCEEEEEBCCCTTTSCCC T ss_pred HHHCCCEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCC T ss_conf 98649989998670684578876557998999999998775403037898986247877888612779987779766537 Q ss_pred CH-----------------------HHHHH------HHCCCCCEEECCCCHHHHHHHHHH-H-CCC-------------- Q ss_conf 06-----------------------77677------732364023010000168886542-0-000-------------- Q gi|254780636|r 63 AP-----------------------NLVGM------LVDEKREKIFHYGRFDIAVLFYTF-G-VRV-------------- 97 (207) Q Consensus 63 ~~-----------------------~L~~l------l~d~~i~KV~Hn~~~D~~~L~~~~-g-i~~-------------- 97 (207) +. .+.++ .-++++.||.|++-+|+..|.+.+ | -.| T Consensus 100 ~~Si~fL~~~GfDF~k~~~~GI~~~~f~ell~~s~~~~~~~v~wv~f~g~yD~~~L~k~l~g~~LP~~~~~F~~~~~~~F 179 (252) T 2d5r_A 100 QDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFF 179 (252) T ss_dssp HHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTTTSSSSSSCEEEESSCHHHHHHHHHHHHTSCCCSSHHHHHHHHHHHC T ss_pred HHHHHHHHHCCCCHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC T ss_conf 78999999869977899980973899999888611432589737871345789999999809999977899999999977 Q ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 00045789886521100000088777654200246752003656544323689999864599999999999999974 Q gi|254780636|r 98 RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRL 174 (207) Q Consensus 98 ~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~~ 174 (207) ..++||...++-+.+ .+-||..+++. ||+. .. -+. +=|..|+..+..+|-++.+.+-.. T Consensus 180 p~~yD~K~i~~~~~~--~~~~L~~la~~-L~v~---r~---------g~~---H~AG~DSllT~~~F~~l~~~~~~~ 238 (252) T 2d5r_A 180 PVIYDVKYLMKSCKN--LKGGLQEVAEQ-LELE---RI---------GPQ---HQAGSDSLLTGMAFFKMREMFFED 238 (252) T ss_dssp SCEEEHHHHGGGCTT--CCSSHHHHHHH-HTCC---CC---------SST---TSHHHHHHHHHHHHHHHHHHTSCS T ss_pred CHHEEHHHHHHHCCC--CCCHHHHHHHH-CCCC---CC---------CCC---CCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 346046989844566--57649999997-6999---87---------987---653678999999999999997147 |
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} | Back alignment and structure |
---|
Probab=97.57 E-value=0.00034 Score=42.38 Aligned_cols=133 Identities=14% Similarity=0.123 Sum_probs=72.4 Q ss_pred CEEEECCCCCCCCCCCEEEEEEEEE-----CCCC----E-EEECCCCCCCCCH------------------------HHH Q ss_conf 2799717778985445079999841-----8942----8-9974657785706------------------------776 Q gi|254780636|r 22 AIAVDTETLGLMPRRDRLCIVQLSP-----GDGT----V-DIIRIAAGQKNAP------------------------NLV 67 (207) Q Consensus 22 ~iaiDtEt~~l~~~~~~l~LiQl~~-----~~~~----~-~l~~~~~~~~~~~------------------------~L~ 67 (207) .|.+|+||||.++....-..|||+. .++. + .++.+.......+ .+. T Consensus 33 ~vv~D~EtTg~~~~~~~~eIIEiGaV~~d~~~~~i~~~f~~~vkP~~~~~i~~~~~~itgIt~e~l~~a~~~~ev~~~f~ 112 (224) T 2xri_A 33 FLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVD 112 (224) T ss_dssp EEEECCEECCCC-CCSSCCEEEEEEEEEETTTCCEEEEEEEECCCSSSCSCCHHHHHHHCCCHHHHTTCCCHHHHHHHHH T ss_pred EEEEEEECCCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCHHHHEECCCCHHHCCCCCCHHHHHHHHH T ss_conf 99999836899998897818999999998999869889999999798887896781530113565113463777899999 Q ss_pred HHHHCCCC------CEEECCCCHHHHHH-HH---HHHCCC----CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC Q ss_conf 77732364------02301000016888-65---420000----000457898865211000000887776542002467 Q gi|254780636|r 68 GMLVDEKR------EKIFHYGRFDIAVL-FY---TFGVRV----RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 (207) Q Consensus 68 ~ll~d~~i------~KV~Hn~~~D~~~L-~~---~~gi~~----~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK 133 (207) .++++..+ .-+.++++||...+ .. ..|+.. ....||+-..+...+...+++|..+++ ++|++... T Consensus 113 ~~l~~~~lv~~~~~~~~~~~~~fD~~~~l~~~~~~~~~~~p~~~~~~iD~~~~~~~~~~~~~~~~L~~l~~-~~gi~~~~ 191 (224) T 2xri_A 113 EWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNK-GLSLQHIG 191 (224) T ss_dssp HHHHHTTTTSTTSCEEEEESSSHHHHTHHHHHHHHHTCCCCGGGSCEEEHHHHHHHHHTSCCTTTHHHHHH-HTTCCCCS T ss_pred HHHCCCEEEEECCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHHHHHHHHCCCCCCCHHHHHH-HCCCCCCC T ss_conf 99658859940552799965166657899999997499987434312349999999718777876999999-86999999 Q ss_pred CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5200365654432368999986459999999999999 Q gi|254780636|r 134 AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 134 ~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +-+-|..||..+.+|+.+|.++ T Consensus 192 ---------------~~H~Al~DA~~ta~l~~~Ll~~ 213 (224) T 2xri_A 192 ---------------RPHSGIDDCKNIANIMKTLAYR 213 (224) T ss_dssp ---------------CTTCHHHHHHHHHHHHHHHHHT T ss_pred ---------------CCCCHHHHHHHHHHHHHHHHHC T ss_conf ---------------8738599999999999999977 |
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymerase, POL alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 3a2f_A* 2jgu_A* 1d5a_A | Back alignment and structure |
---|
Probab=97.56 E-value=0.0023 Score=37.56 Aligned_cols=165 Identities=18% Similarity=0.189 Sum_probs=91.9 Q ss_pred EEECCCCCCHHH----HC--------CCCCCEEEECCCCCCC---CCCCEEEEEEEEECCCCEEEECCCCCC-------- Q ss_conf 153257888578----42--------4898279971777898---544507999984189428997465778-------- Q gi|254780636|r 4 IRVHEGDIPAEC----AA--------RYVDAIAVDTETLGLM---PRRDRLCIVQLSPGDGTVDIIRIAAGQ-------- 60 (207) Q Consensus 4 ~~~~~~dl~~~~----~l--------~~~~~iaiDtEt~~l~---~~~~~l~LiQl~~~~~~~~l~~~~~~~-------- 60 (207) +.+++.|+|-.. +. ..-.++++|.||.+.. +..+++..|.++...... ++...... T Consensus 107 ~~~~E~dI~~~~r~lid~~l~p~~~~~~l~i~s~DIE~~~~~~~~~~~d~I~~Is~~~~~~~~-vi~~~~~d~~~v~~~~ 185 (775) T 1qht_A 107 VDIYEYDIPFAKRYLIDKGLIPMEGDEELTMLAFAIATLYHEGEEFGTGPILMISYADGSEAR-VITWKKIDLPYVDVVS 185 (775) T ss_dssp EEEESCSSCHHHHHHHHTTCCTTCSCCCCCEEEEEEEECCCTTCCTTCSCEEEEEEECSSCEE-EEESSCCCCSSEEECS T ss_pred CCEECCCCCCHHEEEEECCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEECCCCCE-EEECCCCCCCEEEECC T ss_conf 635715888054277877878567899836999998757876888777988999996389707-9967787876278719 Q ss_pred ---CCCHHHHHHH--HCCCCCEEECCC-CHHHHHHHHH---HHCC----------------------CCC--HHHHHHHH Q ss_conf ---5706776777--323640230100-0016888654---2000----------------------000--04578988 Q gi|254780636|r 61 ---KNAPNLVGML--VDEKREKIFHYG-RFDIAVLFYT---FGVR----------------------VRP--VFCTKIAS 107 (207) Q Consensus 61 ---~~~~~L~~ll--~d~~i~KV~Hn~-~~D~~~L~~~---~gi~----------------------~~~--i~DT~ias 107 (207) .....+..++ .||+|+ +|||. .||+..|... +|+. ..+ ++|+.-.. T Consensus 186 ~E~~LL~~F~~~i~~~dPDII-~GyN~~~FDlpyL~~R~~~l~i~~~~~r~~~~~~~~~~~~~~~~~i~Gri~iDl~~~~ 264 (775) T 1qht_A 186 TEKEMIKRFLRVVREKDPDVL-ITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVI 264 (775) T ss_dssp CHHHHHHHHHHHHHHHCCSEE-EESSTTTTHHHHHHHHHHHTTCCCCCSTTSCCCEEEEETTEEEEECTTSEEEEHHHHH T ss_pred CHHHHHHHHHHHHHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCCEECCCCCCCCEEECCCEEEEEECCEEEEEHHHHH T ss_conf 999999999999987199889-8708877529999999998298101035688765434486689988798999839999 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCC--CE-ECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 652110000008877765420024675--20-03656544323689999864599999999999999 Q gi|254780636|r 108 RLTRTYTNQHGLKDNLKELLGINISKA--QQ-SSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 108 ~l~~~~~~~~~L~~L~~~~lg~~ldK~--~q-~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) +-. ....+++|.+++++++|.....- .. .--|...+-...-+.|+..||..+..|..++.... T Consensus 265 ~~~-~~l~sy~L~~Va~~~lg~~K~d~~~~~i~~~~~~~~~~~~~~~Y~~~D~~lv~~L~~kl~~~~ 330 (775) T 1qht_A 265 RRT-INLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESGEGLERVARYSMEDAKVTYELGREFFPME 330 (775) T ss_dssp HHH-SCCSCCCHHHHHHHHHCCCCCCCCHHHHHHHHTTTCSHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_pred HHH-CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 764-667666689999998499755569999999875263299999996999999999988787999 |
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 | Back alignment and structure |
---|
Probab=97.50 E-value=0.0014 Score=38.81 Aligned_cols=140 Identities=14% Similarity=0.197 Sum_probs=80.8 Q ss_pred HCCCCCCEEEECCCCCCCCCC-------------------CEEEEEEEE----ECC-------CCEEEECCC--CCC--C Q ss_conf 424898279971777898544-------------------507999984----189-------428997465--778--5 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPRR-------------------DRLCIVQLS----PGD-------GTVDIIRIA--AGQ--K 61 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~~-------------------~~l~LiQl~----~~~-------~~~~l~~~~--~~~--~ 61 (207) .+...+.||+|||++|+.... +.+.+||++ ..+ ..++.+.+. ... . T Consensus 34 ~i~~~~fVAiD~Ef~Gi~~~~~~~~~~t~~~rY~~lk~nv~~~~iiQlGlt~f~~~g~~~~~~~~~w~FNf~~~~~~~~~ 113 (289) T 1uoc_A 34 LVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIM 113 (289) T ss_dssp HTTTSCEEEEEEEEEC----------CHHHHHHHHHHHHHTTCEEEEEEEEEECTTCCCCSSSCSEEEEEBCCCTTCCCC T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCCC T ss_conf 98339989996251784578886668999999999998664363246999987048876888714789977448620232 Q ss_pred CCH-----------------------HHHH------HHHCCCCCEEECCCCHHHHHHHHHH-HC-CC------------- Q ss_conf 706-----------------------7767------7732364023010000168886542-00-00------------- Q gi|254780636|r 62 NAP-----------------------NLVG------MLVDEKREKIFHYGRFDIAVLFYTF-GV-RV------------- 97 (207) Q Consensus 62 ~~~-----------------------~L~~------ll~d~~i~KV~Hn~~~D~~~L~~~~-gi-~~------------- 97 (207) .+. ...+ ++.++++.||+||+-+|+..|.+.+ |- .| T Consensus 114 ~~~Si~fL~~~G~DFnk~~~~GI~~~~f~~~~~~s~l~~~~~~~wv~f~g~yD~~yl~k~l~~~~LP~~~~~F~~~~~~~ 193 (289) T 1uoc_A 114 STESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQY 193 (289) T ss_dssp CHHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTSSCSSCTTSEEEESSTTHHHHHHHHHHTTSCCCSSHHHHHHHHHHH T ss_pred CHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHCCHHHCCCCEEEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 57789999985998689997199888888998750044247862896043557999999971898999999999999998 Q ss_pred -CCHHHHHHHHHHHHHHCC-------------CHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf -000457898865211000-------------000887776542002467520036565443236899998645999999 Q gi|254780636|r 98 -RPVFCTKIASRLTRTYTN-------------QHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHAL 163 (207) Q Consensus 98 -~~i~DT~ias~l~~~~~~-------------~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L 163 (207) ..++||...++.+.+... +.||..+++. +|++ +. ..-+=|+.|+..+-.+ T Consensus 194 Fp~iyDtK~~~~~~~~l~~~~~~~~~~~~~~~~~~L~~va~~-l~v~-------------r~--g~~HeAG~DS~lTg~~ 257 (289) T 1uoc_A 194 MPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADE-LGLP-------------RF--SIFTTTGGQSLLMLLS 257 (289) T ss_dssp CSSEEEHHHHHHHHTTTCC-------------CCSHHHHHHH-TTCC-------------CC--GGGGSHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-CCCC-------------CC--CCCCCCHHHHHHHHHH T ss_conf 762613999998621335754343322101234888899987-2998-------------77--8886607899999999 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780636|r 164 RLQFTEKL 171 (207) Q Consensus 164 ~~~l~~~L 171 (207) +-++.+.+ T Consensus 258 F~~l~~~~ 265 (289) T 1uoc_A 258 FCQLSKLS 265 (289) T ss_dssp HHHHHHHT T ss_pred HHHHHHHH T ss_conf 99999987 |
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1 | Back alignment and structure |
---|
Probab=97.45 E-value=0.0011 Score=39.34 Aligned_cols=145 Identities=17% Similarity=0.203 Sum_probs=76.7 Q ss_pred CCCCEEEECCCCCC------CCCCCEEEEEEEEEC--CC--CEEEECCC------------------CCCCCCHHHHHHH Q ss_conf 89827997177789------854450799998418--94--28997465------------------7785706776777 Q gi|254780636|r 19 YVDAIAVDTETLGL------MPRRDRLCIVQLSPG--DG--TVDIIRIA------------------AGQKNAPNLVGML 70 (207) Q Consensus 19 ~~~~iaiDtEt~~l------~~~~~~l~LiQl~~~--~~--~~~l~~~~------------------~~~~~~~~L~~ll 70 (207) .-.+++||.|+.+- +|.+++..+||++.. ++ .+++.... ........+..++ T Consensus 189 ~lrilsfDIE~~s~~~~~fPdp~~~~~~ii~I~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~f~sEkeLL~~F~~~i 268 (847) T 1s5j_A 189 KIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNTEYELLGRFFDIL 268 (847) T ss_dssp CCCEEEEEEEECCSSSSCCCCTTTCCSCEEEEEEEETTSCEEEEEECSSCCCCCCEEETTEEEEEESSHHHHHHHHHHHH T ss_pred CCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHC T ss_conf 84499999887888889998943477428999999568998999981677776654579958999898999999999742 Q ss_pred HCCCCCEEECCC-CHHHHHHHHH---HHCCCCC----------------H-HHH-HHH----HHHHH--HHCCCHHHHHH Q ss_conf 323640230100-0016888654---2000000----------------0-457-898----86521--10000008877 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYT---FGVRVRP----------------V-FCT-KIA----SRLTR--TYTNQHGLKDN 122 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~---~gi~~~~----------------i-~DT-~ia----s~l~~--~~~~~~~L~~L 122 (207) .||+|+ +|||+ .||+..|.+. +|+.... + +|. ... .+... ....+++|.++ T Consensus 269 ~dpDII-~GyNi~~FDlpYL~~Ra~~lg~~~~~~~~~~~g~~~~~~~~~~~~d~~~~~~~d~~~~~~~~~~l~sy~L~~V 347 (847) T 1s5j_A 269 LEYPIV-LTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAV 347 (847) T ss_dssp TTCSEE-EESSTTTTHHHHHHHHHHTTTCCGGGCSEECCSTTCCEETTSEEEEHHHHHTSHHHHHHTSTTCCSSCSHHHH T ss_pred CCCCEE-EEEECCCCCHHHHHHHHHHCCCCCCCCEEECCCCEEEEEEEEEEEEEEEEEHHHHHHHHHHHCCCCCCCHHHH T ss_conf 289979-8831056658999999998099832042530573235786206886533575989999876413020779999 Q ss_pred HHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 765420024675200365654432368999986459999999999 Q gi|254780636|r 123 LKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 123 ~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) ++++||..- ..-...+.... .+.-+.|+..||..+..|...+ T Consensus 348 a~~~Lg~~K--~~~~~~~~~~d-~~~l~~Y~~~D~~l~~~L~~~~ 389 (847) T 1s5j_A 348 AKALLGTSK--VKVDTLISFLD-VEKLIEYNFRDAEITLQLTTFN 389 (847) T ss_dssp HHHHHCCCC--C--SSCTTTCC-HHHHHHHHHHHHHHHHHTTTHH T ss_pred HHHHHCCCC--CCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 999838884--22222020100-6889888755568888999875 |
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A* | Back alignment and structure |
---|
Probab=97.34 E-value=0.0035 Score=36.51 Aligned_cols=142 Identities=11% Similarity=0.049 Sum_probs=74.6 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCC-EEEECCCCCCCCCHHHHHHHH--CCCCCEEECCCCHHHHHHHHHHHC- Q ss_conf 9827997177789854450799998418942-899746577857067767773--236402301000016888654200- Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGT-VDIIRIAAGQKNAPNLVGMLV--DEKREKIFHYGRFDIAVLFYTFGV- 95 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~-~~l~~~~~~~~~~~~L~~ll~--d~~i~KV~Hn~~~D~~~L~~~~gi- 95 (207) -+++.+|.||+ .+....++..+-+....+. .+-+. .....+.+.+. ||.| +|||.+||..++..++.. T Consensus 6 ~~~~~~D~Et~-~~~~~~~~~~~~~~~~~~~~~~~~~-----~~l~~f~~~i~~~dpdi--~~hNl~FD~~~i~~~~~~~ 77 (575) T 2py5_A 6 RKMYSCAFETT-TKVEDCRVWAYGYMNIEDHSEYKIG-----NSLDEFMAWVLKVQADL--YFHNLKFAGAFIINWLERN 77 (575) T ss_dssp CCEEEEEEEEC-CBTTBCCEEEEEEEESSCTTCEEEE-----SCHHHHHHHHHHHCCEE--EETTHHHHHHHHHHHHHHT T ss_pred CEEEEEEEEEC-CCCCCCEEEEEEEEECCCCEEEEHH-----HHHHHHHHHHHHCCCCE--EEECCCCCHHHHHHHHHHC T ss_conf 51799999706-8977731479999717984077708-----99999999998659979--9988757999999999970 Q ss_pred --CCCCHHH----------H-HHH---------------HHHHHHHC-CCHHHHHHHHHHHCCCCCCCC---EECCCCCC Q ss_conf --0000045----------7-898---------------86521100-000088777654200246752---00365654 Q gi|254780636|r 96 --RVRPVFC----------T-KIA---------------SRLTRTYT-NQHGLKDNLKELLGINISKAQ---QSSDWSAD 143 (207) Q Consensus 96 --~~~~i~D----------T-~ia---------------s~l~~~~~-~~~~L~~L~~~~lg~~ldK~~---q~SdW~~r 143 (207) ....-.+ . .+. -.+.+++. .+.||.++++.+ +....|.. ...+|... T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~DS~~l~~~SL~~va~~f-~l~~~K~~~~~~~~~~~~~ 156 (575) T 2py5_A 78 GFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDF-KLTVLKGDIDYHKERPVGY 156 (575) T ss_dssp TCEECTTCCTTEEEEEEBTTCCEEEEEEEEEEETTEEEEEEEEEHHHHSCSCHHHHHHHT-TCCCCSSCCCTTSCCCTTC T ss_pred CCCCEECCCCCCCCCEEEECCEEEEEEEEEEECCEEEEEEEEEECCCCCCCCHHHHHHHH-CCCCCCCCCCHHHCCHHHH T ss_conf 986203246766652267354579998999603301368999842144844799999873-7454556477444102233 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 432368999986459999999999999 Q gi|254780636|r 144 DLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 144 pLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) .+.++.+.|+..||..|.+++..+.+. T Consensus 157 ~~~~~~~~Y~~~Dv~ll~~i~~~~~~~ 183 (575) T 2py5_A 157 KITPEEYAYIKNDIQIIAEALLIQFKQ 183 (575) T ss_dssp CCCHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 232989999999999999999999998 |
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A | Back alignment and structure |
---|
Probab=97.31 E-value=0.00094 Score=39.80 Aligned_cols=140 Identities=18% Similarity=0.244 Sum_probs=84.0 Q ss_pred HCCCCCCEEEECCCCCCCCC-----C--------------CEEEEEEEE----ECCC------CEEEECCC----CCCCC Q ss_conf 42489827997177789854-----4--------------507999984----1894------28997465----77857 Q gi|254780636|r 16 AARYVDAIAVDTETLGLMPR-----R--------------DRLCIVQLS----PGDG------TVDIIRIA----AGQKN 62 (207) Q Consensus 16 ~l~~~~~iaiDtEt~~l~~~-----~--------------~~l~LiQl~----~~~~------~~~l~~~~----~~~~~ 62 (207) .++..+.||+|||++|+... . +.+.+||++ ..++ .++-+.+. ..... T Consensus 41 ~I~~~~fVAiDtEFpGiv~~p~~~~~~t~d~rY~~lr~nVd~l~iIQlGLt~~~~~g~~p~~~~twqFNF~f~~~~d~~~ 120 (333) T 2p51_A 41 LIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLRANVDSLKIIQIGLALSDEEGNAPVEACTWQFNFTFNLQDDMYA 120 (333) T ss_dssp HTTTSCEEEEEEECCCCCCCCCSCCSSSHHHHHHHHHHHHHHSCCCEEEEEEECTTSCCCTTCSEEEEEBCCCTTTSCCC T ss_pred HHHCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCCCC T ss_conf 98459989995331772567876668978999999997542145147999977258887888637999879778665504 Q ss_pred C-----------------------HHHHH------HHHCCCCCEEECCCCHHHHHHHHHHH----------------CCC Q ss_conf 0-----------------------67767------77323640230100001688865420----------------000 Q gi|254780636|r 63 A-----------------------PNLVG------MLVDEKREKIFHYGRFDIAVLFYTFG----------------VRV 97 (207) Q Consensus 63 ~-----------------------~~L~~------ll~d~~i~KV~Hn~~~D~~~L~~~~g----------------i~~ 97 (207) + ..+.+ ++-++++.||.|++.+|+..|.+.+- ... T Consensus 121 ~~SI~fL~~~G~DF~k~~~~GI~~~~F~ell~~sglv~~~~v~Wvtfhg~yD~~yLlk~l~g~~LP~~~~eF~~~l~~~F 200 (333) T 2p51_A 121 PESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKILCIYF 200 (333) T ss_dssp HHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTTTSSSCTTCEEEESSCHHHHHHHHHHHHCSCCCSSHHHHHHHHHHHS T ss_pred HHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 78999999749677889860998888899998505541688739980661679999999708878867899999999977 Q ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0004578988652110000008877765420024675200365654432368999986459999999999999997 Q gi|254780636|r 98 RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 98 ~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ..++||...++-+.+ .+-||..+++. ||+. .. -++ +=|..|+..+..+|-+|.+..-. T Consensus 201 P~vYD~Kyia~~~~~--~~~gL~~lA~~-L~v~---r~---------g~~---HqAGsDSllT~~~F~kl~~~~f~ 258 (333) T 2p51_A 201 PKNYDIKYIMKSVLN--NSKGLQDIADD-LQIH---RI---------GPQ---HQAGSDALLTARIFFEIRSRYFD 258 (333) T ss_dssp SSEEEHHHHHTTTTC--CCCCHHHHHHH-TTCC---CC---------SCT---TSHHHHHHHHHHHHHHHHHHHHT T ss_pred CHHHHHHHHHHHCCC--CCCCHHHHHHH-CCCC---CC---------CCC---CCCHHHHHHHHHHHHHHHHHHCC T ss_conf 628718999976156--67659999997-4998---76---------776---45305899999999999998659 |
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli k-12} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A* | Back alignment and structure |
---|
Probab=95.83 E-value=0.0074 Score=34.60 Aligned_cols=142 Identities=15% Similarity=0.098 Sum_probs=73.7 Q ss_pred CCCEEEECCCCCCCCCCCEEEEEEEEECCCC-EEEECCCC-CC--------------CCCHHHHHHH--HCCCCCEEECC Q ss_conf 9827997177789854450799998418942-89974657-78--------------5706776777--32364023010 Q gi|254780636|r 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGT-VDIIRIAA-GQ--------------KNAPNLVGML--VDEKREKIFHY 81 (207) Q Consensus 20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~~~-~~l~~~~~-~~--------------~~~~~L~~ll--~d~~i~KV~Hn 81 (207) -.+++||.|+.+-+ ++.-|.+...... ++.+.... .. .....+..++ .||+|+ +||| T Consensus 153 l~vlsfDIE~~~~~----~i~~I~~~~~~~~~v~~~~~~~~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDII-~GyN 227 (786) T 3k59_A 153 LKWVSIDIETTRHG----ELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVI-IGWN 227 (786) T ss_dssp CCEEEEEEEECTTS----CEEEEEEEETTEEEEEEESSCCSCCTTCSSEEEEESSHHHHHHHHHHHHHHHCCSEE-EESS T ss_pred CEEEEEEEEECCCC----CEEEEEEECCCCCEEEEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCEE-EECC T ss_conf 14899988975889----889999856998389999467777777753899969999999999999997099999-9728 Q ss_pred C-CHHHHHHHHHH---HCC-------------------------CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC Q ss_conf 0-00168886542---000-------------------------000--0457898865211000000887776542002 Q gi|254780636|r 82 G-RFDIAVLFYTF---GVR-------------------------VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGIN 130 (207) Q Consensus 82 ~-~~D~~~L~~~~---gi~-------------------------~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ 130 (207) . .||+..|.+.. |+. ..+ ++|+.-..+-.-....+++|.++++++||.. T Consensus 228 i~~FDlpyL~~Ra~~~~i~~~lgr~~~~~~~~~~~~~~~~~~~~i~Gr~~iD~~~~~~~~~~~~~sy~L~~va~~~L~~~ 307 (786) T 3k59_A 228 VVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG 307 (786) T ss_dssp TTTTHHHHHHHHHHHHTCCCCCBTTTBCCEEEECSSSTTCEEEECTTCEEEEHHHHHHHTTCCCSCCSHHHHHHHHHCCC T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEEEHHHHHHHHHHHHCCCCCCHHHHHHHHCCCC T ss_conf 86867999999999818973026767502300134346537871076880899999999752554378899999975788 Q ss_pred CCC--C-CEECC----CCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 467--5-20036----56544323689999864599999999999 Q gi|254780636|r 131 ISK--A-QQSSD----WSADDLSDEQLQYAASDVVHLHALRLQFT 168 (207) Q Consensus 131 ldK--~-~q~Sd----W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~ 168 (207) ..- . ..... |... ...-..|+..|+..+..|.+++. T Consensus 308 k~~~~~~~~~~~~~~~~~~~--~~~~~~Y~~~D~~L~~~L~~kl~ 350 (786) T 3k59_A 308 KSIDNPWDRMDEIDRRFAED--KPALATYNLKNCELVTQIFHKTE 350 (786) T ss_dssp CC-CCHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCCCCHHHHHHHHHHCCHHH--HHHHHHHHHHHHHHHHHHHHHHC T ss_conf 66678677534554246145--88999999888999999999856 |
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A | Back alignment and structure |
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Probab=94.39 E-value=0.22 Score=26.07 Aligned_cols=134 Identities=10% Similarity=0.088 Sum_probs=66.8 Q ss_pred CCEEEECCCCCCCCCCCE-EEEEEEEE-----CCCC------EE-EECCCCCCCC-----------------CH------ Q ss_conf 827997177789854450-79999841-----8942------89-9746577857-----------------06------ Q gi|254780636|r 21 DAIAVDTETLGLMPRRDR-LCIVQLSP-----GDGT------VD-IIRIAAGQKN-----------------AP------ 64 (207) Q Consensus 21 ~~iaiDtEt~~l~~~~~~-l~LiQl~~-----~~~~------~~-l~~~~~~~~~-----------------~~------ 64 (207) ..|.||+||||+++.++. --.|||+. ..+. +. ++.+...... ++ T Consensus 20 ~~vViD~ETTg~~~~~d~~~EIIEIgaV~vd~~~~~i~~~~~F~~~VkP~~~~~ls~~~~~ltGIt~e~v~~ap~f~evl 99 (308) T 3cg7_A 20 TLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKNCVDFTGIPQRSIDTADTFDVVY 99 (308) T ss_dssp EEEEEEEEECCBTTBCSCCCCEEEEEEEEEETTTTEEEEEEEEEEECBCSSBCSCCHHHHHHHCCCHHHHHTSCBHHHHH T ss_pred EEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCEEEECCEEEEEECCCCCCCCCHHHHHHCCCCHHHHHCCCHHHHHH T ss_conf 18999976089987889996079999999980599897841888778988888679889987197989943110045668 Q ss_pred -HHHHHHHCCCC----CEEECCCCHHHH-HHHHHH---HCCC----CCHHHHHHHH-HHHH-----HHCCCHHHHHHHHH Q ss_conf -77677732364----023010000168-886542---0000----0004578988-6521-----10000008877765 Q gi|254780636|r 65 -NLVGMLVDEKR----EKIFHYGRFDIA-VLFYTF---GVRV----RPVFCTKIAS-RLTR-----TYTNQHGLKDNLKE 125 (207) Q Consensus 65 -~L~~ll~d~~i----~KV~Hn~~~D~~-~L~~~~---gi~~----~~i~DT~ias-~l~~-----~~~~~~~L~~L~~~ 125 (207) .+.+++.+..+ .-+.+++.+|.. ++.+.+ |+.. .+.+|++-.. .... ....+++|..++++ T Consensus 100 ~~f~~~l~~~~l~~~~~~f~~~~~~D~~~~L~~~~~~~~i~~P~~~~~~iDl~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 179 (308) T 3cg7_A 100 EQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEY 179 (308) T ss_dssp HHHHHHHHHHCCCTTSEEEEESSSHHHHTHHHHHHHHTTCCCCGGGSEEEEHHHHHHHHHHHHCCCCCCCCSHHHHHHHH T ss_pred HHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHHHHHHCCCCCCCCHHHHHHH T ss_conf 89999973677323289993154566999999999980999872013244599999999997432277777789999997 Q ss_pred HHCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 420024675200365654432368999986459999999999999 Q gi|254780636|r 126 LLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 126 ~lg~~ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +|++.. . +-+-|..||..+.+|+.+|.++ T Consensus 180 -~gI~~~---------g------~aH~ALdDA~~tA~Il~kLl~~ 208 (308) T 3cg7_A 180 -YDLPTI---------G------RAHDAMDDCLNIATILQRMINM 208 (308) T ss_dssp -TTCCCC---------S------CTTCHHHHHHHHHHHHHHHHHT T ss_pred -CCCCCC---------C------CCCCHHHHHHHHHHHHHHHHHC T ss_conf -699999---------9------8968099999999999999977 |
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 | Back alignment and structure |
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Probab=98.58 E-value=2.5e-07 Score=60.56 Aligned_cols=82 Identities=20% Similarity=0.158 Sum_probs=55.0 Q ss_pred CCCEEECCC-CHHHHHHHHHH---HCCC--C-CHHHHHHHHHHHHH---------HCCCHHHHHHHHHHHCCCCCCCCEE Q ss_conf 640230100-00168886542---0000--0-00457898865211---------0000008877765420024675200 Q gi|254780636|r 74 KREKIFHYG-RFDIAVLFYTF---GVRV--R-PVFCTKIASRLTRT---------YTNQHGLKDNLKELLGINISKAQQS 137 (207) Q Consensus 74 ~i~KV~Hn~-~~D~~~L~~~~---gi~~--~-~i~DT~ias~l~~~---------~~~~~~L~~L~~~~lg~~ldK~~q~ 137 (207) ....|+||+ +||..+|.+.+ |+.+ . ...||+-.++.+.. ...+++|.+|++++.|.. T Consensus 113 ~~~~v~hn~~~FD~~~L~~~~~r~~~~~~~~~~~iDtl~~~~~l~~~~~~~~~~~~~~~~~L~~l~~~~~~~~------- 185 (238) T 1y97_A 113 PICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAE------- 185 (238) T ss_dssp SEEEEETTTTTTHHHHHHHHHHHHTCCCCTTCEEEEHHHHHHHHHHHC----------CCSHHHHHHHHHSSC------- T ss_pred CCEEEEECCHHHHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCC------- T ss_conf 8269996518778999999999808988889878778999999735075444566668858999999964999------- Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3656544323689999864599999999999999 Q gi|254780636|r 138 SDWSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 (207) Q Consensus 138 SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L 171 (207) ..+-+-|..||..+.+|+.++...+ T Consensus 186 ---------~~~aH~Al~Da~~t~~i~~~l~~~~ 210 (238) T 1y97_A 186 ---------PSAAHSAEGDVHTLLLIFLHRAAEL 210 (238) T ss_dssp ---------CC---CHHHHHHHHHHHHHHTHHHH T ss_pred ---------CCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf ---------8978898999999999999999999 |
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PSI, MCSG, protein structure initiative; 2.09A {Pseudomonas aeruginosa PAO1} SCOP: c.55.3.5 | Back alignment and structure |
---|
Probab=98.58 E-value=3.9e-07 Score=59.44 Aligned_cols=86 Identities=16% Similarity=0.181 Sum_probs=53.5 Q ss_pred CEEECCCCHHHHHHHHHH---HCCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHHHH Q ss_conf 023010000168886542---0000--00045789886521100000088777654200246752003656544323689 Q gi|254780636|r 76 EKIFHYGRFDIAVLFYTF---GVRV--RPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDEQL 150 (207) Q Consensus 76 ~KV~Hn~~~D~~~L~~~~---gi~~--~~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~Qi 150 (207) .-|+||..||..++...+ |+.. .+.+|+....+......+..+|.++++. +|++++.. + . T Consensus 128 ~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~~---------~-----a 192 (224) T 2f96_A 128 ILVGHNSSFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQA-AGMEFDNR---------E-----A 192 (224) T ss_dssp EEEETTHHHHHHHHHHHHHHHTCCCCCEEEEEEEEHHHHHHHHHSCCSHHHHHHH-TTCCCCTT---------S-----C T ss_pred EECCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHH-CCCCCCCC---------C-----C T ss_conf 2215347889999999999819998864113589999998754796439999998-29999989---------7-----6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 99986459999999999999997491 Q gi|254780636|r 151 QYAASDVVHLHALRLQFTEKLQRLGR 176 (207) Q Consensus 151 ~YAA~Dv~~l~~L~~~l~~~L~~~~~ 176 (207) +=|..||..+.+||.+|.+++++.+. T Consensus 193 H~Al~Da~~ta~l~~kl~~~~~~~~~ 218 (224) T 2f96_A 193 HSARYDTEKTAELFCGIVNRWKEMGG 218 (224) T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHTTS T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 78899999999999999999998189 |
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase, disease mutation, DNA replication, DNA-binding, DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo sapiens} | Back alignment and structure |
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Probab=98.19 E-value=2.3e-06 Score=54.93 Aligned_cols=99 Identities=16% Similarity=0.132 Sum_probs=68.4 Q ss_pred CCCCEEECCCCHHHHHHHHHHHCCCCC--HHHHHHHHHHHHH-------------------------------------- Q ss_conf 364023010000168886542000000--0457898865211-------------------------------------- Q gi|254780636|r 73 EKREKIFHYGRFDIAVLFYTFGVRVRP--VFCTKIASRLTRT-------------------------------------- 112 (207) Q Consensus 73 ~~i~KV~Hn~~~D~~~L~~~~gi~~~~--i~DT~ias~l~~~-------------------------------------- 112 (207) +++ -||||..||-......+.+...+ ++|||=++--..| T Consensus 194 ~rl-VVGHNVsyDRaRi~EeY~l~~s~~rFlDTMSLHvavsGm~S~QR~~w~~~kk~~~~~~~~~~~~~~~~~~~~~~~~ 272 (1172) T 3ikm_A 194 EQL-VVGHNVSFDRAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGKHKVQPPTKQGQKSQRKARRGPA 272 (1172) T ss_dssp CCC-CBCBCSSSSTTGGGTSSCSSCCCCCCCBTTHHHHHHSCCCHHHHHHHHHHHHC----------------------- T ss_pred CCE-EEECCCCCCHHHHHHHHHHCCCCCEEEEHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 637-9856755108888888731456763221034655402566242689987423132200123333321333212652 Q ss_pred --------HCC--CHHHHHHHHHHH-CCCCCCCCEECCCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --------000--000887776542-002467520036565443------2368999986459999999999999997 Q gi|254780636|r 113 --------YTN--QHGLKDNLKELL-GINISKAQQSSDWSADDL------SDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 113 --------~~~--~~~L~~L~~~~l-g~~ldK~~q~SdW~~rpL------s~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) .+. ..||.++.+-+| |+.+||+.|- .+..-++ -++-+.|||.||.++.++|.++-+...+ T Consensus 273 ~~~~~W~~~sS~~~NSL~dV~~lhcg~~~ldK~~Rd-~Fv~~~~~dI~~~fq~Lm~YCA~DV~aT~~V~~kl~P~Fle 349 (1172) T 3ikm_A 273 ISSWDWLDISSVNSNSLAEVHRLYVGGPPLEKEPRE-LFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPLFLE 349 (1172) T ss_dssp ---CCCCCCCCTTSHHHHHHHTCSSCSCS--SCSSS-STTTTCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT T ss_pred CCCCCHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH T ss_conf 234330002344536499999974799877877888-88529999999989999999998899999999987768785 |
>3nae_A DNA polymerase, GP43; RB69 DNA polymerase; HET: DNA G35 DOC DTP; 2.00A {Enterobacteria phage RB69} PDB: 3lzi_A* 3lzj_A* 1ig9_A* 1q9x_A* 2atq_A* 2dy4_A* 2oyq_A* 2ozm_A* 2ozs_A* 2p5g_A* 2p5o_A* 1q9y_A* 3l8b_A* 3lds_A* 3cq8_A* 1ih7_A* 1clq_A* 1waf_A* 1waj_A* 3cfr_A* ... | Back alignment and structure |
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Probab=96.79 E-value=0.0059 Score=35.15 Aligned_cols=97 Identities=10% Similarity=-0.041 Sum_probs=55.0 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCC-------------------------------C--CCHHHHHHHHH-HHHHHCC Q ss_conf 323640230100-00168886542000-------------------------------0--00045789886-5211000 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVR-------------------------------V--RPVFCTKIASR-LTRTYTN 115 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~-------------------------------~--~~i~DT~ias~-l~~~~~~ 115 (207) .||+|+ +|||+ .||+..|.+..... + ..++|.+-..+ ....... T Consensus 208 ~dPDII-~GyN~~~FD~pYL~~R~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~G~~~lD~~~l~~k~~~~~~~ 286 (903) T 3nae_A 208 KTPVIL-TGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQP 286 (903) T ss_dssp TCCSEE-ECSSTTTTHHHHHHHHHHHHHCHHHHGGGSTTSCEEEEEEEETTEEEEEEEETTCEECCHHHHHHHHSCCCCS T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEECEEEEEHHHHHHHHHHHCCC T ss_conf 599899-9689877679999999998557632211254567652100002355314666043675289999998760201 Q ss_pred CHHHHHHHHHHHCCCCCCCC-EECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00088777654200246752-0036565443236899998645999999999999 Q gi|254780636|r 116 QHGLKDNLKELLGINISKAQ-QSSDWSADDLSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 116 ~~~L~~L~~~~lg~~ldK~~-q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) +++|..++..++|..-.+.. ...++.... ...-+.|...|+..+.+|.+++.- T Consensus 287 sy~Ld~va~~~Lg~~k~~~~~~~~~~~~~~-~~~~~~Y~~~D~~L~~~L~~kl~~ 340 (903) T 3nae_A 287 SYSLDYISEFELNVGKLKYDGPISKLRESN-HQRYISYNIIAVYRVLQIDAKRQF 340 (903) T ss_dssp CCCHHHHHHHHHCCCCCCCSSCGGGHHHHH-HHHHHHHHHHHHHHHHHHHHHHCH T ss_pred CCHHHHHHHHHCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 123999999972888764421032330467-888988743279999999999878 |
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1 strain kos} PDB: 1dml_B* | Back alignment and structure |
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Probab=96.73 E-value=0.0046 Score=35.82 Aligned_cols=97 Identities=10% Similarity=-0.026 Sum_probs=56.2 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHH----CCC------------------------------CC--HHHHHHHHHHHHHH Q ss_conf 323640230100-001688865420----000------------------------------00--04578988652110 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFG----VRV------------------------------RP--VFCTKIASRLTRTY 113 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~g----i~~------------------------------~~--i~DT~ias~l~~~~ 113 (207) .||+|+ +|||+ .||+..|..... ..+ .+ ++|++-..+-- .. T Consensus 415 ~dPDII-tGYNi~~FDlpYL~~Ra~~l~~~~~~~~gR~~~~~~~~~~~~~~~~~~~~~~~~i~Gri~iDl~~~~k~~-~k 492 (1193) T 2gv9_A 415 YGPEFV-TGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQKRSKIKVNGMVNIDMYGIITDK-IK 492 (1193) T ss_dssp HCCSEE-EESSTTTTHHHHHHHHHHHTTCCCCTTTSSBSSSCCEEECC----------CEEETTBEEEEHHHHHTTT-CC T ss_pred CCCCEE-EEECCCCCCHHHHHHHHHHHCCCCHHHHCCCCCCCCCEECCCCCCCCCCCCEEEECCEEEEEHHHHHHHH-CC T ss_conf 399889-9725547747899999999779987882755765662020356665565404623466998437887663-04 Q ss_pred CCCHHHHHHHHHHHCCCCCC-CC-EEC-CCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00000887776542002467-52-003-6565443-236899998645999999999999 Q gi|254780636|r 114 TNQHGLKDNLKELLGINISK-AQ-QSS-DWSADDL-SDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 114 ~~~~~L~~L~~~~lg~~ldK-~~-q~S-dW~~rpL-s~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) ..+++|.++++++||.+-.. +. ... -|...|- ...-..|+..|+..+..|+.++.. T Consensus 493 L~sY~L~~Va~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~lv~~L~~kl~~ 552 (1193) T 2gv9_A 493 LSSYKLNAVAEAVLKDKKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLP 552 (1193) T ss_dssp CSCCCHHHHHHHTSCCCCCCCCTTTHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCH T ss_pred CCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 666889999999727777666888888887656778999999998879999999999878 |
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA- binding, DNA-directed DNA polymerase, exonuclease; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} | Back alignment and structure |
---|
Probab=96.52 E-value=0.012 Score=33.43 Aligned_cols=102 Identities=17% Similarity=0.056 Sum_probs=60.0 Q ss_pred HHHHH--HCCCCCEEECCC-CHHHHHHHHHH---HCC----------------------------------CCC--HHHH Q ss_conf 76777--323640230100-00168886542---000----------------------------------000--0457 Q gi|254780636|r 66 LVGML--VDEKREKIFHYG-RFDIAVLFYTF---GVR----------------------------------VRP--VFCT 103 (207) Q Consensus 66 L~~ll--~d~~i~KV~Hn~-~~D~~~L~~~~---gi~----------------------------------~~~--i~DT 103 (207) +..++ .||+|+ +|||+ .||+..|.+.. |+. +.+ ++|+ T Consensus 320 F~~~i~~~DPDII-~GyNi~~FDlpYL~~Ra~~l~i~~~~~~gr~~~~~~~~~~~~~~~~~~g~~~~~~~~i~Gr~~iDl 398 (919) T 3iay_A 320 WRNFIIKVDPDVI-IGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKESVFSSKAYGTRETKNVNIDGRLQLDL 398 (919) T ss_dssp HHHHHHHHCCSEE-EESSTTTTHHHHHHHHHHHTTCTTCSCCSSBTTCCCCBCCEEEEETTTEEEEECCBCCTTCEEEEH T ss_pred HHHHHHHCCCCEE-EEECCCCCCHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEEEEH T ss_conf 9999866299879-875785753799999999858751433176577664456564345433564422898737899877 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-C-CEECC-CCCCC-CCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 898865211000000887776542002467-5-20036-56544-3236899998645999999999999 Q gi|254780636|r 104 KIASRLTRTYTNQHGLKDNLKELLGINISK-A-QQSSD-WSADD-LSDEQLQYAASDVVHLHALRLQFTE 169 (207) Q Consensus 104 ~ias~l~~~~~~~~~L~~L~~~~lg~~ldK-~-~q~Sd-W~~rp-Ls~~Qi~YAA~Dv~~l~~L~~~l~~ 169 (207) .-..+-. ....+++|.+++++++|.+-.. . ...++ |...+ -...-+.|+..||..+..|.+++.- T Consensus 399 ~~~~~~~-~kl~sy~L~~Va~~~lg~~K~dv~~~~i~~~~~~~~e~~~~l~~Y~l~Da~l~~~L~~kl~~ 467 (919) T 3iay_A 399 LQFIQRE-YKLRSYTLNAVSAHFLGEQKEDVHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMA 467 (919) T ss_dssp HHHHHHH-CCCSCCCHHHHHHHHHCCC------CCHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHTTH T ss_pred HHHHHHH-CCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999875-65672328999987715887643044435777535267999999985436889999999999 |
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 | Back alignment and structure |
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Probab=95.45 E-value=0.11 Score=27.77 Aligned_cols=77 Identities=12% Similarity=0.223 Sum_probs=42.7 Q ss_pred EECCCCHHH-HHHHHHH---HCCC----CCHHHHHHHH-HHHHHHCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCHH Q ss_conf 301000016-8886542---0000----0004578988-65211000000887776542002467520036565443236 Q gi|254780636|r 78 IFHYGRFDI-AVLFYTF---GVRV----RPVFCTKIAS-RLTRTYTNQHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148 (207) Q Consensus 78 V~Hn~~~D~-~~L~~~~---gi~~----~~i~DT~ias-~l~~~~~~~~~L~~L~~~~lg~~ldK~~q~SdW~~rpLs~~ 148 (207) +.++..+|. .+|...+ ++.. ..++|++-.. ...+....+++|..+++. +|++.+. T Consensus 109 ~~~~~~~d~~~~l~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~kL~~l~~~-~gi~~~~--------------- 172 (204) T 1w0h_A 109 LLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEK-LGMDYDG--------------- 172 (204) T ss_dssp EEESSTTTTHHHHHHHHHHHTCCCCGGGSEEEEHHHHHHHHHTCCGGGCSHHHHHHH-TTCCCCS--------------- T ss_pred HHCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHCCCCCCCCHHHHHHH-CCCCCCC--------------- T ss_conf 211035648999999999818998642451676888888875034578899999998-6999999--------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999986459999999999999 Q gi|254780636|r 149 QLQYAASDVVHLHALRLQFTEK 170 (207) Q Consensus 149 Qi~YAA~Dv~~l~~L~~~l~~~ 170 (207) +-+-|..||..+-+|+.+|.++ T Consensus 173 ~aH~Al~Da~~ta~i~~~ll~~ 194 (204) T 1w0h_A 173 RPHCGLDDSKNIARIAVRMLQD 194 (204) T ss_dssp CTTCHHHHHHHHHHHHHHHHHT T ss_pred CCCCHHHHHHHHHHHHHHHHHC T ss_conf 8848799999999999999987 |
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, cytoplasm, exonuclease, hydrolase, magnesium, metal-binding, nonsense- mediated mRNA decay; HET: 7MG GDP; 3.00A {Mus musculus} | Back alignment and structure |
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Probab=95.39 E-value=0.023 Score=31.78 Aligned_cols=99 Identities=17% Similarity=0.104 Sum_probs=58.9 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHH-HCCC--------------CCHHHHHHHHHHH--HHHCCCHHHHHHHHHHHCCC-- Q ss_conf 732364023010000168886542-0000--------------0004578988652--11000000887776542002-- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTF-GVRV--------------RPVFCTKIASRLT--RTYTNQHGLKDNLKELLGIN-- 130 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~-gi~~--------------~~i~DT~ias~l~--~~~~~~~~L~~L~~~~lg~~-- 130 (207) +.+.+.+.||||+-+|+..+.+.| |..| ..++||...+... ......-+|..+.+.+-... T Consensus 272 l~~~kkpiVgHN~~~Dl~~l~~~F~gpLP~~~~eFk~~v~~lFP~i~DTK~la~~~~~~~~~~~t~L~~l~~~l~~~~~~ 351 (507) T 3d45_A 272 IANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFD 351 (507) T ss_dssp HHHHCCEEEESSCHHHHHHHHHHHTCSCCSSHHHHHHHHHHHCSCEEEHHHHTTSTTHHHHCCCCCHHHHHHHTTSTTCC T ss_pred HHHCCCEEEEECCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCC T ss_conf 97259839992438889999998428899679999999999777505888776316744467787699999998325789 Q ss_pred -----CCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf -----4675200365654432368999986459999999999999997 Q gi|254780636|r 131 -----ISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 131 -----ldK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ........+++. ++.+=|+.|++.|-.++-++...|.. T Consensus 352 ~~~i~~~~~~~~~~~~~-----~~~HeAGyDA~mTg~vF~~l~~~l~~ 394 (507) T 3d45_A 352 PPKVESAEGFPSYDTAS-----EQLHEAGYDAYITGLCFISMANYLGS 394 (507) T ss_dssp CCCEEECTTSCCCC---------CCCCHHHHHHHHHHHHHHHHHHHCC T ss_pred CCCEECCCCCCCCCCCC-----CCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 98342265666555678-----88735388899999999999999731 |
>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A* | Back alignment and structure |
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Probab=95.14 E-value=0.14 Score=27.20 Aligned_cols=95 Identities=8% Similarity=-0.043 Sum_probs=51.8 Q ss_pred HCCCCCEEECCC-CHHHHHHHHHHHCC-------------------------------CC--CHHHHHHHHHHH-HHHCC Q ss_conf 323640230100-00168886542000-------------------------------00--004578988652-11000 Q gi|254780636|r 71 VDEKREKIFHYG-RFDIAVLFYTFGVR-------------------------------VR--PVFCTKIASRLT-RTYTN 115 (207) Q Consensus 71 ~d~~i~KV~Hn~-~~D~~~L~~~~gi~-------------------------------~~--~i~DT~ias~l~-~~~~~ 115 (207) .||+|+ +|||. .||+..|.+..... .. ..+|.+-..+.. ..... T Consensus 205 ~dPDiI-~G~N~~~FD~pYL~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~d~l~~~~~~~~~~~~ 283 (388) T 1noy_A 205 KRPAIF-TGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKLLQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLP 283 (388) T ss_dssp SCCSEE-ECSSTTTTHHHHHHHHHHHHHHHHHHGGGSTTSCEEEEECCGGGCSCEEEEETTSEECCHHHHHHHHTCCCCS T ss_pred CCCCEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEECCCHHHHHHHHHHHHHCCCCC T ss_conf 388889-8706788517899999998526421011375676642255402565225642142167899999976303423 Q ss_pred CHHHHHHHHHHHCCCCCC-CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000887776542002467-5200365654432368999986459999999999 Q gi|254780636|r 116 QHGLKDNLKELLGINISK-AQQSSDWSADDLSDEQLQYAASDVVHLHALRLQF 167 (207) Q Consensus 116 ~~~L~~L~~~~lg~~ldK-~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207) +.+|.......++..... ......|.... .+.-+.|+..||..+++|.+++ T Consensus 284 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d-~~kli~Yn~~D~~l~~~L~~kl 335 (388) T 1noy_A 284 SFSLESVAQHETKKGKLPYDGPINKLRETN-HQRYISYNIIDVESVQAIDKIR 335 (388) T ss_dssp CCSHHHHHHHHHSCCCCCCSSCGGGHHHHH-HHHHHHHHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHCCCCCCCCHHHHHHHHHHC-HHHHHHHHHHHHHHHHHHHHHH T ss_conf 202888999866887667256666665418-9999999999999999999997 |
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase/RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A | Back alignment and structure |
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Probab=92.85 E-value=0.18 Score=26.48 Aligned_cols=99 Identities=18% Similarity=0.097 Sum_probs=57.3 Q ss_pred HHCCCCCEEECCCCHHHHHHHHHHH-CCC--------------CCHHHHHHHHHH--HHHHCCCHHHHHHHHHHHCCCC- Q ss_conf 7323640230100001688865420-000--------------000457898865--2110000008877765420024- Q gi|254780636|r 70 LVDEKREKIFHYGRFDIAVLFYTFG-VRV--------------RPVFCTKIASRL--TRTYTNQHGLKDNLKELLGINI- 131 (207) Q Consensus 70 l~d~~i~KV~Hn~~~D~~~L~~~~g-i~~--------------~~i~DT~ias~l--~~~~~~~~~L~~L~~~~lg~~l- 131 (207) +.+.+...||||+-.|+..+...|- ..| ..++||+..+.- +......-+|..+.+.+-.... T Consensus 277 l~~~~kpiVgHN~~~Dl~~~~~~f~~~LP~~~~eFk~~v~~~FP~i~DTK~l~~~~~~~~~~~~t~L~~l~~~l~~~~~~ 356 (430) T 2a1r_A 277 IANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFN 356 (430) T ss_dssp HHHHCCEEEESSCHHHHHHHHHHHTCCCCSSHHHHHHHHHHHCSSEEEHHHHHTSTTTTTTCSCCSHHHHHHHTTSTTCC T ss_pred HHHCCCCEEECCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCEEEHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCC T ss_conf 98659977866428889999987158999789999999998767300437653136644678886689999997206789 Q ss_pred ------CCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ------675200365654432368999986459999999999999997 Q gi|254780636|r 132 ------SKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQR 173 (207) Q Consensus 132 ------dK~~q~SdW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~~ 173 (207) ..+.+..++ ...+.+=|+-|++.|=.++-+|...|.. T Consensus 357 ~p~i~~~~~~~~~~~-----~~~~~HeAGyDA~mTG~vF~~l~~~l~~ 399 (430) T 2a1r_A 357 PPKVESAEGFPSYDT-----ASEQLHEAGYDAYITGLCFISMANYLGS 399 (430) T ss_dssp CCCEEECTTCCCC----------CCCCHHHHHHHHHHHHHHHHHHHGG T ss_pred CCCEECCCCCCCCCC-----CCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 983433766665568-----8998617088999999999999998741 |
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, X-RAY diffraction, hydrolase; 2.30A {Xanthomonas campestris PV} | Back alignment and structure |
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Probab=96.14 E-value=0.0022 Score=37.62 Aligned_cols=28 Identities=29% Similarity=0.387 Sum_probs=22.7 Q ss_pred CCCCCCEEEECCCCCCCCCCCEEEEEEEEE Q ss_conf 248982799717778985445079999841 Q gi|254780636|r 17 ARYVDAIAVDTETLGLMPRRDRLCIVQLSP 46 (207) Q Consensus 17 l~~~~~iaiDtEt~~l~~~~~~l~LiQl~~ 46 (207) ....+.|.+||||||++|.++++ ||+|. T Consensus 6 ~~~~~lV~lD~ETTGLdp~~d~I--IEIaa 33 (194) T 2gbz_A 6 AGNDRLIWIDLEMTGLDTDRDSI--IEIAT 33 (194) T ss_dssp --CCEEEEEEEEESCSCTTTCCE--EEEEE T ss_pred CCCCCEEEEEEECCCCCCCCCEE--EEEEE T ss_conf 77899899987789999999837--99999 |
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli K12} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A | Back alignment and structure |
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Probab=96.01 E-value=0.0028 Score=37.09 Aligned_cols=27 Identities=33% Similarity=0.572 Sum_probs=21.8 Q ss_pred CCCCCEEEECCCCCCCCCCCEEEEEEEEE Q ss_conf 48982799717778985445079999841 Q gi|254780636|r 18 RYVDAIAVDTETLGLMPRRDRLCIVQLSP 46 (207) Q Consensus 18 ~~~~~iaiDtEt~~l~~~~~~l~LiQl~~ 46 (207) ++.++|.+|+||||++|.++++ ||||. T Consensus 3 ~~~~lv~lD~ETTGL~p~~D~I--IeIaa 29 (180) T 2igi_A 3 NENNLIWIDLEMTGLDPERDRI--IEIAT 29 (180) T ss_dssp GGGCEEEEEEEESSSCTTTCCE--EEEEE T ss_pred CCCCEEEEEEECCCCCCCCCEE--EEEEE T ss_conf 8897899986789999999847--99999 |
Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
Identity | Alignment graph | Length | Definition | E-value |
207 | ribonuclease D [Candidatus Liberibacter asiaticus str. | |||
d2hbka2 | 292 | c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 { | 5e-21 | |
d1vk0a_ | 206 | c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cre | 3e-19 | |
d1yt3a3 | 193 | c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Es | 9e-19 | |
d2hhva1 | 171 | c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic | 3e-15 | |
d1kfsa1 | 195 | c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic | 4e-12 |
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 292 | Back information, alignment and structure |
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class: Alpha and beta proteins (a/b) fold: Ribonuclease H-like motif superfamily: Ribonuclease H-like family: DnaQ-like 3'-5' exonuclease domain: Exosome complex exonuclease RRP6 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] Score = 94.9 bits (235), Expect = 5e-21 Identities = 39/170 (22%), Positives = 61/170 (35%), Gaps = 3/170 (1%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 IAVD E +C++Q+S + ++ ++N L + + K+FH Sbjct: 105 KEIAVDLEHHDYRSYYGIVCLMQISTRERDY-LVDTLKLRENLHILNEVFTNPSIVKVFH 163 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 DI L G+ V +F T AS+ +H L L+ SK Q +DW Sbjct: 164 GAFMDIIWLQRDLGLYVVGLFDTYHASKAIGLP--RHSLAYLLENFANFKTSKKYQLADW 221 Query: 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 LS A +D L + Q KL + + R Sbjct: 222 RIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVLYESRNVAKR 271 |
>d1vk0a_ c.55.3.5 (A:) Hypothetical protein AT5G06450 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 206 | Back information, alignment and structure |
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class: Alpha and beta proteins (a/b) fold: Ribonuclease H-like motif superfamily: Ribonuclease H-like family: DnaQ-like 3'-5' exonuclease domain: Hypothetical protein AT5G06450 species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702] Score = 88.5 bits (219), Expect = 3e-19 Identities = 25/161 (15%), Positives = 56/161 (34%), Gaps = 14/161 (8%) Query: 22 AIAVDTETLGLMPRRD--------RLCIVQLSPGDGTVDIIRI-AAGQKNAPNLVGMLVD 72 A+ D P + L V+LS + + +R+ N +L Sbjct: 48 AVIFDVYWDVGFPETETKTKTSGWSLSSVKLSTRNLCL-FLRLPKPFHDNLKDLYRFFAS 106 Query: 73 EKREKIFHYGRFDIAVLFYTFGVRVRPVF-CTKIASRLT-RTYTNQHGLKDNLKELLGIN 130 + + D+ +L G+ +R K+A+ G ++ +L + Sbjct: 107 KFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSD 166 Query: 131 ISKA-QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEK 170 + + + W +EQL+ AA + + + Q +++ Sbjct: 167 LGQLDSIEAKWE-KAGPEEQLEAAAIEGWLIVNVWDQLSDE 206 |
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Length = 193 | Back information, alignment and structure |
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class: Alpha and beta proteins (a/b) fold: Ribonuclease H-like motif superfamily: Ribonuclease H-like family: DnaQ-like 3'-5' exonuclease domain: Ribonuclease D, catalytic domain species: Escherichia coli [TaxId: 562] Score = 87.3 bits (215), Expect = 9e-19 Identities = 43/170 (25%), Positives = 73/170 (42%), Gaps = 3/170 (1%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 AIA+DTE + +L ++Q DG + G + L +L D K H Sbjct: 23 PAIALDTEFVRTRTYYPQLGLIQ--LFDGEHLALIDPLGITDWSPLKAILRDPSITKFLH 80 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 G D+ V FG +P+ T+I + G ++E G+ + K++ +DW Sbjct: 81 AGSEDLEVFLNVFGELPQPLIDTQILAA-FCGRPMSWGFASMVEEYSGVTLDKSESRTDW 139 Query: 141 SADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 A L++ Q +YAA+DV +L + + + + G A C + R Sbjct: 140 LARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAALDECRLMQMR 189 |
>d2hhva1 c.55.3.5 (A:298-468) Exonuclease domain of prokaryotic DNA polymerase {Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]} Length = 171 | Back information, alignment and structure |
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class: Alpha and beta proteins (a/b) fold: Ribonuclease H-like motif superfamily: Ribonuclease H-like family: DnaQ-like 3'-5' exonuclease domain: Exonuclease domain of prokaryotic DNA polymerase species: Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422] Score = 75.6 bits (185), Expect = 3e-15 Identities = 20/155 (12%), Positives = 40/155 (25%), Gaps = 5/155 (3%) Query: 21 DAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIFH 80 D A+ E + IV ++ + P V L DE ++K Sbjct: 17 DKAALVVEVVEENYHDAP--IVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMF 74 Query: 81 YGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSDW 140 + L + F +A+ L + K + + Sbjct: 75 DSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGK 134 Query: 141 SADDLS---DEQLQYAASDVVHLHALRLQFTEKLQ 172 A ++ + L F ++L+ Sbjct: 135 GAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELR 169 |
>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokary |
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