Psyllid ID: psy12447
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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Close Homologs for Annotation Transfer
Close Homologs in SWISS-PROT Database Detected by BLAST 
Original result of BLAST against SWISS-PROT Database
| ID | Alignment graph | Length |
Definition |
RBH(Q2H) |
RBH(H2Q) |
Q cover |
H cover |
Identity |
E-value |
| Query | 551 | 2.2.26 [Sep-21-2011] | |||||||
| P54358 | 1092 | DNA polymerase delta cata | yes | N/A | 0.751 | 0.379 | 0.499 | 1e-153 | |
| P28340 | 1107 | DNA polymerase delta cata | yes | N/A | 0.731 | 0.364 | 0.407 | 1e-110 | |
| P28339 | 1106 | DNA polymerase delta cata | yes | N/A | 0.731 | 0.364 | 0.4 | 1e-109 | |
| P97283 | 1103 | DNA polymerase delta cata | N/A | N/A | 0.731 | 0.365 | 0.385 | 1e-103 | |
| P52431 | 1105 | DNA polymerase delta cata | yes | N/A | 0.731 | 0.364 | 0.385 | 1e-102 | |
| O54747 | 1103 | DNA polymerase delta cata | yes | N/A | 0.731 | 0.365 | 0.385 | 1e-102 | |
| Q54N97 | 1104 | DNA polymerase delta cata | yes | N/A | 0.720 | 0.359 | 0.351 | 8e-88 | |
| Q9LVN7 | 1095 | DNA polymerase delta cata | yes | N/A | 0.725 | 0.365 | 0.368 | 3e-86 | |
| Q9LRE6 | 1105 | DNA polymerase delta cata | yes | N/A | 0.724 | 0.361 | 0.365 | 2e-84 | |
| O48901 | 1088 | DNA polymerase delta cata | yes | N/A | 0.716 | 0.363 | 0.360 | 4e-79 |
| >sp|P54358|DPOD1_DROME DNA polymerase delta catalytic subunit OS=Drosophila melanogaster GN=DNApol-delta PE=2 SV=2 | Back alignment and function desciption |
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Score = 543 bits (1398), Expect = e-153, Method: Compositional matrix adjust.
Identities = 273/547 (49%), Positives = 341/547 (62%), Gaps = 133/547 (24%)
Query: 1 PECQQTSDKWSRAPPPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVT 60
PE Q TS++WSR PPPEL+P + + FQQ+ +E+Y G+P+PGMPG+Q+ PVP+VRMFGVT
Sbjct: 52 PENQTTSERWSRPPPPELDPSKHNLEFQQLDVENYLGQPLPGMPGAQIGPVPVVRMFGVT 111
Query: 61 MEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVE 120
MEGNSVCCHVHGF PY Y+ AP +F HC ++AL++ +IAD+R NKD +QEAVLMVE
Sbjct: 112 MEGNSVCCHVHGFCPYFYIEAPSQFEEHHCEKLQKALDQKVIADIRNNKDNVQEAVLMVE 171
Query: 121 IVQKQTVFGFWGEELENFLKIT----------------ESVFPTFPTHTYKAFESNIDFD 164
+V+K + G+ G++ + ++KI+ E + +AFE+NIDFD
Sbjct: 172 LVEKLNIHGYNGDKKQRYIKISVTLPRFVAAASRLLKKEVIMSEIDFQDCRAFENNIDFD 231
Query: 165 IRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPC-VSRCQLEIDVSTDDIVSHAPEE 223
IRFMVD D+VGCNWIE+P G W++R H ++P SRCQ+E+D
Sbjct: 232 IRFMVDTDVVGCNWIELPMGHWRIRNSH-----SKPLPESRCQIEVD------------- 273
Query: 224 IDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGAS 283
V+ D +SH PEGEWSKVAP RILSFDIECAGRKGIFP+ DP+IQIANM I QG
Sbjct: 274 --VAFDRFISHEPEGEWSKVAPFRILSFDIECAGRKGIFPEAKIDPVIQIANMVIRQGER 331
Query: 284 ENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNT 343
E F++NVFTLN CAPI+GSQV+C ET++LDKWSAF+
Sbjct: 332 EP-FIRNVFTLNECAPIIGSQVLCHDKETQMLDKWSAFV--------------------- 369
Query: 344 CAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403
RE+DPDI TGYNI NFDFPYL+NRA HL V+NF
Sbjct: 370 --------------------------REVDPDILTGYNINNFDFPYLLNRAAHLKVRNFE 403
Query: 404 FLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVI 463
+LGR+K+IRSVIK+ +QSKQMG+REN+ +NFEG
Sbjct: 404 YLGRIKNIRSVIKEQMLQSKQMGRRENQYVNFEG-------------------------- 437
Query: 464 KDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQH 523
RV FDLLFVLLR+YKLRSYTLN+VSYHFLQEQKEDV H
Sbjct: 438 ----------------------RVPFDLLFVLLRDYKLRSYTLNAVSYHFLQEQKEDVHH 475
Query: 524 SIISDLQ 530
SII+DLQ
Sbjct: 476 SIITDLQ 482
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Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex. Drosophila melanogaster (taxid: 7227) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7 |
| >sp|P28340|DPOD1_HUMAN DNA polymerase delta catalytic subunit OS=Homo sapiens GN=POLD1 PE=1 SV=2 | Back alignment and function description |
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| >sp|P28339|DPOD1_BOVIN DNA polymerase delta catalytic subunit OS=Bos taurus GN=POLD1 PE=1 SV=1 | Back alignment and function description |
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| >sp|P97283|DPOD1_MESAU DNA polymerase delta catalytic subunit OS=Mesocricetus auratus GN=POLD1 PE=2 SV=1 | Back alignment and function description |
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| >sp|P52431|DPOD1_MOUSE DNA polymerase delta catalytic subunit OS=Mus musculus GN=Pold1 PE=1 SV=2 | Back alignment and function description |
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| >sp|O54747|DPOD1_RAT DNA polymerase delta catalytic subunit OS=Rattus norvegicus GN=Pold1 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q54N97|DPOD1_DICDI DNA polymerase delta catalytic subunit OS=Dictyostelium discoideum GN=pold1 PE=3 SV=1 | Back alignment and function description |
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| >sp|Q9LVN7|DPOD1_ARATH DNA polymerase delta catalytic subunit OS=Arabidopsis thaliana GN=POLD1 PE=2 SV=2 | Back alignment and function description |
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| >sp|Q9LRE6|DPOD1_ORYSJ DNA polymerase delta catalytic subunit OS=Oryza sativa subsp. japonica GN=POLD1 PE=2 SV=1 | Back alignment and function description |
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| >sp|O48901|DPOD1_SOYBN DNA polymerase delta catalytic subunit OS=Glycine max GN=POLD1 PE=2 SV=1 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 551 | ||||||
| 324120740 | 1094 | DNA polymerase delta catalytic subunit [ | 0.760 | 0.382 | 0.553 | 1e-168 | |
| 324120732 | 1091 | DNA polymerase delta catalytic subunit [ | 0.754 | 0.381 | 0.518 | 1e-162 | |
| 195127716 | 1092 | GI13419 [Drosophila mojavensis] gi|19391 | 0.753 | 0.380 | 0.514 | 1e-157 | |
| 324120692 | 1097 | DNA polymerase delta catalytic subunit [ | 0.754 | 0.379 | 0.509 | 1e-156 | |
| 350397570 | 1090 | PREDICTED: DNA polymerase delta catalyti | 0.753 | 0.380 | 0.521 | 1e-156 | |
| 324120706 | 1088 | DNA polymerase delta catalytic subunit [ | 0.744 | 0.376 | 0.510 | 1e-156 | |
| 66511388 | 1105 | PREDICTED: DNA polymerase delta catalyti | 0.753 | 0.375 | 0.529 | 1e-156 | |
| 350397573 | 1104 | PREDICTED: DNA polymerase delta catalyti | 0.753 | 0.375 | 0.521 | 1e-156 | |
| 380019903 | 1105 | PREDICTED: DNA polymerase delta catalyti | 0.753 | 0.375 | 0.529 | 1e-155 | |
| 195377844 | 1092 | GJ11779 [Drosophila virilis] gi|19415485 | 0.753 | 0.380 | 0.507 | 1e-155 |
| >gi|324120740|dbj|BAJ78761.1| DNA polymerase delta catalytic subunit [Bemisia tabaci] | Back alignment and taxonomy information |
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Score = 598 bits (1543), Expect = e-168, Method: Compositional matrix adjust.
Identities = 305/551 (55%), Positives = 356/551 (64%), Gaps = 132/551 (23%)
Query: 1 PECQQTSDKWSRAPPPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVT 60
PE + T+ KWSR PP+L+P++D IVFQQIS++ YTGEP+ GMPGSQL PVPI R+FG+T
Sbjct: 59 PETRSTNQKWSRPAPPDLDPEKDGIVFQQISLDSYTGEPVKGMPGSQLGPVPIFRIFGIT 118
Query: 61 MEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVE 120
MEGNSVC HVHGFSPY +V+AP FN +HCR FK+ALNR I+ DMRGNK IQEAVLMVE
Sbjct: 119 MEGNSVCAHVHGFSPYFFVTAPAGFNESHCRPFKDALNRTILNDMRGNKSGIQEAVLMVE 178
Query: 121 IVQKQTVFGFWGEELENFLKIT----------------ESVFPTFPTHTYKAFESNIDFD 164
IV+KQT+FG+WG+E+++FLKIT E+VFP+FP H YKAFESNIDFD
Sbjct: 179 IVRKQTMFGYWGDEVKDFLKITVALPRLIAAGKRLLEKEAVFPSFPNHAYKAFESNIDFD 238
Query: 165 IRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEI 224
IRFMVD +IVGC+W+E+ G WQ R T SRCQ+E+DV
Sbjct: 239 IRFMVDKNIVGCSWVELGKGTWQRRPHSDLRVT-----SRCQIEVDV------------- 280
Query: 225 DVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASE 284
S +D++SH PEGEWSKVAP RILSFDIECAGRKGIFP+PNHDP+IQIANM + QG E
Sbjct: 281 --SCEDLISHLPEGEWSKVAPFRILSFDIECAGRKGIFPEPNHDPVIQIANMVVQQGEPE 338
Query: 285 NIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTC 344
IF++NVFTL CAPIVG QVI C TE ELL +WS F+
Sbjct: 339 -IFIRNVFTLKECAPIVGCQVISCDTEMELLQRWSDFV---------------------- 375
Query: 345 APIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTF 404
RE DPD+FTGYNI NFDFPYLINRAKHL V NF+F
Sbjct: 376 -------------------------RESDPDVFTGYNINNFDFPYLINRAKHLNVHNFSF 410
Query: 405 LGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIK 464
LGR+KD RSVIKD IQSKQMG+RENK INFEG
Sbjct: 411 LGRIKDTRSVIKDQIIQSKQMGRRENKNINFEG--------------------------- 443
Query: 465 DSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHS 524
RV FDLLFVLLR+YKLRSYTLN+VSYHFLQEQKEDV H+
Sbjct: 444 ---------------------RVPFDLLFVLLRDYKLRSYTLNAVSYHFLQEQKEDVHHN 482
Query: 525 IISDLQIALLQ 535
+I++LQ Q
Sbjct: 483 MITELQEGTAQ 493
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Source: Bemisia tabaci Species: Bemisia tabaci Genus: Bemisia Family: Aleyrodidae Order: Hemiptera Class: Insecta Phylum: Arthropoda Superkingdom: Eukaryota |
| >gi|324120732|dbj|BAJ78757.1| DNA polymerase delta catalytic subunit [Thrips palmi] | Back alignment and taxonomy information |
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| >gi|195127716|ref|XP_002008314.1| GI13419 [Drosophila mojavensis] gi|193919923|gb|EDW18790.1| GI13419 [Drosophila mojavensis] | Back alignment and taxonomy information |
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| >gi|324120692|dbj|BAJ78737.1| DNA polymerase delta catalytic subunit [Thermobia domestica] | Back alignment and taxonomy information |
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| >gi|350397570|ref|XP_003484917.1| PREDICTED: DNA polymerase delta catalytic subunit-like isoform 1 [Bombus impatiens] | Back alignment and taxonomy information |
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| >gi|324120706|dbj|BAJ78744.1| DNA polymerase delta catalytic subunit [Aposthonia japonica] | Back alignment and taxonomy information |
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| >gi|66511388|ref|XP_623795.1| PREDICTED: DNA polymerase delta catalytic subunit [Apis mellifera] | Back alignment and taxonomy information |
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| >gi|350397573|ref|XP_003484918.1| PREDICTED: DNA polymerase delta catalytic subunit-like isoform 2 [Bombus impatiens] | Back alignment and taxonomy information |
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| >gi|380019903|ref|XP_003693840.1| PREDICTED: DNA polymerase delta catalytic subunit-like [Apis florea] | Back alignment and taxonomy information |
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| >gi|195377844|ref|XP_002047697.1| GJ11779 [Drosophila virilis] gi|194154855|gb|EDW70039.1| GJ11779 [Drosophila virilis] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 551 | ||||||
| FB|FBgn0263600 | 1092 | DNApol-delta "DNA-polymerase-d | 0.548 | 0.276 | 0.544 | 1.4e-133 | |
| ZFIN|ZDB-GENE-060429-1 | 1105 | pold1 "polymerase (DNA directe | 0.591 | 0.295 | 0.441 | 7e-113 | |
| UNIPROTKB|E2R5W5 | 1107 | POLD1 "DNA polymerase" [Canis | 0.531 | 0.264 | 0.453 | 2.8e-99 | |
| UNIPROTKB|J9NS34 | 1131 | POLD1 "DNA polymerase" [Canis | 0.531 | 0.259 | 0.453 | 3.8e-99 | |
| UNIPROTKB|F1RH32 | 1107 | POLD1 "DNA polymerase" [Sus sc | 0.531 | 0.264 | 0.432 | 4.9e-96 | |
| UNIPROTKB|P28340 | 1107 | POLD1 "DNA polymerase delta ca | 0.531 | 0.264 | 0.438 | 7.1e-96 | |
| UNIPROTKB|P28339 | 1106 | POLD1 "DNA polymerase delta ca | 0.531 | 0.264 | 0.435 | 2.3e-94 | |
| RGD|621839 | 1103 | Pold1 "polymerase (DNA directe | 0.531 | 0.265 | 0.420 | 5.7e-94 | |
| UNIPROTKB|O54747 | 1103 | Pold1 "DNA polymerase delta ca | 0.531 | 0.265 | 0.420 | 5.7e-94 | |
| MGI|MGI:97741 | 1105 | Pold1 "polymerase (DNA directe | 0.531 | 0.265 | 0.414 | 2.6e-91 |
| FB|FBgn0263600 DNApol-delta "DNA-polymerase-delta" [Drosophila melanogaster (taxid:7227)] | Back alignment and assigned GO terms |
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Score = 976 (348.6 bits), Expect = 1.4e-133, Sum P(2) = 1.4e-133
Identities = 185/340 (54%), Positives = 239/340 (70%)
Query: 1 PECQQTSDKWSRAPPPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVT 60
PE Q TS++WSR PPPEL+P + + FQQ+ +E+Y G+P+PGMPG+Q+ PVP+VRMFGVT
Sbjct: 52 PENQTTSERWSRPPPPELDPSKHNLEFQQLDVENYLGQPLPGMPGAQIGPVPVVRMFGVT 111
Query: 61 MEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVE 120
MEGNSVCCHVHGF PY Y+ AP +F HC ++AL++ +IAD+R NKD +QEAVLMVE
Sbjct: 112 MEGNSVCCHVHGFCPYFYIEAPSQFEEHHCEKLQKALDQKVIADIRNNKDNVQEAVLMVE 171
Query: 121 IVQKQTVFGFWGEELENFLKIT----------------ESVFPTFPTHTYKAFESNIDFD 164
+V+K + G+ G++ + ++KI+ E + +AFE+NIDFD
Sbjct: 172 LVEKLNIHGYNGDKKQRYIKISVTLPRFVAAASRLLKKEVIMSEIDFQDCRAFENNIDFD 231
Query: 165 IRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCV-SRCQLEIDVSTDDIVSHAPEE 223
IRFMVD D+VGCNWIE+P G W++R H ++P SRCQ+E+DV+ D +SH PE
Sbjct: 232 IRFMVDTDVVGCNWIELPMGHWRIRNSH-----SKPLPESRCQIEVDVAFDRFISHEPE- 285
Query: 224 IDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGAS 283
GEWSKVAP RILSFDIECAGRKGIFP+ DP+IQIANM I QG
Sbjct: 286 --------------GEWSKVAPFRILSFDIECAGRKGIFPEAKIDPVIQIANMVIRQGER 331
Query: 284 ENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIR 323
E F++NVFTLN CAPI+GSQV+C ET++LDKWSAF+R
Sbjct: 332 EP-FIRNVFTLNECAPIIGSQVLCHDKETQMLDKWSAFVR 370
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| ZFIN|ZDB-GENE-060429-1 pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Danio rerio (taxid:7955)] | Back alignment and assigned GO terms |
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| UNIPROTKB|E2R5W5 POLD1 "DNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
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| UNIPROTKB|J9NS34 POLD1 "DNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
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| UNIPROTKB|F1RH32 POLD1 "DNA polymerase" [Sus scrofa (taxid:9823)] | Back alignment and assigned GO terms |
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| UNIPROTKB|P28340 POLD1 "DNA polymerase delta catalytic subunit" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
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| UNIPROTKB|P28339 POLD1 "DNA polymerase delta catalytic subunit" [Bos taurus (taxid:9913)] | Back alignment and assigned GO terms |
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| RGD|621839 Pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
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| UNIPROTKB|O54747 Pold1 "DNA polymerase delta catalytic subunit" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
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| MGI|MGI:97741 Pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Mus musculus (taxid:10090)] | Back alignment and assigned GO terms |
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Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
No confident hit for EC number transfering in SWISSPROT detected by BLAST
EC Number Prediction by EFICAz Software
| Prediction Level | EC number | Confidence of Prediction |
| 3rd Layer | 2.7.7 | LOW CONFIDENCE prediction! |
Prediction of Functionally Associated Proteins
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 551 | |||
| PTZ00166 | 1054 | PTZ00166, PTZ00166, DNA polymerase delta catalytic | 1e-142 | |
| cd05777 | 230 | cd05777, DNA_polB_delta_exo, DEDDy 3'-5' exonuclea | 1e-111 | |
| pfam03104 | 254 | pfam03104, DNA_pol_B_exo1, DNA polymerase family B | 7e-54 | |
| smart00486 | 474 | smart00486, POLBc, DNA polymerase type-B family | 5e-32 | |
| cd05160 | 199 | cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclea | 1e-30 | |
| COG0417 | 792 | COG0417, PolB, DNA polymerase elongation subunit ( | 2e-30 | |
| COG0417 | 792 | COG0417, PolB, DNA polymerase elongation subunit ( | 5e-17 | |
| cd05778 | 231 | cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' e | 3e-15 | |
| cd05780 | 195 | cd05780, DNA_polB_Kod1_like_exo, DEDDy 3'-5' exonu | 5e-12 | |
| PRK05762 | 786 | PRK05762, PRK05762, DNA polymerase II; Reviewed | 2e-11 | |
| cd05776 | 234 | cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' | 1e-10 | |
| cd05784 | 193 | cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease | 2e-10 | |
| cd05781 | 188 | cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease | 6e-09 | |
| PHA02528 | 881 | PHA02528, 43, DNA polymerase; Provisional | 4e-08 | |
| cd05785 | 207 | cd05785, DNA_polB_like2_exo, Uncharacterized bacte | 1e-07 | |
| cd05779 | 204 | cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonucl | 5e-07 | |
| PRK05762 | 786 | PRK05762, PRK05762, DNA polymerase II; Reviewed | 2e-04 | |
| pfam03104 | 254 | pfam03104, DNA_pol_B_exo1, DNA polymerase family B | 4e-04 | |
| cd05783 | 204 | cd05783, DNA_polB_B1_exo, DEDDy 3'-5' exonuclease | 0.001 | |
| TIGR00592 | 1172 | TIGR00592, pol2, DNA polymerase (pol2) | 0.002 | |
| PRK05761 | 787 | PRK05761, PRK05761, DNA polymerase I; Reviewed | 0.003 | |
| cd05781 | 188 | cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease | 0.004 |
| >gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional | Back alignment and domain information |
|---|
Score = 437 bits (1127), Expect = e-142
Identities = 186/545 (34%), Positives = 268/545 (49%), Gaps = 146/545 (26%)
Query: 12 RAPPPELNPKEDKIVFQQISIEHY------TGEPIPGMPGSQLKPVPIVRMFGVTMEGNS 65
R P P ++ ++D +VF Q+ ++ G P + G + VPI+R++GVT EG+S
Sbjct: 30 RRPLPPISLQKD-LVFFQLDADYTEKDDKSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHS 88
Query: 66 VCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQ 125
V +VH F PY Y+ AP F + K LN + + + Q VL +EIV+K+
Sbjct: 89 VLVNVHNFFPYFYIEAPPNFLPEDSQKLKRELNAQL--SEQSQFKKYQNTVLDIEIVKKE 146
Query: 126 TVFGFWGEELENFLKITESVFPTFPT-------------------HTYKAFESNIDFDIR 166
++ + G ++FLKIT + P ++ +ESN+ F +R
Sbjct: 147 SLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVVCGGGWDGIRLFQTYESNVPFVLR 206
Query: 167 FMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDV 226
F++DN+I G +W+ +P GK+++R K S CQ+E+D S +D++ PE
Sbjct: 207 FLIDNNITGGSWLTLPKGKYKIRPPKKK-------TSTCQIEVDCSYEDLIPLPPE---- 255
Query: 227 STDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGI-FPDPNHDPIIQIANMCISQGASEN 285
GE+ +APLRILSFDIEC KG+ FP+ +DP+IQI+++ +QG E
Sbjct: 256 -----------GEYLTIAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEE 304
Query: 286 IFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCA 345
K +FTL CA I G+ V+ F
Sbjct: 305 PLTKFIFTLKECASIAGANVLS-------------F------------------------ 327
Query: 346 PIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFL 405
+TE ELL W+ F+ +DPD TGYNI NFD PYL+NRAK
Sbjct: 328 ----------ETEKELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAK---------- 367
Query: 406 GRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKD 465
L + +F +LGR+K RSVIKD
Sbjct: 368 --------------------------------------ALKLNDFKYLGRIKSTRSVIKD 389
Query: 466 SFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSI 525
S SKQMG RE+K IN EGR+ FD++ ++ R+YKL+SY+LN VS+ FL+EQKEDV +SI
Sbjct: 390 SKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSI 449
Query: 526 ISDLQ 530
ISDLQ
Sbjct: 450 ISDLQ 454
|
Length = 1054 |
| >gnl|CDD|99820 cd05777, DNA_polB_delta_exo, DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >gnl|CDD|217371 pfam03104, DNA_pol_B_exo1, DNA polymerase family B, exonuclease domain | Back alignment and domain information |
|---|
| >gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family | Back alignment and domain information |
|---|
| >gnl|CDD|176646 cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >gnl|CDD|99821 cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >gnl|CDD|99823 cd05780, DNA_polB_Kod1_like_exo, DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|99819 cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|99824 cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|99828 cd05785, DNA_polB_like2_exo, Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|99822 cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|217371 pfam03104, DNA_pol_B_exo1, DNA polymerase family B, exonuclease domain | Back alignment and domain information |
|---|
| >gnl|CDD|99826 cd05783, DNA_polB_B1_exo, DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2) | Back alignment and domain information |
|---|
| >gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|99824 cd05781, DNA_polB_B3_exo, DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 551 | |||
| KOG0969|consensus | 1066 | 100.0 | ||
| PTZ00166 | 1054 | DNA polymerase delta catalytic subunit; Provisiona | 100.0 | |
| PF03104 | 325 | DNA_pol_B_exo1: DNA polymerase family B, exonuclea | 100.0 | |
| cd05777 | 230 | DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain | 100.0 | |
| PRK05762 | 786 | DNA polymerase II; Reviewed | 100.0 | |
| cd05778 | 231 | DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease | 100.0 | |
| KOG0970|consensus | 1429 | 100.0 | ||
| cd05780 | 195 | DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease dom | 100.0 | |
| cd05779 | 204 | DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai | 100.0 | |
| cd05784 | 193 | DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of | 100.0 | |
| PRK05761 | 787 | DNA polymerase I; Reviewed | 100.0 | |
| TIGR00592 | 1172 | pol2 DNA polymerase (pol2). This family is based o | 100.0 | |
| cd05776 | 234 | DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas | 99.98 | |
| cd05781 | 188 | DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of | 99.97 | |
| cd05785 | 207 | DNA_polB_like2_exo Uncharacterized bacterial subgr | 99.97 | |
| COG0417 | 792 | PolB DNA polymerase elongation subunit (family B) | 99.97 | |
| KOG0968|consensus | 1488 | 99.97 | ||
| cd05160 | 199 | DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain | 99.97 | |
| PHA02528 | 881 | 43 DNA polymerase; Provisional | 99.96 | |
| KOG1798|consensus | 2173 | 99.96 | ||
| PHA03036 | 1004 | DNA polymerase; Provisional | 99.96 | |
| cd05783 | 204 | DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of | 99.96 | |
| PHA02524 | 498 | 43A DNA polymerase subunit A; Provisional | 99.95 | |
| smart00486 | 471 | POLBc DNA polymerase type-B family. DNA polymerase | 99.94 | |
| TIGR00592 | 1172 | pol2 DNA polymerase (pol2). This family is based o | 99.92 | |
| cd05782 | 208 | DNA_polB_like1_exo Uncharacterized bacterial subgr | 99.79 | |
| KOG0969|consensus | 1066 | 99.48 | ||
| PHA03334 | 1545 | putative DNA polymerase catalytic subunit; Provisi | 99.43 | |
| PF10108 | 209 | DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate | 99.12 | |
| PF13482 | 164 | RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A | 98.26 | |
| PTZ00166 | 1054 | DNA polymerase delta catalytic subunit; Provisiona | 97.82 | |
| COG3359 | 278 | Predicted exonuclease [DNA replication, recombinat | 97.69 | |
| cd05777 | 230 | DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain | 97.45 | |
| cd05778 | 231 | DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease | 97.4 | |
| PRK06309 | 232 | DNA polymerase III subunit epsilon; Validated | 97.24 | |
| cd06125 | 96 | DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonucleas | 97.18 | |
| PRK08517 | 257 | DNA polymerase III subunit epsilon; Provisional | 97.1 | |
| PRK05601 | 377 | DNA polymerase III subunit epsilon; Validated | 97.06 | |
| PRK06310 | 250 | DNA polymerase III subunit epsilon; Validated | 97.04 | |
| cd06138 | 183 | ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o | 97.02 | |
| cd06136 | 177 | TREX1_2 DEDDh 3'-5' exonuclease domain of three pr | 97.02 | |
| TIGR01405 | 1213 | polC_Gram_pos DNA polymerase III, alpha chain, Gra | 96.92 | |
| PRK06063 | 313 | DNA polymerase III subunit epsilon; Provisional | 96.91 | |
| PRK06807 | 313 | DNA polymerase III subunit epsilon; Validated | 96.86 | |
| PRK05711 | 240 | DNA polymerase III subunit epsilon; Provisional | 96.82 | |
| TIGR01406 | 225 | dnaQ_proteo DNA polymerase III, epsilon subunit, P | 96.78 | |
| cd06130 | 156 | DNA_pol_III_epsilon_like an uncharacterized bacter | 96.65 | |
| PRK07883 | 557 | hypothetical protein; Validated | 96.55 | |
| PRK07942 | 232 | DNA polymerase III subunit epsilon; Provisional | 96.53 | |
| cd06131 | 167 | DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl | 96.46 | |
| PRK06195 | 309 | DNA polymerase III subunit epsilon; Validated | 96.41 | |
| cd06127 | 159 | DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh | 96.36 | |
| COG2176 | 1444 | PolC DNA polymerase III, alpha subunit (gram-posit | 96.3 | |
| PRK07740 | 244 | hypothetical protein; Provisional | 96.29 | |
| TIGR01407 | 850 | dinG_rel DnaQ family exonuclease/DinG family helic | 96.16 | |
| smart00479 | 169 | EXOIII exonuclease domain in DNA-polymerase alpha | 96.04 | |
| PRK08074 | 928 | bifunctional ATP-dependent DNA helicase/DNA polyme | 96.04 | |
| PRK09146 | 239 | DNA polymerase III subunit epsilon; Validated | 95.91 | |
| TIGR00573 | 217 | dnaq exonuclease, DNA polymerase III, epsilon subu | 95.9 | |
| PHA02524 | 498 | 43A DNA polymerase subunit A; Provisional | 95.79 | |
| PRK07748 | 207 | sporulation inhibitor KapD; Provisional | 95.63 | |
| PRK07247 | 195 | DNA polymerase III subunit epsilon; Validated | 95.58 | |
| PRK07246 | 820 | bifunctional ATP-dependent DNA helicase/DNA polyme | 95.4 | |
| cd06134 | 189 | RNaseT DEDDh 3'-5' exonuclease domain of RNase T. | 95.04 | |
| PRK11779 | 476 | sbcB exonuclease I; Provisional | 94.93 | |
| cd06144 | 152 | REX4_like DEDDh 3'-5' exonuclease domain of RNA ex | 94.65 | |
| cd06137 | 161 | DEDDh_RNase DEDDh 3'-5' exonuclease domain of the | 94.45 | |
| PRK05168 | 211 | ribonuclease T; Provisional | 94.41 | |
| TIGR01298 | 200 | RNaseT ribonuclease T. in gamma-subdivision Proteo | 94.23 | |
| PRK05359 | 181 | oligoribonuclease; Provisional | 94.03 | |
| TIGR03491 | 457 | RecB family nuclease, putative, TM0106 family. Mem | 93.72 | |
| cd06133 | 176 | ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o | 93.28 | |
| COG0847 | 243 | DnaQ DNA polymerase III, epsilon subunit and relat | 92.78 | |
| cd05776 | 234 | DNA_polB_alpha_exo inactive DEDDy 3'-5' exonucleas | 92.37 | |
| cd06145 | 150 | REX1_like DEDDh 3'-5' exonuclease domain of RNA ex | 91.88 | |
| PRK00448 | 1437 | polC DNA polymerase III PolC; Validated | 91.86 | |
| PRK09145 | 202 | DNA polymerase III subunit epsilon; Validated | 91.85 | |
| cd05779 | 204 | DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domai | 90.85 | |
| PRK09182 | 294 | DNA polymerase III subunit epsilon; Validated | 90.6 | |
| cd06135 | 173 | Orn DEDDh 3'-5' exonuclease domain of oligoribonuc | 89.72 | |
| PHA02528 | 881 | 43 DNA polymerase; Provisional | 87.69 | |
| PRK06722 | 281 | exonuclease; Provisional | 84.87 | |
| cd05784 | 193 | DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of | 84.12 | |
| PHA03036 | 1004 | DNA polymerase; Provisional | 83.85 | |
| PF03104 | 325 | DNA_pol_B_exo1: DNA polymerase family B, exonuclea | 82.04 | |
| PF01612 | 176 | DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 | 80.63 |
| >KOG0969|consensus | Back alignment and domain information |
|---|
Probab=100.00 E-value=1.3e-81 Score=664.41 Aligned_cols=411 Identities=57% Similarity=0.965 Sum_probs=368.0
Q ss_pred ccCcCCCCCCCCCCCCCCceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCC
Q psy12447 6 TSDKWSRAPPPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEF 85 (551)
Q Consensus 6 ~~~~w~~~~~~~~~~~~~~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~ 85 (551)
.++.|.||++|.++|.+..+.||++|++.|...+ ......+|++|+||.|.+|.|||+|||||.||||+++|.++
T Consensus 56 ~~~~w~Rp~~p~~~p~~~~i~fqq~~~e~y~~~~-----~~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g~ 130 (1066)
T KOG0969|consen 56 EHSRWARPALPALDPIKNDIEFQQIDIEFYVENG-----SGTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNGF 130 (1066)
T ss_pred ccccccCCCCCccCcccccceEEEeehhhhccCC-----CcccCCCceEEEeeeccCCCeEEEEEecccceEEecCCCCC
Confidence 3578999999999999999999999999997533 23456789999999999999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEccc------------CC---CcC
Q psy12447 86 NSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESV------------FP---TFP 150 (551)
Q Consensus 86 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~------------~~---~l~ 150 (551)
.++++..+...|+..+.. ..+..+++|++..+|||++..+.+|+||+... .+ ...
T Consensus 131 ~~e~i~~~~~~l~~~~~~----------~av~~ve~~~k~~l~~~~g~~k~~f~kit~~lP~~~~~~r~~lergv~~~~~ 200 (1066)
T KOG0969|consen 131 GPEHIGKFQQALDVKVTA----------HAVDHVEVVSKESLYGYQGDTKQPFLKITVTLPRMVAAARRLLERGVFISGK 200 (1066)
T ss_pred CHHHHHHHHHHHHHHHHH----------hHHHHHHHHhhhhhheecCCCCceeEEEecccHHHHHHhHHHHHhccccccc
Confidence 999999888888766532 14567889999999999998899999999421 01 011
Q ss_pred --CCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCC
Q psy12447 151 --THTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVST 228 (551)
Q Consensus 151 --~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~ 228 (551)
...+++||+||+|.+|||+|.+|.||+|++++.++|..+. .+.|.|++|+++.+.+
T Consensus 201 ~~~~~~~~yEsNi~f~lrfmvd~~iVG~~wi~lp~gk~~~~~---------~~~s~cqlEv~v~y~~------------- 258 (1066)
T KOG0969|consen 201 GEKVGFTTYESNIDFVLRFMVDCDIVGMNWIELPAGKYRIRD---------NRVSRCQLEVSVNYKD------------- 258 (1066)
T ss_pred CcceeeeEecCCccEEEEEEecCccccceeEEeccchheecc---------chhcccceEEEEeecc-------------
Confidence 1346899999999999999999999999999999998763 3799999999999999
Q ss_pred CcccccCCCCCcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeee
Q psy12447 229 DDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICC 308 (551)
Q Consensus 229 ~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~ 308 (551)
+++++++++|..+||+++|||||||.+++|.||.|+.|||++|+..+...|..+
T Consensus 259 --lishp~eG~w~~~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~------------------------ 312 (1066)
T KOG0969|consen 259 --LISHPAEGEWSKIAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENE------------------------ 312 (1066)
T ss_pred --cccccccCcccccccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCc------------------------
Confidence 678888899999999999999999999999999999999999997765555443
Q ss_pred cchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChH
Q psy12447 309 KTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFP 388 (551)
Q Consensus 309 ~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~ 388 (551)
|+.+++|++++|.++.|++|++|.+|++||..|..+|++.|||+|+|||+.+||+|
T Consensus 313 ------------------------pf~rnvf~l~~capI~G~~V~~~~~e~elL~~W~~firevDPDvI~GYNi~nFDiP 368 (1066)
T KOG0969|consen 313 ------------------------PFVRNVFTLKTCAPIVGSNVHSYETEKELLESWRKFIREVDPDVIIGYNICNFDIP 368 (1066)
T ss_pred ------------------------hHHHhhhcccCcCCCCCceeEEeccHHHHHHHHHHHHHhcCCCeEecccccccccc
Confidence 78888999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccc
Q psy12447 389 YLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFI 468 (551)
Q Consensus 389 yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~ 468 (551)
||++||+.||+..|..|||+++.. ..|.|+.+
T Consensus 369 Yll~RA~~L~Ie~Fp~LGRikn~~------------------------------------------------s~irDttf 400 (1066)
T KOG0969|consen 369 YLLNRAKTLGIENFPYLGRIKNSR------------------------------------------------SVIRDSTF 400 (1066)
T ss_pred eecChHhhcCcccccccceecccc------------------------------------------------eeeecccc
Confidence 999999999999999999987643 23445678
Q ss_pred cccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------ccc
Q psy12447 469 QSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSN 542 (551)
Q Consensus 469 ~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~ 542 (551)
+|+++|.|+.+.+.|.||+.+||+.++++++||+||+|+.|+.||||++|+|+++.-|+++.+++.+.|+| |||
T Consensus 401 SSkq~GtRetK~v~I~GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDA 480 (1066)
T KOG0969|consen 401 SSKQYGTRETKEVNIDGRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDA 480 (1066)
T ss_pred chhhcCcccceEEeecceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred ccccccCCC
Q psy12447 543 AAPLRYSPK 551 (551)
Q Consensus 543 ~l~~rl~~~ 551 (551)
+||+|||+|
T Consensus 481 YLPlRLlek 489 (1066)
T KOG0969|consen 481 YLPLRLLEK 489 (1066)
T ss_pred cchHHHHHH
Confidence 999999975
|
|
| >PTZ00166 DNA polymerase delta catalytic subunit; Provisional | Back alignment and domain information |
|---|
| >PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included | Back alignment and domain information |
|---|
| >cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >PRK05762 DNA polymerase II; Reviewed | Back alignment and domain information |
|---|
| >cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >KOG0970|consensus | Back alignment and domain information |
|---|
| >cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases | Back alignment and domain information |
|---|
| >PRK05761 DNA polymerase I; Reviewed | Back alignment and domain information |
|---|
| >TIGR00592 pol2 DNA polymerase (pol2) | Back alignment and domain information |
|---|
| >cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
|---|
| >COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >KOG0968|consensus | Back alignment and domain information |
|---|
| >cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
|---|
| >PHA02528 43 DNA polymerase; Provisional | Back alignment and domain information |
|---|
| >KOG1798|consensus | Back alignment and domain information |
|---|
| >PHA03036 DNA polymerase; Provisional | Back alignment and domain information |
|---|
| >cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases | Back alignment and domain information |
|---|
| >PHA02524 43A DNA polymerase subunit A; Provisional | Back alignment and domain information |
|---|
| >smart00486 POLBc DNA polymerase type-B family | Back alignment and domain information |
|---|
| >TIGR00592 pol2 DNA polymerase (pol2) | Back alignment and domain information |
|---|
| >cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases | Back alignment and domain information |
|---|
| >KOG0969|consensus | Back alignment and domain information |
|---|
| >PHA03334 putative DNA polymerase catalytic subunit; Provisional | Back alignment and domain information |
|---|
| >PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins | Back alignment and domain information |
|---|
| >PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A | Back alignment and domain information |
|---|
| >PTZ00166 DNA polymerase delta catalytic subunit; Provisional | Back alignment and domain information |
|---|
| >COG3359 Predicted exonuclease [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >PRK06309 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily | Back alignment and domain information |
|---|
| >PRK08517 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
|---|
| >PRK05601 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >PRK06310 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins | Back alignment and domain information |
|---|
| >cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins | Back alignment and domain information |
|---|
| >TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type | Back alignment and domain information |
|---|
| >PRK06063 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
|---|
| >PRK06807 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >PRK05711 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
|---|
| >TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial | Back alignment and domain information |
|---|
| >cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III | Back alignment and domain information |
|---|
| >PRK07883 hypothetical protein; Validated | Back alignment and domain information |
|---|
| >PRK07942 DNA polymerase III subunit epsilon; Provisional | Back alignment and domain information |
|---|
| >cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins | Back alignment and domain information |
|---|
| >PRK06195 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd06127 DEDDh DEDDh 3'-5' exonuclease domain family | Back alignment and domain information |
|---|
| >COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >PRK07740 hypothetical protein; Provisional | Back alignment and domain information |
|---|
| >TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative | Back alignment and domain information |
|---|
| >smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases | Back alignment and domain information |
|---|
| >PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >PRK09146 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family | Back alignment and domain information |
|---|
| >PHA02524 43A DNA polymerase subunit A; Provisional | Back alignment and domain information |
|---|
| >PRK07748 sporulation inhibitor KapD; Provisional | Back alignment and domain information |
|---|
| >PRK07247 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T | Back alignment and domain information |
|---|
| >PRK11779 sbcB exonuclease I; Provisional | Back alignment and domain information |
|---|
| >cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins | Back alignment and domain information |
|---|
| >cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins | Back alignment and domain information |
|---|
| >PRK05168 ribonuclease T; Provisional | Back alignment and domain information |
|---|
| >TIGR01298 RNaseT ribonuclease T | Back alignment and domain information |
|---|
| >PRK05359 oligoribonuclease; Provisional | Back alignment and domain information |
|---|
| >TIGR03491 RecB family nuclease, putative, TM0106 family | Back alignment and domain information |
|---|
| >cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins | Back alignment and domain information |
|---|
| >COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] | Back alignment and domain information |
|---|
| >cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins | Back alignment and domain information |
|---|
| >PRK00448 polC DNA polymerase III PolC; Validated | Back alignment and domain information |
|---|
| >PRK09145 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase | Back alignment and domain information |
|---|
| >PRK09182 DNA polymerase III subunit epsilon; Validated | Back alignment and domain information |
|---|
| >cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins | Back alignment and domain information |
|---|
| >PHA02528 43 DNA polymerase; Provisional | Back alignment and domain information |
|---|
| >PRK06722 exonuclease; Provisional | Back alignment and domain information |
|---|
| >cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases | Back alignment and domain information |
|---|
| >PHA03036 DNA polymerase; Provisional | Back alignment and domain information |
|---|
| >PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included | Back alignment and domain information |
|---|
| >PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides | Back alignment and domain information |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
| ID | Alignment Graph | Length |
Definition |
E-value | |
| Query | 551 | ||||
| 3iay_A | 919 | Ternary Complex Of Dna Polymerase Delta Length = 91 | 3e-78 | ||
| 2gv9_A | 1193 | Crystal Structure Of The Herpes Simplex Virus Type | 2e-14 | ||
| 2jgu_A | 775 | Crystal Structure Of Dna-directed Dna Polymerase Le | 6e-07 | ||
| 4ahc_A | 775 | Crystal Structure Of An Evolved Replicating Dna Pol | 2e-06 | ||
| 4flt_A | 793 | Pyrococcus Abyssi B Family Dna Polymerase Bound To | 2e-06 | ||
| 4fm2_A | 793 | Pyrococcus Abyssi B Family Dna Polymerase (Triple M | 3e-06 | ||
| 3a2f_A | 775 | Crystal Structure Of Pyrococcus Furiosus Dna Polyme | 3e-06 | ||
| 1qht_A | 775 | Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon | 6e-06 | ||
| 1tgo_A | 773 | Thermostable B Type Dna Polymerase From Thermococcu | 1e-05 | ||
| 1qqc_A | 773 | Crystal Structure Of An Archaebacterial Dna Polymer | 2e-05 | ||
| 1d5a_A | 733 | Crystal Structure Of An Archaebacterial Dna Polymer | 2e-05 | ||
| 1wns_A | 774 | Crystal Structure Of Family B Dna Polymerase From H | 5e-05 | ||
| 1wn7_A | 774 | Crystal Structure Of Archaeal Family B Dna Polymera | 5e-05 | ||
| 2xhb_A | 773 | Crystal Structure Of Dna Polymerase From Thermococc | 1e-04 | ||
| 2vwj_A | 773 | Uracil Recognition In Archaeal Dna Polymerases Capt | 1e-04 | ||
| 2vwk_A | 773 | Uracil Recognition In Archaeal Dna Polymerases Capt | 1e-04 | ||
| 1noz_A | 388 | T4 Dna Polymerase Fragment (Residues 1-388) At 110k | 2e-04 |
| >pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta Length = 919 | Back alignment and structure |
|
| >pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna Polymerase Length = 1193 | Back alignment and structure |
| >pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase Length = 775 | Back alignment and structure |
| >pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase Length = 775 | Back alignment and structure |
| >pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A Dsdna, In Edition Mode Length = 793 | Back alignment and structure |
| >pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound To A Dsdna, In Edition Mode Length = 793 | Back alignment and structure |
| >pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA Monomer Mutant Complex Length = 775 | Back alignment and structure |
| >pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon Length = 775 | Back alignment and structure |
| >pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus Gorgonarius Length = 773 | Back alignment and structure |
| >pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok Length = 773 | Back alignment and structure |
| >pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok. Deposition Of Second Native Structure At 2.4 Angstrom Length = 733 | Back alignment and structure |
| >pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1 Length = 774 | Back alignment and structure |
| >pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant Length = 774 | Back alignment and structure |
| >pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus Gorgonarius In Complex With Hypoxanthine-Containing Dna Length = 773 | Back alignment and structure |
| >pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography Length = 773 | Back alignment and structure |
| >pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography. V93q Polymerase Variant Length = 773 | Back alignment and structure |
| >pdb|1NOZ|A Chain A, T4 Dna Polymerase Fragment (Residues 1-388) At 110k Length = 388 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} Length = 919 | Back alignment and structure |
|---|
Score = 375 bits (964), Expect = e-120
Identities = 178/544 (32%), Positives = 243/544 (44%), Gaps = 148/544 (27%)
Query: 4 QQTSDKWSRAP-PPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTME 62
+ + R P + +P I FQQI E I +VR FGVT E
Sbjct: 25 EHDLSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENT-----STVVRFFGVTSE 79
Query: 63 GNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIV 122
G+SV C+V GF YLYV AP ++ + ++ + A+ +E+V
Sbjct: 80 GHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVHY--------LNETFDHAIDSIEVV 131
Query: 123 QKQTVFGFWGEELENFLKIT----------------ESVFPTFPTHTYKAFESNIDFDIR 166
KQ+++G+ G+ F KI + NI + +R
Sbjct: 132 SKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNSWFSNGTTTYDNIAYTLR 191
Query: 167 FMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDV 226
MVD IVG +WI +P GK+ + + VS CQLE+ ++ ++++H E
Sbjct: 192 LMVDCGIVGMSWITLPKGKYSMIEPNN-------RVSSCQLEVSINYRNLIAHPAE---- 240
Query: 227 STDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENI 286
G+WS APLRI+SFDIECAGR G+FP+P +DP+IQIAN+ GA +
Sbjct: 241 -----------GDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKKP- 288
Query: 287 FVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAP 346
F++NVFTLNTC+P
Sbjct: 289 -----------------------------------------------FIRNVFTLNTCSP 301
Query: 347 IVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLG 406
I GS + TE E+L W FI ++DPD+ GYN NFD PYL+NRAK
Sbjct: 302 ITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKA---------- 351
Query: 407 RVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDS 466
L V +F + GR+K ++ IK+S
Sbjct: 352 --------------------------------------LKVNDFPYFGRLKTVKQEIKES 373
Query: 467 FIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSII 526
SK G RE K +N +GR+ DLL + REYKLRSYTLN+VS HFL EQKEDV +SII
Sbjct: 374 VFSSKAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSII 433
Query: 527 SDLQ 530
SDLQ
Sbjct: 434 SDLQ 437
|
| >2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* Length = 1193 | Back alignment and structure |
|---|
| >1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1 Length = 847 | Back alignment and structure |
|---|
| >3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A* Length = 786 | Back alignment and structure |
|---|
| >1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A Length = 775 | Back alignment and structure |
|---|
| >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* Length = 388 | Back alignment and structure |
|---|
| >3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 3spz_A* 3ne6_A* 3nhg_A* 3si6_A* 3scx_A* 3sjj_A* 3snn_A* 3ngi_A* 3lzi_A* 3lzj_A* 3ndk_A* ... Length = 903 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 551 | |||
| 3iay_A | 919 | DNA polymerase delta catalytic subunit; protein-DN | 100.0 | |
| 2gv9_A | 1193 | DNA polymerase; polymerase alpha fold, transferase | 100.0 | |
| 3k59_A | 786 | POL II, DNA polymerase II; protein-DNA complex, DN | 100.0 | |
| 1qht_A | 775 | Protein (DNA polymerase); archaea, hyperthermostab | 100.0 | |
| 1s5j_A | 847 | DNA polymerase I; replication, disulfide bonds, tr | 100.0 | |
| 1noy_A | 388 | Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas | 100.0 | |
| 3qex_A | 903 | DNA polymerase, GP43; difluorotoluene nucleoside; | 99.95 | |
| 2py5_A | 575 | DNA polymerase; protein-DNA complex, replication, | 97.67 | |
| 2p1j_A | 186 | POLIII, DNA polymerase III POLC-type; structural g | 97.63 | |
| 3mxm_B | 242 | Three prime repair exonuclease 1; RNAse H-like fol | 97.62 | |
| 3u3y_B | 314 | Three prime repair exonuclease 1; RNAse H fold, 3' | 97.59 | |
| 1y97_A | 238 | Three prime repair exonuclease 2; TREX2, hydrolase | 97.43 | |
| 2f96_A | 224 | Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas | 97.1 | |
| 3v9w_A | 235 | Ribonuclease T; DEDD nucleases family, EXO-nucleas | 97.03 | |
| 1zbh_A | 299 | 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif | 96.88 | |
| 1w0h_A | 204 | 3'-5' exonuclease ERI1; nuclease domain, hydrolase | 96.77 | |
| 2qxf_A | 482 | Exodeoxyribonuclease I; alpha-beta domain, DNAQ su | 96.69 | |
| 2gui_A | 194 | DNA polymerase III epsilon subunit; DNA polymerase | 96.58 | |
| 3iay_A | 919 | DNA polymerase delta catalytic subunit; protein-DN | 96.28 | |
| 1zbu_A | 349 | ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; | 96.19 | |
| 3tr8_A | 186 | Oligoribonuclease; transcription, hydrolase; 2.50A | 94.88 | |
| 2igi_A | 180 | Oligoribonuclease; RNAse, exoribonuclease, exonucl | 93.48 | |
| 2xri_A | 224 | ERI1 exoribonuclease 3; hydrolase, metal binding; | 92.77 | |
| 1noy_A | 388 | Protein (DNA polymerase (E.C.2.7.7.7)); exonucleas | 92.66 | |
| 2gbz_A | 194 | Oligoribonuclease; ORN, deddh, structural genomics | 92.08 | |
| 3cg7_A | 308 | CRN-4, cell death-related nuclease 4; hydrolase, a | 85.83 | |
| 2gv9_A | 1193 | DNA polymerase; polymerase alpha fold, transferase | 81.22 |
| >3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
Probab=100.00 E-value=2.4e-72 Score=645.97 Aligned_cols=413 Identities=45% Similarity=0.784 Sum_probs=337.5
Q ss_pred ccccCcCCCCCCCC-CCCCCCceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCC
Q psy12447 4 QQTSDKWSRAPPPE-LNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAP 82 (551)
Q Consensus 4 ~~~~~~w~~~~~~~-~~~~~~~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~ 82 (551)
+++...|.|||+|+ ++|..+.+.||++|+||+.. ++. .+.+++|+|+|||+|++|.+|||+||||+|||||..+
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~f~~ld~~~~~~---~~~--~~~~~~~virlfg~t~~G~sv~v~V~gf~PYFYv~~~ 99 (919)
T 3iay_A 25 EHDLSSFERKKLPTDFDPSLYDISFQQIDAEQSVL---NGI--KDENTSTVVRFFGVTSEGHSVLCNVTGFKNYLYVPAP 99 (919)
T ss_dssp ----CCCCCCCCCTTCCTTTCCEEEEEEEEEEEEC---SSS--CBTTBCEEEEEEEEETTSCEEEEEEESCCCEEEEECC
T ss_pred cccccCcCCCCCCcccCCCCCceEEEEEecccccc---ccc--cccCCeeEEEEEEEeCCCCEEEEEECCcCCEEEEEcC
Confidence 34567899999866 99999999999999999862 223 2345789999999999999999999999999999998
Q ss_pred CC---CChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEcccCCC-----------
Q psy12447 83 KE---FNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPT----------- 148 (551)
Q Consensus 83 ~~---~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~~~~----------- 148 (551)
++ ++.++++.+...|++.+ ...+.++++|+|+++|||+++.+.+|+||+......
T Consensus 100 ~~~~~~~~~~~~~~~~~L~~~~-----------~~~v~~ve~v~K~~l~gy~~~~~~~~lKI~~~~p~~v~~~r~~l~~g 168 (919)
T 3iay_A 100 NSSDANDQEQINKFVHYLNETF-----------DHAIDSIEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERG 168 (919)
T ss_dssp SSGGGGCHHHHHHHHHHHHTTT-----------TTCEEEEEEEEEEESSCCSCSCCEEEEEEEESSTTHHHHHHHHHHHS
T ss_pred CcccccchhHHHHHHHHHHHhh-----------cCCceEEEEEeeeccccCCCCCceEEEEEEEcCHHHHHHHHHHHHcc
Confidence 87 77666666555554321 346899999999999999876679999999533211
Q ss_pred ------cCCCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCc
Q psy12447 149 ------FPTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPE 222 (551)
Q Consensus 149 ------l~~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~ 222 (551)
+....+++|| ||+|++|||+|++|.||+|++++++.+..+... .+.|+|++|++|.+++
T Consensus 169 ~~~~~~~~~~~~~~yE-dI~~~~RfliD~~I~g~~W~~i~~~~~~~~~~~-------~~~S~c~~Ev~v~~~~------- 233 (919)
T 3iay_A 169 HLSFNSWFSNGTTTYD-NIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPN-------NRVSSCQLEVSINYRN------- 233 (919)
T ss_dssp CCCGGGSSTTCCCCBC-CCCHHHHHHHHHTCCTTCEEEECTTSEEECCGG-------GCCBCCSEEEEEETTT-------
T ss_pred ccccccccccCccccc-CCChHhhheeecCCccceEEEEecCcceecccc-------CCccceeEEEEeeccc-------
Confidence 1113578999 999999999999999999999998888765432 3689999999999988
Q ss_pred ccccCCCcccccCCCCCcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccC
Q psy12447 223 EIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVG 302 (551)
Q Consensus 223 ~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~ 302 (551)
++++.++.+|..+||+++|||||||.+++|.||+|++|+|+|||+++..+|...
T Consensus 234 --------l~~~~~~~~~~~~PplrilSfDIEt~~~~g~fP~~~~D~Ii~IS~~v~~~g~~~------------------ 287 (919)
T 3iay_A 234 --------LIAHPAEGDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKK------------------ 287 (919)
T ss_dssp --------CEEECSSGGGSCCCCCEEEEEEEEECCCTTSCCCTTTCCEEEEEEEEEETTCSS------------------
T ss_pred --------cccccccccccCCCCceEEEEEEEECCCCCCCCCCCCCcEEEEEEEEecCCCcc------------------
Confidence 455555667878999999999999999988899999999999999886665433
Q ss_pred ceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecc
Q psy12447 303 SQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNI 382 (551)
Q Consensus 303 ~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi 382 (551)
|+.+.+|+++.|+++.|..|..|++|++||.+|+++|+++|||||+|||+
T Consensus 288 ------------------------------~~~r~~f~l~~~~~~~~~~V~~~~sE~eLL~~F~~~i~~~DPDIIvGyNi 337 (919)
T 3iay_A 288 ------------------------------PFIRNVFTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNT 337 (919)
T ss_dssp ------------------------------CSEEEEEEESCCCCBTTBEEEEESSHHHHHHHHHHHHHHHCCSEEEESST
T ss_pred ------------------------------cceeEEEEecCCCCCCCCeEEECCCHHHHHHHHHHHHHHhCCCEEEecCC
Confidence 44466788888888889999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccc
Q psy12447 383 QNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSV 462 (551)
Q Consensus 383 ~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~ 462 (551)
.+||||||.+||..+|++.|..+||.++.....+
T Consensus 338 ~~FDlpyL~~Ra~~lgi~~~~~lGR~~~~~~~~~---------------------------------------------- 371 (919)
T 3iay_A 338 TNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIK---------------------------------------------- 371 (919)
T ss_dssp TTTHHHHHHHHHHHTTCTTCSCCSSBTTCCCCBC----------------------------------------------
T ss_pred ccCCHHHHHHHHHHcCCCchhhhccccCcccccc----------------------------------------------
Confidence 9999999999999999998888999865421111
Q ss_pred cccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---
Q psy12447 463 IKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP--- 539 (551)
Q Consensus 463 i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~--- 539 (551)
+..+++++||.+....+.++||+++|+|+++++++++.||+|++||+++||++|+++++++|.+||.+++..+.+
T Consensus 372 --~~~~~~~~~g~~~~~~~~i~GR~~lDl~~~~k~~~~l~sysL~~Va~~~Lg~~K~dv~~~~I~~l~~~~~~~~~~L~~ 449 (919)
T 3iay_A 372 --ESVFSSKAYGTRETKNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSIISDLQNGDSETRRRLAV 449 (919)
T ss_dssp --CEEEEETTTEEEEECCBCCTTCEEEEHHHHHHHHCCCSCCCHHHHHHHHHCCC------CCHHHHHTSCHHHHHHHHH
T ss_pred --ccccccccccccccceeEEcCeEEEEhHHHHHhhcCCCCCCHHHHHHHhcccCCCCCCHHHHHHHHhcChhhHHHHHH
Confidence 123445567766656689999999999999999999999999999999999999999999999999977655554
Q ss_pred ---cccccccccCCC
Q psy12447 540 ---KSNAAPLRYSPK 551 (551)
Q Consensus 540 ---~D~~l~~rl~~~ 551 (551)
+||+|+++||.|
T Consensus 450 Y~~~Da~l~~~L~~k 464 (919)
T 3iay_A 450 YCLKDAYLPLRLMEK 464 (919)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999753
|
| >2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* | Back alignment and structure |
|---|
| >3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A* | Back alignment and structure |
|---|
| >1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A | Back alignment and structure |
|---|
| >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 |
|---|
| >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 |
|---|
| >3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ... | Back alignment and structure |
|---|
| >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 |
|---|
| >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 |
|---|
| >3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A | Back alignment and structure |
|---|
| >3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B* | Back alignment and structure |
|---|
| >1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 | Back alignment and structure |
|---|
| >2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5 | Back alignment and structure |
|---|
| >3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A | Back alignment and structure |
|---|
| >1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} | Back alignment and structure |
|---|
| >1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 | Back alignment and structure |
|---|
| >2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A* | Back alignment and structure |
|---|
| >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* 2xy8_A* | Back alignment and structure |
|---|
| >3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae} | Back alignment and structure |
|---|
| >1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} | Back alignment and structure |
|---|
| >3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} | Back alignment and structure |
|---|
| >2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A | Back alignment and structure |
|---|
| >2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} | Back alignment and structure |
|---|
| >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 |
|---|
| >2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} | Back alignment and structure |
|---|
| >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 |
|---|
| >2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 551 | ||||
| d1s5ja1 | 410 | c.55.3.5 (A:40-449) Exonuclease domain of family B | 2e-44 | |
| d1q8ia1 | 388 | c.55.3.5 (A:2-389) Exonuclease domain of family B | 3e-24 | |
| d1tgoa1 | 347 | c.55.3.5 (A:1-347) Exonuclease domain of family B | 1e-22 | |
| d1noya_ | 372 | c.55.3.5 (A:) Exonuclease domain of family B DNA p | 1e-09 | |
| d1ih7a1 | 375 | c.55.3.5 (A:1-375) Exonuclease domain of family B | 8e-08 |
| >d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]} Length = 410 | Back information, alignment and structure |
|---|
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 family B DNA polymerases species: Sulfolobus solfataricus [TaxId: 2287]
Score = 160 bits (405), Expect = 2e-44
Identities = 65/478 (13%), Positives = 114/478 (23%), Gaps = 148/478 (30%)
Query: 52 PIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDE 111
+ ++F + G PY V + + ++
Sbjct: 26 AVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIPKIVRD---------------- 69
Query: 112 IQEAVLMVEIVQKQTVFGFWGEELENFLKITESVFPTFP---THTYKAFESNIDFDIRFM 168
+ +E V K + KI KA+E++I + +M
Sbjct: 70 --PSFDHIETVSKID---PYTWNKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYM 124
Query: 169 VDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVST 228
D ++ + GK + L +D + + A + D T
Sbjct: 125 YDIGLIPGMPYVVKNGKLESVY----------------LSLDEKDVEEIKKAFADSDEMT 168
Query: 229 DDIVSHAPEGEWSKVAPLRILSFDIEC-AGRKGIFPDPNHDPIIQIANMCISQGASENIF 287
+ +++ ++ ++ DIE KG PD I+ + +
Sbjct: 169 RQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVL 228
Query: 288 VKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPI 347
V N +N +
Sbjct: 229 VLNRNDVN----------------------------------------------EGSVKL 242
Query: 348 VGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
G V TE ELL ++ + + I +N +FD PY+ RA LG
Sbjct: 243 DGISVERFNTEYELLGRFFDILL--EYPIVLTFNGDDFDLPYIYFRALKLG--------- 291
Query: 408 VKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSF 467
I GK E
Sbjct: 292 -------YFPEEIPIDVAGKDE-------------------------------------- 306
Query: 468 IQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSI 525
I+ + E K Y L++V+ L K V I
Sbjct: 307 -----AKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKVDTLI 359
|
| >d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} Length = 388 | Back information, alignment and structure |
|---|
| >d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Length = 347 | Back information, alignment and structure |
|---|
| >d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]} Length = 372 | Back information, alignment and structure |
|---|
| >d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]} Length = 375 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 551 | |||
| d1s5ja1 | 410 | Exonuclease domain of family B DNA polymerases {Su | 100.0 | |
| d1tgoa1 | 347 | Exonuclease domain of family B DNA polymerases {Ar | 100.0 | |
| d1q8ia1 | 388 | Exonuclease domain of family B DNA polymerases {Es | 100.0 | |
| d1ih7a1 | 375 | Exonuclease domain of family B DNA polymerases {Ba | 99.96 | |
| d1noya_ | 372 | Exonuclease domain of family B DNA polymerases {Ba | 99.96 | |
| d1x9ma1 | 204 | Exonuclease domain of T7 DNA polymerase {Bacteriop | 98.8 | |
| d3b6oa1 | 226 | Three prime repair exonuclease 1, TREX1 {Mouse (Mu | 96.71 | |
| d2guia1 | 174 | N-terminal exonuclease domain of the epsilon subun | 95.48 | |
| d2qxfa1 | 467 | Exonuclease I {Escherichia coli K12 (Escherichia c | 94.45 | |
| d1y97a1 | 228 | Three prime repair exonuclease 2, TREX2 {Human (Ho | 93.77 | |
| d1w0ha_ | 200 | Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 | 92.68 | |
| d1wlja_ | 173 | Interferon-stimulated gene 20 kDa protein, ISG20 { | 85.72 | |
| d2igia1 | 180 | Oligoribonuclease {Escherichia coli [TaxId: 562]} | 81.49 |
| >d1s5ja1 c.55.3.5 (A:40-449) Exonuclease domain of family B DNA polymerases {Sulfolobus solfataricus [TaxId: 2287]} | Back information, alignment and structure |
|---|
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 family B DNA polymerases species: Sulfolobus solfataricus [TaxId: 2287]
Probab=100.00 E-value=2.8e-50 Score=426.08 Aligned_cols=368 Identities=19% Similarity=0.195 Sum_probs=248.0
Q ss_pred CCCceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCCChhHHHHHHHHHHHH
Q psy12447 21 KEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRA 100 (551)
Q Consensus 21 ~~~~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~~~~~~~~~~~~l~~~ 100 (551)
..+...|+++|++|... .++|+|++||++.+|.+||+.++||+|||||..|.+ .+..+.
T Consensus 6 ~~~~~~~~ll~~~Y~~~-----------~~~~vi~~~g~~~~~~~v~~~~~gf~PYFyv~~~~~----~~~~~~------ 64 (410)
T d1s5ja1 6 AQENKIYFLLQVDYDGK-----------KGKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPD----KVGKIP------ 64 (410)
T ss_dssp CCTTCEEEEEEEEEETT-----------TTEEEEEEEETTTTEEEEEECCSCCCCEEEESSCHH----HHTTCH------
T ss_pred cccCCcEEEEEeEEeee-----------CCEEEEEEEeecCCcEEEEEeCCCccceEEEECCcc----hHHHHH------
Confidence 45678999999998862 378999999999999999999999999999987632 111111
Q ss_pred HHHHhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEccc---CCCcCCCcccccccCcchhhhhhhhCCCCcce
Q psy12447 101 IIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESV---FPTFPTHTYKAFESNIDFDIRFMVDNDIVGCN 177 (551)
Q Consensus 101 l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~---~~~l~~~~~~vyEa~I~~~~rFliD~~I~g~~ 177 (551)
...+ ...+..++.|+|..++++ ++.+|+||+... .+.++....++|||||+|+.|||+|++|.||+
T Consensus 65 --~~~~------~~~~~~~e~v~k~~~~~~---~~~~~~ki~~~~p~~v~~~r~~~~~~~EadI~~~~RfliD~~l~~~~ 133 (410)
T d1s5ja1 65 --KIVR------DPSFDHIETVSKIDPYTW---NKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGM 133 (410)
T ss_dssp --HHHT------CTTEEEEEEEEEECTTTC---CEEEEEEEEESSHHHHHHHTTSSSCEESCSSCHHHHHHHHHTCCTTS
T ss_pred --HHhh------hcccceEEEEEEEeccCC---cceeEEEEEEcCHHHHHHHHHHhhhhcccccCchhcEEEEcCCccce
Confidence 1111 135678999999998775 467999999543 33444555589999999999999999999999
Q ss_pred EEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEecc
Q psy12447 178 WIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAG 257 (551)
Q Consensus 178 Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~ 257 (551)
|+++.+.......... .....+.++..+...++. ... . .....+ ....++|++++|||||||.+
T Consensus 134 w~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~-----~~~-~---~~~~~~-~~~~~~p~l~~lsfDIE~~~ 197 (410)
T d1s5ja1 134 PYVVKNGKLESVYLSL------DEKDVEEIKKAFADSDEM-----TRQ-M---AVDWLP-IFETEIPKIKRVAIDIEVYT 197 (410)
T ss_dssp EEEEETTEEEECCCCC------CHHHHHHHHHHTTTSCHH-----HHH-H---HHHHTH-HHHSCCCCCCEEEEEEEECC
T ss_pred EEEecCCccccccccc------Ccchhhhhccccccccch-----hhc-c---cccccc-ccccCCCCceEEEEEEEECC
Confidence 9999887654332110 011111111000000000 000 0 000000 01235799999999999987
Q ss_pred C-CCCCCCCCCC--cEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCce
Q psy12447 258 R-KGIFPDPNHD--PIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIF 334 (551)
Q Consensus 258 ~-~~~fP~~~~d--~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~ 334 (551)
. ++.||+|+.+ +|+||++.- .++.. .++.++.+
T Consensus 198 ~~~~~fP~p~~~~~~ii~I~~~~-~~~~~------~v~~~~~~------------------------------------- 233 (410)
T d1s5ja1 198 PVKGRIPDSQKAEFPIISIALAG-SDGLK------KVLVLNRN------------------------------------- 233 (410)
T ss_dssp SSSSCCCCTTTCCSCEEEEEEEE-TTSCE------EEEEECSS-------------------------------------
T ss_pred CCCCCCCCccccCceEEEEEEEc-ccCCE------EEEEEccC-------------------------------------
Confidence 6 4579999865 777777642 22221 12222110
Q ss_pred eeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccc-cccccccccc
Q psy12447 335 VKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT-FLGRVKDIRS 413 (551)
Q Consensus 335 ~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~-~l~R~~~~~~ 413 (551)
.....|..+.++.|+.|++|++||.+|++++. |||||+|||+.+||||||.+||+.+|+.... .++|....
T Consensus 234 ----~~~~~~~~~~~~~v~~~~sE~eLL~~F~~~i~--dpDii~GyN~~~FD~pyL~~Ra~~lg~~~~~~~~~~~~~~-- 305 (410)
T d1s5ja1 234 ----DVNEGSVKLDGISVERFNTEYELLGRFFDILL--EYPIVLTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKD-- 305 (410)
T ss_dssp ----CCCCCCEEETTEEEEEESSHHHHHHHHHHHHT--TCSEEEESSTTTTHHHHHHHHHHTTTCCGGGCSEECCSTT--
T ss_pred ----CCccccccCCCeEEEEECCHHHHHHHHHhhhc--ccceEEEecccCCcHHHHHHHHHHhCCccccccccccCcc--
Confidence 01122445678899999999999999999995 8999999999999999999999999985321 12221110
Q ss_pred ccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHH
Q psy12447 414 VIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLF 493 (551)
Q Consensus 414 ~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~ 493 (551)
..+......+.+.||+++|+|.
T Consensus 306 ----------------------------------------------------------~~~~~~~~~~~~~g~~~~d~~~ 327 (410)
T d1s5ja1 306 ----------------------------------------------------------EAKYLAGLHIDLYKFFFNKAVR 327 (410)
T ss_dssp ----------------------------------------------------------CCEETTSEEEEHHHHHTSHHHH
T ss_pred ----------------------------------------------------------ceeEecceEEEecceeeehHHH
Confidence 0011112357889999999999
Q ss_pred HHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccccCC
Q psy12447 494 VLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYSP 550 (551)
Q Consensus 494 ~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~~ 550 (551)
.++...+|+||+|++||+++||++|.+++... .. .+....+. +||.|+++|+.
T Consensus 328 ~~~~~~~l~sy~Ld~Va~~~Lg~~K~d~~~~~-~~---~~~~~l~~Y~~~D~~L~~~L~~ 383 (410)
T d1s5ja1 328 NYAFEGKYNEYNLDAVAKALLGTSKVKVDTLI-SF---LDVEKLIEYNFRDAEITLQLTT 383 (410)
T ss_dssp HHTSTTCCSSCSHHHHHHHHHCCCCC--SSCT-TT---CCHHHHHHHHHHHHHHHHHTTT
T ss_pred HHhhccCCCCCCHHHHHHHHhCcCcccCCCcc-cc---CCHHHHHHhhHHHHHHHHHHHh
Confidence 99999999999999999999999999886421 00 11111122 99999999985
|
| >d1tgoa1 c.55.3.5 (A:1-347) Exonuclease domain of family B DNA polymerases {Archaeon Thermococcus gorgonarius [TaxId: 71997]} | Back information, alignment and structure |
|---|
| >d1q8ia1 c.55.3.5 (A:2-389) Exonuclease domain of family B DNA polymerases {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d1ih7a1 c.55.3.5 (A:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]} | Back information, alignment and structure |
|---|
| >d1noya_ c.55.3.5 (A:) Exonuclease domain of family B DNA polymerases {Bacteriophage T4 [TaxId: 10665]} | Back information, alignment and structure |
|---|
| >d1x9ma1 c.55.3.5 (A:1-210) Exonuclease domain of T7 DNA polymerase {Bacteriophage T7 [TaxId: 10760]} | Back information, alignment and structure |
|---|
| >d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} | Back information, alignment and structure |
|---|
| >d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|
| >d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} | Back information, alignment and structure |
|---|
| >d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} | Back information, alignment and structure |
|---|
| >d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} | Back information, alignment and structure |
|---|