Psyllid ID: psy12450

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
MLRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLYC
cccccccccEEEEEEEEccccccHHHHHHcEEEHHHccccHHHHHccccccccccccccccccccEEcccccccccccEEEEEcccccHHHHHHHccccccccccccccccccccccEEEcccccEEcccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHccc
ccccEEHHHHHHHHHHccccccHHHHccccHHHHHHHHHHHHHHHcccEEEcccccccccccEEEEEEccccccccccEEEEEEccHHHHHHHHcccccccEccccHHHHcccccccEEEcccccEEEcHcHHHcHHHHHHHHHHHHHHHHHHHHHHccccccEEEEc
mlrhvtwrdgletvrrdnspLVANMINTCLQKLlinrdpdgavtqknfiiptyhggqgedqfegatviepkkgyyadpiatldfsslypsIMMAHNlcyttlltpqtitkleltpdqysktpcgnfflksslrkgLLPEILENLLSARKQAKNDLKKETDELTQVLYC
mlrhvtwrdgletvrrdnsplvaNMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQakndlkketdeltqvlyc
MLRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLYC
*****TWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLL***********************
**R*VTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAV**********************TVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDE*TQVLYC
MLRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLYC
MLRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLYC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLRHVTWRDGLETVRRDNSPLVANMINTCLQKLLINRDPDGAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEIxxxxxxxxxxxxxxxxxxxxxLTQVLYC
no confident homologs detected

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 ?
Query168 2.2.26 [Sep-21-2011]
P54358 1092 DNA polymerase delta cata yes N/A 0.684 0.105 0.655 2e-39
P28340 1107 DNA polymerase delta cata yes N/A 0.720 0.109 0.666 8e-38
P28339 1106 DNA polymerase delta cata yes N/A 0.720 0.109 0.666 1e-37
P97283 1103 DNA polymerase delta cata N/A N/A 0.720 0.109 0.658 2e-37
P46588 1038 DNA polymerase delta cata N/A N/A 0.690 0.111 0.629 3e-37
P52431 1105 DNA polymerase delta cata yes N/A 0.654 0.099 0.702 4e-37
O54747 1103 DNA polymerase delta cata yes N/A 0.720 0.109 0.650 4e-37
Q9LRE6 1105 DNA polymerase delta cata yes N/A 0.726 0.110 0.560 2e-34
Q9LVN7 1095 DNA polymerase delta cata yes N/A 0.726 0.111 0.552 5e-34
P30316 1086 DNA polymerase delta cata yes N/A 0.726 0.112 0.593 7e-34
>sp|P54358|DPOD1_DROME DNA polymerase delta catalytic subunit OS=Drosophila melanogaster GN=DNApol-delta PE=2 SV=2 Back     alignment and function desciption
 Score =  161 bits (407), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 78/119 (65%), Positives = 95/119 (79%), Gaps = 4/119 (3%)

Query: 46  KNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTP 105
           K FI+P+Y     ++Q+EGATVIEPK+GYYADPI+TLDF+SLYPSIMMAHNLCYTTL+  
Sbjct: 550 KGFIMPSYTSQGSDEQYEGATVIEPKRGYYADPISTLDFASLYPSIMMAHNLCYTTLVLG 609

Query: 106 QTITKLE----LTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
            T  KL     L  DQ  +TP  N+F+KS +R+GLLPEILE+LL+ARK+AKNDLK ETD
Sbjct: 610 GTREKLRQQENLQDDQVERTPANNYFVKSEVRRGLLPEILESLLAARKRAKNDLKVETD 668
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
>sp|P28339|DPOD1_BOVIN DNA polymerase delta catalytic subunit OS=Bos taurus GN=POLD1 PE=1 SV=1 Back     alignment and function description
>sp|P97283|DPOD1_MESAU DNA polymerase delta catalytic subunit OS=Mesocricetus auratus GN=POLD1 PE=2 SV=1 Back     alignment and function description
>sp|P46588|DPOD_CANAX DNA polymerase delta catalytic subunit OS=Candida albicans GN=POL3 PE=3 SV=2 Back     alignment and function description
>sp|P52431|DPOD1_MOUSE DNA polymerase delta catalytic subunit OS=Mus musculus GN=Pold1 PE=1 SV=2 Back     alignment and function description
>sp|O54747|DPOD1_RAT DNA polymerase delta catalytic subunit OS=Rattus norvegicus GN=Pold1 PE=2 SV=1 Back     alignment and function description
>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
>sp|Q9LVN7|DPOD1_ARATH DNA polymerase delta catalytic subunit OS=Arabidopsis thaliana GN=POLD1 PE=2 SV=2 Back     alignment and function description
>sp|P30316|DPOD_SCHPO DNA polymerase delta catalytic subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pol3 PE=1 SV=2 Back     alignment and function description

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 ?
Query168
324120694 1097 DNA polymerase delta catalytic subunit [ 0.702 0.107 0.779 4e-48
324120690 1006 DNA polymerase delta catalytic subunit [ 0.714 0.119 0.75 4e-46
324120696 1007 DNA polymerase delta catalytic subunit [ 0.714 0.119 0.741 9e-46
324120740 1094 DNA polymerase delta catalytic subunit [ 0.714 0.109 0.741 2e-45
324120692 1097 DNA polymerase delta catalytic subunit [ 0.714 0.109 0.741 3e-45
324120698 1095 DNA polymerase delta catalytic subunit [ 0.714 0.109 0.716 3e-45
324120744 1036 DNA polymerase delta catalytic subunit [ 0.714 0.115 0.725 5e-45
324120714 1035 DNA polymerase delta catalytic subunit [ 0.714 0.115 0.725 1e-44
324120718 1111 DNA polymerase delta catalytic subunit [ 0.714 0.108 0.710 2e-44
324120730 1033 DNA polymerase delta catalytic subunit [ 0.714 0.116 0.7 4e-44
>gi|324120694|dbj|BAJ78738.1| DNA polymerase delta catalytic subunit [Inocellia japonica] Back     alignment and taxonomy information
 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 92/118 (77%), Positives = 103/118 (87%)

Query: 45  QKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
           +K+F+IP Y GG  EDQ+EGATVIEPK+GYY DPIATLDFSSLYPSIMMAHNLCYT+LL 
Sbjct: 559 EKDFVIPAYSGGTQEDQYEGATVIEPKRGYYDDPIATLDFSSLYPSIMMAHNLCYTSLLQ 618

Query: 105 PQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDEL 162
           P    KL LTPDQYS+TP GNFF+K S+RKGLLPEILENLL+ARK+AK DLKKETD L
Sbjct: 619 PGVKEKLGLTPDQYSRTPAGNFFVKQSVRKGLLPEILENLLAARKKAKADLKKETDPL 676

Source: Inocellia japonica

Species: Inocellia japonica

Genus: Inocellia

Family: Inocelliidae

Order: Raphidioptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120690|dbj|BAJ78736.1| DNA polymerase delta catalytic subunit [Nipponatelura sp. 66-1] Back     alignment and taxonomy information
>gi|324120696|dbj|BAJ78739.1| DNA polymerase delta catalytic subunit [Epiophlebia superstes] Back     alignment and taxonomy information
>gi|324120740|dbj|BAJ78761.1| DNA polymerase delta catalytic subunit [Bemisia tabaci] Back     alignment and taxonomy information
>gi|324120692|dbj|BAJ78737.1| DNA polymerase delta catalytic subunit [Thermobia domestica] Back     alignment and taxonomy information
>gi|324120698|dbj|BAJ78740.1| DNA polymerase delta catalytic subunit [Mnais pruinosa pruinosa] Back     alignment and taxonomy information
>gi|324120744|dbj|BAJ78763.1| DNA polymerase delta catalytic subunit [Metylophorus sp. E-43] Back     alignment and taxonomy information
>gi|324120714|dbj|BAJ78748.1| DNA polymerase delta catalytic subunit [Euconocephalus varius] Back     alignment and taxonomy information
>gi|324120718|dbj|BAJ78750.1| DNA polymerase delta catalytic subunit [Oyamia lugubris] Back     alignment and taxonomy information
>gi|324120730|dbj|BAJ78756.1| DNA polymerase delta catalytic subunit [Reticulitermes speratus] Back     alignment and taxonomy information

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 ?
Query168
ZFIN|ZDB-GENE-060429-1 1105 pold1 "polymerase (DNA directe 0.720 0.109 0.674 4e-36
FB|FBgn0263600 1092 DNApol-delta "DNA-polymerase-d 0.684 0.105 0.655 8.2e-36
UNIPROTKB|P28340 1107 POLD1 "DNA polymerase delta ca 0.714 0.108 0.672 4.7e-35
UNIPROTKB|E1BNZ6 984 E1BNZ6 "DNA polymerase" [Bos t 0.720 0.122 0.666 7.8e-35
UNIPROTKB|P28339 1106 POLD1 "DNA polymerase delta ca 0.720 0.109 0.666 9.8e-35
UNIPROTKB|E2R5W5 1107 POLD1 "DNA polymerase" [Canis 0.720 0.109 0.666 9.9e-35
UNIPROTKB|J9NS34 1131 POLD1 "DNA polymerase" [Canis 0.720 0.106 0.666 1e-34
MGI|MGI:97741 1105 Pold1 "polymerase (DNA directe 0.654 0.099 0.702 2.6e-34
UNIPROTKB|F1RH32 1107 POLD1 "DNA polymerase" [Sus sc 0.720 0.109 0.658 2.6e-34
RGD|621839 1103 Pold1 "polymerase (DNA directe 0.720 0.109 0.650 3.3e-34
ZFIN|ZDB-GENE-060429-1 pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 401 (146.2 bits), Expect = 4.0e-36, P = 4.0e-36
 Identities = 83/123 (67%), Positives = 97/123 (78%)

Query:    45 QKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
             +++ ++P      GED + GATVIEP+KGYY+ PIATLDFSSLYPSIMMAHNLCYTTLL 
Sbjct:   569 KQDLVMPVVKTEGGED-YTGATVIEPEKGYYSVPIATLDFSSLYPSIMMAHNLCYTTLLQ 627

Query:   105 PQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELT- 163
                I KL L PD + KTP G+ F+KSS+RKGLLPEILENLLSARK+AK +LKKETD    
Sbjct:   628 KSQIEKLGLGPDDFIKTPTGDLFVKSSVRKGLLPEILENLLSARKRAKAELKKETDPFKK 687

Query:   164 QVL 166
             QVL
Sbjct:   688 QVL 690
GO:0000166 "nucleotide binding" evidence=IEA
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
GO:0003887 "DNA-directed DNA polymerase activity" evidence=IEA;IBA
GO:0006260 "DNA replication" evidence=IEA;IMP
GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA
GO:0008408 "3'-5' exonuclease activity" evidence=IBA
GO:0007346 "regulation of mitotic cell cycle" evidence=IBA
GO:0019985 "translesion synthesis" evidence=IBA
GO:0043137 "DNA replication, removal of RNA primer" evidence=IBA
GO:0045004 "DNA replication proofreading" evidence=IBA
GO:0006297 "nucleotide-excision repair, DNA gap filling" evidence=IBA
GO:0043625 "delta DNA polymerase complex" evidence=IBA
GO:0005634 "nucleus" evidence=IBA
GO:0006287 "base-excision repair, gap-filling" evidence=IBA
GO:0000084 "S phase of mitotic cell cycle" evidence=IBA
GO:0016779 "nucleotidyltransferase activity" evidence=IEA
GO:0016740 "transferase activity" evidence=IEA
FB|FBgn0263600 DNApol-delta "DNA-polymerase-delta" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|P28340 POLD1 "DNA polymerase delta catalytic subunit" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E1BNZ6 E1BNZ6 "DNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P28339 POLD1 "DNA polymerase delta catalytic subunit" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R5W5 POLD1 "DNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|J9NS34 POLD1 "DNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:97741 Pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1RH32 POLD1 "DNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|621839 Pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
O48901DPOD1_SOYBN2, ., 7, ., 7, ., 70.55280.72610.1121yesN/A
Q9LRE6DPOD1_ORYSJ2, ., 7, ., 7, ., 70.56090.72610.1104yesN/A
P52431DPOD1_MOUSE2, ., 7, ., 7, ., 70.70270.65470.0995yesN/A
P15436DPOD_YEAST2, ., 7, ., 7, ., 70.57520.66660.1020yesN/A
P54358DPOD1_DROME2, ., 7, ., 7, ., 70.65540.68450.1053yesN/A
P90829DPOD1_CAEEL2, ., 7, ., 7, ., 70.5440.70230.1091yesN/A
Q9LVN7DPOD1_ARATH2, ., 7, ., 7, ., 70.55280.72610.1114yesN/A
O54747DPOD1_RAT2, ., 7, ., 7, ., 70.65040.72020.1097yesN/A
P28339DPOD1_BOVIN2, ., 7, ., 7, ., 70.66660.72020.1094yesN/A
Q54N97DPOD1_DICDI2, ., 7, ., 7, ., 70.59010.70230.1068yesN/A
P30316DPOD_SCHPO2, ., 7, ., 7, ., 70.59340.72610.1123yesN/A
P28340DPOD1_HUMAN2, ., 7, ., 7, ., 70.66660.72020.1093yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.691

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 ?
Query168
cd05533 393 cd05533, POLBc_delta, DNA polymerase type-B delta 2e-60
PTZ00166 1054 PTZ00166, PTZ00166, DNA polymerase delta catalytic 2e-54
pfam00136 458 pfam00136, DNA_pol_B, DNA polymerase family B 2e-36
smart00486474 smart00486, POLBc, DNA polymerase type-B family 4e-31
COG0417 792 COG0417, PolB, DNA polymerase elongation subunit ( 1e-29
cd00145 323 cd00145, POLBc, DNA polymerase type-B family catal 8e-27
cd05534 451 cd05534, POLBc_zeta, DNA polymerase type-B zeta su 1e-23
cd05532 400 cd05532, POLBc_alpha, DNA polymerase type-B alpha 2e-22
PRK05762 786 PRK05762, PRK05762, DNA polymerase II; Reviewed 7e-20
cd05536 371 cd05536, POLBc_B3, DNA polymerase type-B B3 subfam 2e-18
cd05533393 cd05533, POLBc_delta, DNA polymerase type-B delta 8e-14
TIGR00592 1172 TIGR00592, pol2, DNA polymerase (pol2) 2e-12
cd05531 352 cd05531, POLBc_B2, DNA polymerase type-B B2 subfam 4e-11
PTZ00166 1054 PTZ00166, PTZ00166, DNA polymerase delta catalytic 9e-11
PRK05761 787 PRK05761, PRK05761, DNA polymerase I; Reviewed 2e-09
PHA02528 881 PHA02528, 43, DNA polymerase; Provisional 8e-09
cd05530 372 cd05530, POLBc_B1, DNA polymerase type-B B1 subfam 2e-08
PHA03036 1004 PHA03036, PHA03036, DNA polymerase; Provisional 3e-08
cd05537 371 cd05537, POLBc_Pol_II, DNA polymerase type-II subf 9e-08
pfam00136458 pfam00136, DNA_pol_B, DNA polymerase family B 7e-06
COG0417792 COG0417, PolB, DNA polymerase elongation subunit ( 1e-05
PHA02524498 PHA02524, 43A, DNA polymerase subunit A; Provision 9e-05
PHA03334 1545 PHA03334, PHA03334, putative DNA polymerase cataly 0.002
cd00145323 cd00145, POLBc, DNA polymerase type-B family catal 0.003
cd05534451 cd05534, POLBc_zeta, DNA polymerase type-B zeta su 0.004
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily catalytic domain Back     alignment and domain information 
 Score =  191 bits (488), Expect = 2e-60
 Identities = 74/105 (70%), Positives = 86/105 (81%), Gaps = 2/105 (1%)

Query: 60  DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
           +Q+EGATVIEP KGYY  PIATLDF+SLYPSIMMAHNLCYTTLL   T  KL   P+ Y 
Sbjct: 1   EQYEGATVIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTTLLNKNTAKKLP--PEDYI 58

Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQ 164
           KTP G++F+KSS+RKGLLPEILE LL+ARK+AK DLK+ETD   +
Sbjct: 59  KTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEETDPFKK 103

Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. Length = 393
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B Back     alignment and domain information
>gnl|CDD|214691 smart00486, POLBc, DNA polymerase type-B family 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|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain Back     alignment and domain information
>gnl|CDD|99917 cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed Back     alignment and domain information
>gnl|CDD|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2) Back     alignment and domain information
>gnl|CDD|99914 cd05531, POLBc_B2, DNA polymerase type-B B2 subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>gnl|CDD|235594 PRK05761, PRK05761, DNA polymerase I; Reviewed Back     alignment and domain information
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional Back     alignment and domain information
>gnl|CDD|99913 cd05530, POLBc_B1, DNA polymerase type-B B1 subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional Back     alignment and domain information
>gnl|CDD|99920 cd05537, POLBc_Pol_II, DNA polymerase type-II subfamily catalytic domain Back     alignment and domain information
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B 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|164925 PHA02524, 43A, DNA polymerase subunit A; Provisional Back     alignment and domain information
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit; Provisional Back     alignment and domain information
>gnl|CDD|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain Back     alignment and domain information
>gnl|CDD|99917 cd05534, POLBc_zeta, DNA polymerase type-B zeta subfamily catalytic domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 168
KOG0969|consensus 1066 100.0
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 100.0
PHA02524498 43A DNA polymerase subunit A; Provisional 100.0
cd05534 451 POLBc_zeta DNA polymerase type-B zeta subfamily ca 100.0
cd05533 393 POLBc_delta DNA polymerase type-B delta subfamily 99.98
KOG0970|consensus 1429 99.98
PHA02528 881 43 DNA polymerase; Provisional 99.97
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 99.97
PHA03036 1004 DNA polymerase; Provisional 99.96
cd05532 400 POLBc_alpha DNA polymerase type-B alpha subfamily 99.96
cd05536 371 POLBc_B3 DNA polymerase type-B B3 subfamily cataly 99.96
PRK05761 787 DNA polymerase I; Reviewed 99.96
PRK05762 786 DNA polymerase II; Reviewed 99.96
PF00136 466 DNA_pol_B: DNA polymerase family B Several related 99.95
cd00145 323 POLBc DNA polymerase type-B family catalytic domai 99.95
COG0417 792 PolB DNA polymerase elongation subunit (family B) 99.95
cd05530 372 POLBc_B1 DNA polymerase type-B B1 subfamily cataly 99.95
cd05531 352 POLBc_B2 DNA polymerase type-B B2 subfamily cataly 99.94
PHA03334 1545 putative DNA polymerase catalytic subunit; Provisi 99.94
cd05537 371 POLBc_Pol_II DNA polymerase type-II subfamily cata 99.93
smart00486471 POLBc DNA polymerase type-B family. DNA polymerase 99.92
KOG0968|consensus 1488 99.91
cd05538 347 POLBc_Pol_II_B DNA polymerase type-II B subfamily 99.9
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 99.19
KOG0969|consensus 1066 98.23
PHA02563 630 DNA polymerase; Provisional 97.58
KOG0968|consensus 1488 97.23
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 95.98
PF03175 459 DNA_pol_B_2: DNA polymerase type B, organellar and 95.6
cd00145323 POLBc DNA polymerase type-B family catalytic domai 93.44
cd05537371 POLBc_Pol_II DNA polymerase type-II subfamily cata 93.42
cd05533393 POLBc_delta DNA polymerase type-B delta subfamily 93.41
cd05534451 POLBc_zeta DNA polymerase type-B zeta subfamily ca 93.37
cd05531352 POLBc_B2 DNA polymerase type-B B2 subfamily cataly 93.32
cd05535 621 POLBc_epsilon DNA polymerase type-B epsilon subfam 93.05
cd05536371 POLBc_B3 DNA polymerase type-B B3 subfamily cataly 92.72
cd05532400 POLBc_alpha DNA polymerase type-B alpha subfamily 92.53
cd05538347 POLBc_Pol_II_B DNA polymerase type-II B subfamily 91.63
PHA030361004 DNA polymerase; Provisional 91.44
PHA02528881 43 DNA polymerase; Provisional 91.43
COG0417792 PolB DNA polymerase elongation subunit (family B) 91.3
PF00136466 DNA_pol_B: DNA polymerase family B Several related 91.06
cd05530372 POLBc_B1 DNA polymerase type-B B1 subfamily cataly 90.9
PHA02735 716 putative DNA polymerase type B; Provisional 90.55
PRK05761787 DNA polymerase I; Reviewed 90.33
PRK05762786 DNA polymerase II; Reviewed 87.5
>KOG0969|consensus Back     alignment and domain information 
Probab=100.00  E-value=1.4e-36  Score=276.54  Aligned_cols=135  Identities=57%  Similarity=0.991  Sum_probs=121.9

Q ss_pred             HHHHhccCCC--------ccccccceeeeeCCCCCC-CcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccc
Q psy12450         31 QKLLINRDPD--------GAVTQKNFIIPTYHGGQG-EDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTT  101 (168)
Q Consensus        31 ~~lli~r~~~--------~A~~~~~~liP~~~~~~~-~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~T  101 (168)
                      ..+|..|.+.        -++.++++++|+...... .++||||+|+||+.|+|+.||++|||||||||||||||+||+|
T Consensus       507 ~syLltRGqqIKVlSqLlRkakq~~~~~P~i~~~~s~~e~yEGatVIEp~kGfY~~PIATLDFaSLYPSIMmahNLCYtT  586 (1066)
T KOG0969|consen  507 ISYLLTRGQQIKVLSQLLRKAKQKDFVIPNIKSQGSDDEQYEGATVIEPRKGFYDKPIATLDFASLYPSIMMAHNLCYTT  586 (1066)
T ss_pred             HHHHHhCCcchHHHHHHHHHHhhcCeeeeeecccCCccccccccEEeecccccCCCCceeeehhhhhhHHHHHhhhhhee
Confidence            3667777752        578889999999964433 3789999999999999999999999999999999999999999


Q ss_pred             cccccccccCCCCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450        102 LLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY  167 (168)
Q Consensus       102 l~~~~~~~~~~~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l  167 (168)
                      ++.++...+++  +++++.+|+|..|++.+.++|+||++|++||+.||.+|+.||+++||++|++|
T Consensus       587 Ll~~~t~~~l~--~~~~~~TP~g~yFv~~~~rkGlLP~ILe~ll~aRKraK~dlk~ekDp~kr~vl  650 (1066)
T KOG0969|consen  587 LLTKETVEKLG--DEDYTRTPTGDYFVKTEVRKGLLPEILEDLLTARKRAKADLKKEKDPFKRAVL  650 (1066)
T ss_pred             ccccchhhhcC--ccceeECCCCCeeeehhhhccccHHHHHHHHHHHHHHHHHHHhccCHHHHhhh
Confidence            99988766554  78999999999999999999999999999999999999999999999999987

>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>PHA02524 43A DNA polymerase subunit A; Provisional Back     alignment and domain information
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain Back     alignment and domain information
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain Back     alignment and domain information
>KOG0970|consensus Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) Back     alignment and domain information
>PHA03036 DNA polymerase; Provisional Back     alignment and domain information
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain Back     alignment and domain information
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included Back     alignment and domain information
>cd00145 POLBc DNA polymerase type-B family catalytic domain Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain Back     alignment and domain information
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain Back     alignment and domain information
>PHA03334 putative DNA polymerase catalytic subunit; Provisional Back     alignment and domain information
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>KOG0968|consensus Back     alignment and domain information
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) Back     alignment and domain information
>KOG0969|consensus Back     alignment and domain information
>PHA02563 DNA polymerase; Provisional Back     alignment and domain information
>KOG0968|consensus Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>PF03175 DNA_pol_B_2: DNA polymerase type B, organellar and viral; InterPro: IPR004868 This entry is found in DNA polymerase type B proteins Back     alignment and domain information
>cd00145 POLBc DNA polymerase type-B family catalytic domain Back     alignment and domain information
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain Back     alignment and domain information
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain Back     alignment and domain information
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain Back     alignment and domain information
>cd05531 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain Back     alignment and domain information
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain Back     alignment and domain information
>cd05536 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain Back     alignment and domain information
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain Back     alignment and domain information
>cd05538 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain Back     alignment and domain information
>PHA03036 DNA polymerase; Provisional Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>PF00136 DNA_pol_B: DNA polymerase family B Several related DNA polymerases were too dissimilar to be included Back     alignment and domain information
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain Back     alignment and domain information
>PHA02735 putative DNA polymerase type B; Provisional Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed 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 ?
Query168
3iay_A 919 Ternary Complex Of Dna Polymerase Delta Length = 91 8e-33
2gv9_A 1193 Crystal Structure Of The Herpes Simplex Virus Type 7e-16
4fvm_A 910 Crystal Structure Of Yeast Dna Polymerase Alpha Len 2e-11
4fyd_A 910 Crystal Structure Of Yeast Dna Polymerase Alpha Bou 2e-11
4b08_A 910 Crystal Structure Of Yeast Dna Polymerase Alpha, Se 1e-10
4fm2_A 793 Pyrococcus Abyssi B Family Dna Polymerase (Triple M 2e-09
4flt_A 793 Pyrococcus Abyssi B Family Dna Polymerase Bound To 2e-09
1qht_A 775 Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon 5e-08
1wns_A 774 Crystal Structure Of Family B Dna Polymerase From H 8e-08
1wn7_A 774 Crystal Structure Of Archaeal Family B Dna Polymera 8e-08
4ahc_A 775 Crystal Structure Of An Evolved Replicating Dna Pol 8e-08
2xhb_A 773 Crystal Structure Of Dna Polymerase From Thermococc 1e-07
2vwj_A 773 Uracil Recognition In Archaeal Dna Polymerases Capt 1e-07
2vwk_A 773 Uracil Recognition In Archaeal Dna Polymerases Capt 1e-07
1tgo_A 773 Thermostable B Type Dna Polymerase From Thermococcu 1e-07
1d5a_A 733 Crystal Structure Of An Archaebacterial Dna Polymer 2e-07
1qqc_A 773 Crystal Structure Of An Archaebacterial Dna Polymer 2e-07
2jgu_A 775 Crystal Structure Of Dna-directed Dna Polymerase Le 2e-07
3a2f_A 775 Crystal Structure Of Pyrococcus Furiosus Dna Polyme 4e-07
1s5j_A 847 Insight In Dna Replication: The Crystal Structure O 2e-04
3k5l_A 786 Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp 3e-04
1q8i_A 783 Crystal Structure Of Escherichia Coli Dna Polymeras 4e-04
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta Length = 919 Back     alignment and structure 
Iteration: 1

 Score =  135 bits (341), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 65/113 (57%), Positives = 83/113 (73%), Gaps = 1/113 (0%)
Query: 49  IIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTI 108
           +IP       +DQ+EGATVIEP +GYY  PIATLDF+SLYPSIMMAHNLCYTTL    T+
Sbjct: 508 VIPNMQSQASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATV 567
Query: 109 TKLELTPDQ-YSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
            +L L  D+ Y  TP G++F+ +  R+G+LP IL+ L+SARK+AK DL+ E D
Sbjct: 568 ERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKD 620
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna Polymerase Length = 1193 Back     alignment and structure
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Length = 910 Back     alignment and structure
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To Dna/rna And Dgtp Length = 910 Back     alignment and structure
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha, Selenomethionine Protein Length = 910 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|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A Dsdna, In Edition Mode Length = 793 Back     alignment and structure
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon Length = 775 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|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase Length = 775 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|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus Gorgonarius 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|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok Length = 773 Back     alignment and structure
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase Length = 775 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|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna Polymerase B1 From The Archaeon Sulfolobus Solfataricus Length = 847 Back     alignment and structure
>pdb|3K5L|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp Lt(0, 3) Ternary Complex Length = 786 Back     alignment and structure
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii Length = 783 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 1e-46
3iay_A919 DNA polymerase delta catalytic subunit; protein-DN 4e-09
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 3e-40
1qht_A775 Protein (DNA polymerase); archaea, hyperthermostab 9e-09
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 6e-38
3k59_A786 POL II, DNA polymerase II; protein-DNA complex, DN 2e-06
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 2e-35
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 2e-08
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 7e-35
1s5j_A847 DNA polymerase I; replication, disulfide bonds, tr 3e-07
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 1e-07
>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 =  161 bits (408), Expect = 1e-46
 Identities = 65/124 (52%), Positives = 86/124 (69%), Gaps = 1/124 (0%)

Query: 45  QKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLT 104
           + + +IP       +DQ+EGATVIEP +GYY  PIATLDF+SLYPSIMMAHNLCYTTL  
Sbjct: 504 EIDTVIPNMQSQASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCN 563

Query: 105 PQTITKLELTPD-QYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELT 163
             T+ +L L  D  Y  TP G++F+ +  R+G+LP IL+ L+SARK+AK DL+ E D   
Sbjct: 564 KATVERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFK 623

Query: 164 QVLY 167
           + + 
Sbjct: 624 RDVL 627
>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
>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
>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
>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
>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
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* Length = 1193 Back     alignment and structure
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query168
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 100.0
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 99.96
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 99.96
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 99.95
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 99.94
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 99.94
2py5_A 575 DNA polymerase; protein-DNA complex, replication, 98.3
3k59_A786 POL II, DNA polymerase II; protein-DNA complex, DN 95.15
3iay_A919 DNA polymerase delta catalytic subunit; protein-DN 94.98
1qht_A775 Protein (DNA polymerase); archaea, hyperthermostab 94.25
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 91.88
3qex_A903 DNA polymerase, GP43; difluorotoluene nucleoside; 91.28
1s5j_A847 DNA polymerase I; replication, disulfide bonds, tr 91.02
>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=1.2e-35  Score=280.38  Aligned_cols=165  Identities=43%  Similarity=0.701  Sum_probs=130.0

Q ss_pred             ccccchhhhhhhhhccC----cHHHHHHHHHH---HHHHHhccCC--------CccccccceeeeeCCCCCCCcccCccE
Q psy12450          2 LRHVTWRDGLETVRRDN----SPLVANMINTC---LQKLLINRDP--------DGAVTQKNFIIPTYHGGQGEDQFEGAT   66 (168)
Q Consensus         2 ~~~~~~~~~~~~~r~~~----c~Lv~~i~~~~---L~~lli~r~~--------~~A~~~~~~liP~~~~~~~~~~y~Gg~   66 (168)
                      |++|.++|...+.++..    .+....+-..+   +..++ .|..        .++++++|+++|++......++|+||+
T Consensus       447 L~~Y~~~Da~l~~~L~~kl~~l~~~~elArl~Gi~~~~vl-~rG~qi~ves~Llr~a~~~~~ilP~~~~~~~~~~y~Gg~  525 (919)
T 3iay_A          447 LAVYCLKDAYLPLRLMEKLMALVNYTEMARVTGVPFSYLL-ARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGAT  525 (919)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHCCCHHHHH-HSCHHHHHHHHHHHHHHHTTEECBCCCCCCCSSCCCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHcCCCHHHhh-cccchHHHHHHHHHHHhhCCeeCCCcccccccccCCCCE
Confidence            45677777777777633    22222332222   33332 2221        267899999999986445568899999


Q ss_pred             eecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCC-CCceeeCCCceEEeecCCCCcchHHHHHHHH
Q psy12450         67 VIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELT-PDQYSKTPCGNFFLKSSLRKGLLPEILENLL  145 (168)
Q Consensus        67 VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~-~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll  145 (168)
                      |++|++|+|++||++|||+|||||||++|||||||++++.+.++.++. .+++..+|+|.+|++++.++||+|++|++|+
T Consensus       526 V~eP~~G~y~~pV~~lDF~SLYPSIi~~~Nlc~~Tl~~~~~~~~~~~~~~~~~~~~p~g~~f~~~~~~~gilp~~l~~ll  605 (919)
T 3iay_A          526 VIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELI  605 (919)
T ss_dssp             BCCCCCEEECSCEEEEEETTHHHHHHHHTTCSGGGEECHHHHHHTTCCBTTTEEECTTSCEEECTTTCCCHHHHHHHHHH
T ss_pred             EecCCCCceeccEEEEEecccchHHHHhcCcCcccccccchhhhcCCCCCcceeeCCCCcEEeccCCCCCchHHHHHHHH
Confidence            999999999999999999999999999999999999987643334433 3488899999999998889999999999999


Q ss_pred             HHHHHHHHHhccCCChhhhhcc
Q psy12450        146 SARKQAKNDLKKETDELTQVLY  167 (168)
Q Consensus       146 ~~R~~~K~~mk~~~Dp~~k~~l  167 (168)
                      +.|+++|++||+++||+++++|
T Consensus       606 ~~R~~~K~~mk~~~d~~~~~~l  627 (919)
T 3iay_A          606 SARKRAKKDLRDEKDPFKRDVL  627 (919)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHH
T ss_pred             HHHHHHHHHHhhcCChHHHHHH
Confidence            9999999999999999988765
>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
>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
>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
>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
>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
>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
>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
>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
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* 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
>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

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 ?
Query 168
d1ih7a2 528 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacte 4e-29
d1q8ia2 394 e.8.1.1 (A:390-783) Family B DNA polymerase {Esche 8e-28
d1tgoa2 426 e.8.1.1 (A:348-773) Family B DNA polymerase {Archa 2e-27
d1s5ja2 415 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfo 1e-23
d2py5a2 388 e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacterio 7e-09
>d1ih7a2 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacteriophage RB69 [TaxId: 12353]} Length = 528 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Bacteriophage RB69 [TaxId: 12353]

 Score =  109 bits (272), Expect = 4e-29
 Identities = 32/124 (25%), Positives = 51/124 (41%), Gaps = 12/124 (9%)

Query: 46  KNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTP 105
           +N +IP          + GA V EP    Y   + + D +SLYPSI+   N+   T+   
Sbjct: 1   QNKVIPQ-GRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGT 58

Query: 106 QTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKK 157
             +  L        E   D YS +P G  + K   R G++P  +  + + RK+ K  +  
Sbjct: 59  FKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLA 116

Query: 158 ETDE 161
               
Sbjct: 117 AQRN 120
>d1q8ia2 e.8.1.1 (A:390-783) Family B DNA polymerase {Escherichia coli [TaxId: 562]} Length = 394 Back     information, alignment and structure
>d1tgoa2 e.8.1.1 (A:348-773) Family B DNA polymerase {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Length = 426 Back     information, alignment and structure
>d1s5ja2 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfolobus solfataricus [TaxId: 2287]} Length = 415 Back     information, alignment and structure
>d2py5a2 e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Length = 388 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 ?
Query168
d1tgoa2 426 Family B DNA polymerase {Archaeon Thermococcus gor 99.97
d1ih7a2 528 Family B DNA polymerase {Bacteriophage RB69 [TaxId 99.95
d1s5ja2 415 Family B DNA polymerase {Sulfolobus solfataricus [ 99.94
d1q8ia2 394 Family B DNA polymerase {Escherichia coli [TaxId: 99.93
d2py5a2 388 phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 98.63
d1q8ia2394 Family B DNA polymerase {Escherichia coli [TaxId: 88.81
d1tgoa2426 Family B DNA polymerase {Archaeon Thermococcus gor 86.88
d1s5ja2415 Family B DNA polymerase {Sulfolobus solfataricus [ 81.94
d1ih7a2528 Family B DNA polymerase {Bacteriophage RB69 [TaxId 81.58
>d1tgoa2 e.8.1.1 (A:348-773) Family B DNA polymerase {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: DNA polymerase I
domain: Family B DNA polymerase
species: Archaeon Thermococcus gorgonarius [TaxId: 71997]

Probab=99.97  E-value=4.3e-32  Score=235.17  Aligned_cols=116  Identities=30%  Similarity=0.552  Sum_probs=99.4

Q ss_pred             ccccccceeeeeCCCC----CCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCC
Q psy12450         41 GAVTQKNFIIPTYHGG----QGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPD  116 (168)
Q Consensus        41 ~A~~~~~~liP~~~~~----~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~  116 (168)
                      +.++++|+++|+....    ...++|+||+|++|++|+|++ |++|||+|||||||++|||||||+++..+        +
T Consensus        12 ~~~~~~~~~~p~~~~~~~~~~~~~~y~Gg~V~~p~~G~~~~-v~~lDf~SLYPsii~~~Ni~p~T~~~~~~--------~   82 (426)
T d1tgoa2          12 RKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC--------E   82 (426)
T ss_dssp             HHHHHTTBCCCCCCCHHHHHHCCCCCCCCCEECCCCSEEEE-EEEEEESSHHHHHHHHTTCSTTTBTCTTC--------S
T ss_pred             HHHHHCCEEeccCCccccccccccCcCCceEccCCCCcCCC-eEEEEccchhHHHHHHhCCChhhcCCCCc--------c
Confidence            4588899999997421    245689999999999999986 99999999999999999999999988764        2


Q ss_pred             ceeeC-CCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450        117 QYSKT-PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVLY  167 (168)
Q Consensus       117 ~~~~~-p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l  167 (168)
                      ++... +.|++|.+  +++||+|++|++|++.|+++|++||+.+|++++++|
T Consensus        83 ~~~~~~~~g~~~~~--~~~Gilp~~l~~l~~~R~~~K~~~k~~~~~~~~~~~  132 (426)
T d1tgoa2          83 EYDVAPQVGHKFCK--DFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLL  132 (426)
T ss_dssp             SEEECTTTCCEEEC--SSCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             ccccCCCCCceEec--cCCCchHHHHHHHHHHHHHhhhhhhhccchHHHHHH
Confidence            34444 46788987  489999999999999999999999999999988764
>d1ih7a2 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacteriophage RB69 [TaxId: 12353]} Back     information, alignment and structure
>d1s5ja2 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1q8ia2 e.8.1.1 (A:390-783) Family B DNA polymerase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2py5a2 e.8.1.1 (A:188-575) phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 10756]} Back     information, alignment and structure
>d1q8ia2 e.8.1.1 (A:390-783) Family B DNA polymerase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tgoa2 e.8.1.1 (A:348-773) Family B DNA polymerase {Archaeon Thermococcus gorgonarius [TaxId: 71997]} Back     information, alignment and structure
>d1s5ja2 e.8.1.1 (A:450-864) Family B DNA polymerase {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1ih7a2 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacteriophage RB69 [TaxId: 12353]} Back     information, alignment and structure