Psyllid ID: psy12449

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 (MEMSAT_SVM) ?
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--
MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
cccHHHHHHHHHccccHHHHHHHccHHHHHHHHcHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEcccHHHHHHcccccc
cHHHHHHHHHHHHcccccHHHHHcccEEEEEEEccccccccccEccccccHEHHccccccccccHHHEcccccccHHHHHHHHHHHHHHHHHHHHHcccccc
MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISansvygftgaqvgklpcqlwtqcqtcqgslheqvictsrdcpifyMRKKVQIELISQDQIIQRFGTIAW
mvkfgtkelkeamtldefkkKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
***************DEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTI**
********************KVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFG****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW
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 ?
Query102 2.2.26 [Sep-21-2011]
O547471103 DNA polymerase delta cata yes N/A 0.470 0.043 0.75 5e-18
P283401107 DNA polymerase delta cata yes N/A 0.470 0.043 0.75 6e-18
P972831103 DNA polymerase delta cata N/A N/A 0.470 0.043 0.75 6e-18
P524311105 DNA polymerase delta cata yes N/A 0.470 0.043 0.75 6e-18
P283391106 DNA polymerase delta cata yes N/A 0.470 0.043 0.729 2e-17
P543581092 DNA polymerase delta cata yes N/A 0.509 0.047 0.596 1e-15
Q54N971104 DNA polymerase delta cata yes N/A 0.5 0.046 0.557 6e-14
P303161086 DNA polymerase delta cata yes N/A 0.588 0.055 0.523 1e-13
Q9LRE61105 DNA polymerase delta cata yes N/A 0.441 0.040 0.595 1e-12
Q9LVN71095 DNA polymerase delta cata yes N/A 0.441 0.041 0.595 4e-12
>sp|O54747|DPOD1_RAT DNA polymerase delta catalytic subunit OS=Rattus norvegicus GN=Pold1 PE=2 SV=1 Back     alignment and function desciption
 Score = 89.4 bits (220), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 36/48 (75%), Positives = 43/48 (89%)

Query: 51   QLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFG 98
            +LWTQCQ CQGSLHE VICTSRDCPIFYMRKKV+ +L  Q++++QRFG
Sbjct: 1049 RLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQERLLQRFG 1096
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.
Rattus norvegicus (taxid: 10116)
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|P97283|DPOD1_MESAU DNA polymerase delta catalytic subunit OS=Mesocricetus auratus GN=POLD1 PE=2 SV=1 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|P28339|DPOD1_BOVIN DNA polymerase delta catalytic subunit OS=Bos taurus GN=POLD1 PE=1 SV=1 Back     alignment and function description
>sp|P54358|DPOD1_DROME DNA polymerase delta catalytic subunit OS=Drosophila melanogaster GN=DNApol-delta PE=2 SV=2 Back     alignment and function description
>sp|Q54N97|DPOD1_DICDI DNA polymerase delta catalytic subunit OS=Dictyostelium discoideum GN=pold1 PE=3 SV=1 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
>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

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 ?
Query102
324120708 994 DNA polymerase delta catalytic subunit [ 0.519 0.053 0.773 4e-21
324120726 1030 DNA polymerase delta catalytic subunit [ 0.519 0.051 0.735 6e-21
324120710 992 DNA polymerase delta catalytic subunit [ 0.519 0.053 0.754 9e-21
324120706 1088 DNA polymerase delta catalytic subunit [ 0.519 0.048 0.754 1e-20
324120712 1092 DNA polymerase delta catalytic subunit [ 0.5 0.046 0.754 2e-20
324120734 1091 DNA polymerase delta catalytic subunit [ 0.509 0.047 0.788 4e-20
324120724 999 DNA polymerase delta catalytic subunit [ 0.519 0.053 0.735 4e-20
324120730 1033 DNA polymerase delta catalytic subunit [ 0.5 0.049 0.735 5e-20
324120716 1089 DNA polymerase delta catalytic subunit [ 0.509 0.047 0.75 1e-19
324120738 1091 DNA polymerase delta catalytic subunit [ 0.509 0.047 0.769 1e-19
>gi|324120708|dbj|BAJ78745.1| DNA polymerase delta catalytic subunit [Galloisiana yuasai] Back     alignment and taxonomy information
 Score =  105 bits (262), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 41/53 (77%), Positives = 49/53 (92%)

Query: 50  CQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW 102
           C+LWTQCQ CQGSLHE+V+CTSRDCPIFYMRKKVQI+L+SQD+ I+RFG + W
Sbjct: 942 CRLWTQCQRCQGSLHEEVLCTSRDCPIFYMRKKVQIDLVSQDKAIKRFGNVIW 994

Source: Galloisiana yuasai

Species: Galloisiana yuasai

Genus: Galloisiana

Family: Grylloblattidae

Order: Grylloblattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120726|dbj|BAJ78754.1| DNA polymerase delta catalytic subunit [Tenodera aridifolia] Back     alignment and taxonomy information
>gi|324120710|dbj|BAJ78746.1| DNA polymerase delta catalytic subunit [Karoophasma biedouwense] Back     alignment and taxonomy information
>gi|324120706|dbj|BAJ78744.1| DNA polymerase delta catalytic subunit [Aposthonia japonica] Back     alignment and taxonomy information
>gi|324120712|dbj|BAJ78747.1| DNA polymerase delta catalytic subunit [Nomadacris japonica] Back     alignment and taxonomy information
>gi|324120734|dbj|BAJ78758.1| DNA polymerase delta catalytic subunit [Gynaikothrips ficorum] Back     alignment and taxonomy information
>gi|324120724|dbj|BAJ78753.1| DNA polymerase delta catalytic subunit [Zorotypus sp. 154-1] Back     alignment and taxonomy information
>gi|324120730|dbj|BAJ78756.1| DNA polymerase delta catalytic subunit [Reticulitermes speratus] Back     alignment and taxonomy information
>gi|324120716|dbj|BAJ78749.1| DNA polymerase delta catalytic subunit [Teleogryllus emma] Back     alignment and taxonomy information
>gi|324120738|dbj|BAJ78760.1| DNA polymerase delta catalytic subunit [Anacanthocoris striicornis] 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 ?
Query102
ZFIN|ZDB-GENE-060429-11105 pold1 "polymerase (DNA directe 0.470 0.043 0.729 1.7e-30
MGI|MGI:977411105 Pold1 "polymerase (DNA directe 0.470 0.043 0.75 2.4e-29
UNIPROTKB|P283401107 POLD1 "DNA polymerase delta ca 0.470 0.043 0.75 3.1e-29
UNIPROTKB|F1RH321107 POLD1 "DNA polymerase" [Sus sc 0.470 0.043 0.75 3.1e-29
RGD|6218391103 Pold1 "polymerase (DNA directe 0.470 0.043 0.75 8e-29
UNIPROTKB|O547471103 Pold1 "DNA polymerase delta ca 0.470 0.043 0.75 8e-29
FB|FBgn02636001092 DNApol-delta "DNA-polymerase-d 0.509 0.047 0.596 1.1e-28
UNIPROTKB|P283391106 POLD1 "DNA polymerase delta ca 0.470 0.043 0.729 1.7e-28
UNIPROTKB|E2R5W51107 POLD1 "DNA polymerase" [Canis 0.470 0.043 0.729 7.4e-28
DICTYBASE|DDB_G02853811104 polD1 "DNA polymerase delta su 0.5 0.046 0.557 2.3e-26
ZFIN|ZDB-GENE-060429-1 pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 207 (77.9 bits), Expect = 1.7e-30, Sum P(2) = 1.7e-30
 Identities = 35/48 (72%), Positives = 42/48 (87%)

Query:    51 QLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFG 98
             +LWTQCQ CQGSLHE V+CTSRDCPIFYMRKKVQ +L  Q++++ RFG
Sbjct:  1057 RLWTQCQRCQGSLHEDVLCTSRDCPIFYMRKKVQKDLDDQEKLVSRFG 1104
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
MGI|MGI:97741 Pold1 "polymerase (DNA directed), delta 1, catalytic subunit" [Mus musculus (taxid:10090)] 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|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
UNIPROTKB|O54747 Pold1 "DNA polymerase delta catalytic subunit" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
FB|FBgn0263600 DNApol-delta "DNA-polymerase-delta" [Drosophila melanogaster (taxid:7227)] 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
DICTYBASE|DDB_G0285381 polD1 "DNA polymerase delta subunit 1" [Dictyostelium discoideum (taxid:44689)] 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, ., 70.68750.45090.0422yesN/A
Q9LRE6DPOD1_ORYSJ2, ., 7, ., 7, ., 70.59570.44110.0407yesN/A
P52431DPOD1_MOUSE2, ., 7, ., 7, ., 70.750.47050.0434yesN/A
P54358DPOD1_DROME2, ., 7, ., 7, ., 70.59610.50980.0476yesN/A
P90829DPOD1_CAEEL2, ., 7, ., 7, ., 70.71730.45090.0425yesN/A
Q9LVN7DPOD1_ARATH2, ., 7, ., 7, ., 70.59570.44110.0410yesN/A
O54747DPOD1_RAT2, ., 7, ., 7, ., 70.750.47050.0435yesN/A
P28339DPOD1_BOVIN2, ., 7, ., 7, ., 70.72910.47050.0433yesN/A
Q54N97DPOD1_DICDI2, ., 7, ., 7, ., 70.55760.50.0461yesN/A
P28340DPOD1_HUMAN2, ., 7, ., 7, ., 70.750.47050.0433yesN/A
P30316DPOD_SCHPO2, ., 7, ., 7, ., 70.52380.58820.0552yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

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 ?
Query102
PTZ001661054 PTZ00166, PTZ00166, DNA polymerase delta catalytic 1e-25
cd05533 393 cd05533, POLBc_delta, DNA polymerase type-B delta 5e-25
PTZ00166 1054 PTZ00166, PTZ00166, DNA polymerase delta catalytic 4e-19
pfam1426073 pfam14260, zf-C4pol, C4-type zinc-finger of DNA po 5e-15
pfam00136 458 pfam00136, DNA_pol_B, DNA polymerase family B 6e-15
smart00486474 smart00486, POLBc, DNA polymerase type-B family 4e-11
COG0417 792 COG0417, PolB, DNA polymerase elongation subunit ( 4e-10
cd00145 323 cd00145, POLBc, DNA polymerase type-B family catal 1e-08
cd05534 451 cd05534, POLBc_zeta, DNA polymerase type-B zeta su 2e-07
cd05536 371 cd05536, POLBc_B3, DNA polymerase type-B B3 subfam 4e-05
cd05532 400 cd05532, POLBc_alpha, DNA polymerase type-B alpha 5e-05
TIGR00592 1172 TIGR00592, pol2, DNA polymerase (pol2) 1e-04
cd07219 382 cd07219, Pat_PNPLA1, Patatin-like phospholipase do 4e-04
>gnl|CDD|240301 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information 
 Score = 98.6 bits (246), Expect = 1e-25
 Identities = 33/48 (68%), Positives = 40/48 (83%)

Query: 51   QLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFG 98
            QLWTQCQ CQGSLH++VICT+RDCPIFY RKKVQ +L    +++ RFG
Sbjct: 1004 QLWTQCQRCQGSLHQEVICTNRDCPIFYRRKKVQKDLAELQELLSRFG 1051

Length = 1054
>gnl|CDD|99916 cd05533, POLBc_delta, DNA polymerase type-B delta 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|222632 pfam14260, zf-C4pol, C4-type zinc-finger of DNA polymerase delta 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|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 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|233037 TIGR00592, pol2, DNA polymerase (pol2) Back     alignment and domain information
>gnl|CDD|132858 cd07219, Pat_PNPLA1, Patatin-like phospholipase domain containing protein 1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 102
KOG0969|consensus1066 99.61
PTZ001661054 DNA polymerase delta catalytic subunit; Provisiona 99.53
PF1426073 zf-C4pol: C4-type zinc-finger of DNA polymerase de 99.44
KOG0969|consensus 1066 99.21
PTZ00166 1054 DNA polymerase delta catalytic subunit; Provisiona 98.94
cd05533 393 POLBc_delta DNA polymerase type-B delta subfamily 98.9
cd00145 323 POLBc DNA polymerase type-B family catalytic domai 98.86
cd05538 347 POLBc_Pol_II_B DNA polymerase type-II B subfamily 98.86
PHA03036 1004 DNA polymerase; Provisional 98.85
cd05532 400 POLBc_alpha DNA polymerase type-B alpha subfamily 98.82
cd05534 451 POLBc_zeta DNA polymerase type-B zeta subfamily ca 98.78
TIGR00592 1172 pol2 DNA polymerase (pol2). This family is based o 98.72
cd05536 371 POLBc_B3 DNA polymerase type-B B3 subfamily cataly 98.71
PRK05761 787 DNA polymerase I; Reviewed 98.69
cd05530 372 POLBc_B1 DNA polymerase type-B B1 subfamily cataly 98.65
COG0417 792 PolB DNA polymerase elongation subunit (family B) 98.64
PHA03334 1545 putative DNA polymerase catalytic subunit; Provisi 98.6
PF00136 466 DNA_pol_B: DNA polymerase family B Several related 98.42
KOG0968|consensus1488 98.39
PHA02528 881 43 DNA polymerase; Provisional 98.34
cd05531 352 POLBc_B2 DNA polymerase type-B B2 subfamily cataly 98.22
cd05535 621 POLBc_epsilon DNA polymerase type-B epsilon subfam 98.07
KOG0970|consensus 1429 98.04
KOG0968|consensus 1488 98.03
smart00486471 POLBc DNA polymerase type-B family. DNA polymerase 98.03
PRK05762 786 DNA polymerase II; Reviewed 97.82
cd05537 371 POLBc_Pol_II DNA polymerase type-II subfamily cata 97.81
PHA02523 391 43B DNA polymerase subunit B; Provisional 97.46
KOG1798|consensus 2173 94.38
>KOG0969|consensus Back     alignment and domain information 
Probab=99.61  E-value=1.2e-16  Score=138.91  Aligned_cols=67  Identities=54%  Similarity=1.042  Sum_probs=63.3

Q ss_pred             ccccccchhh---ccchhHHHhhccccccccCCccccccCCCcccceehhhhhhhhhHHHHHHhhCcCCC
Q psy12449         36 SVYGFTGAQV---GKLPCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGTIAW  102 (102)
Q Consensus        36 s~Yg~~ga~~---Er~~~~l~~~Cq~C~gs~~~~v~C~s~DCPVfY~R~K~~~~l~~~~~~l~~~~~~~~  102 (102)
                      .+|.....++   |..|+++|++||+|+|+.|++|+|+|+||||||+|.|++++|++..+++++||...|
T Consensus       997 ~lyqk~v~~~~~lee~fsrlWt~Cqrcqgs~h~~vic~~rdCpifymr~kv~keL~~~~~~l~rf~~~~w 1066 (1066)
T KOG0969|consen  997 ELYQKQVSHVNDLEEKFSRLWTECQRCQGSLHEEVICSNRDCPIFYMRQKVRKELQEQVDRLRRFGSFAW 1066 (1066)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhheeccCCCCchhhHHHHHHHHHHHHHHHHhccccCC
Confidence            5777777777   899999999999999999999999999999999999999999999999999999998

>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta Back     alignment and domain information
>KOG0969|consensus Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain Back     alignment and domain information
>cd00145 POLBc DNA polymerase type-B family 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
>cd05532 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain Back     alignment and domain information
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain Back     alignment and domain information
>TIGR00592 pol2 DNA polymerase (pol2) 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
>cd05530 POLBc_B1 DNA polymerase type-B B1 subfamily 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
>PHA03334 putative DNA polymerase catalytic subunit; Provisional 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
>KOG0968|consensus Back     alignment and domain information
>PHA02528 43 DNA polymerase; Provisional 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
>KOG0970|consensus Back     alignment and domain information
>KOG0968|consensus Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>cd05537 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain Back     alignment and domain information
>PHA02523 43B DNA polymerase subunit B; Provisional Back     alignment and domain information
>KOG1798|consensus 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 ?
Query102
3iay_A 919 Ternary Complex Of Dna Polymerase Delta Length = 91 2e-12
2gv9_A 1193 Crystal Structure Of The Herpes Simplex Virus Type 5e-05
2xhb_A 773 Crystal Structure Of Dna Polymerase From Thermococc 3e-04
2vwk_A 773 Uracil Recognition In Archaeal Dna Polymerases Capt 3e-04
2vwj_A 773 Uracil Recognition In Archaeal Dna Polymerases Capt 3e-04
1tgo_A 773 Thermostable B Type Dna Polymerase From Thermococcu 3e-04
1qht_A 775 Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon 3e-04
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta Length = 919 Back     alignment and structure 
Iteration: 1

 Score = 67.4 bits (163), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/100 (41%), Positives = 54/100 (54%), Gaps = 5/100 (5%)
Query: 3   KFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQGS 62
           K   K+L++    D FK+ VL+GRQLALKISANSVYGFTGA VGKLPC   +   T  G 
Sbjct: 609 KRAKKDLRDEK--DPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGR 666
Query: 63  ---LHEQVICTSRDCPIFYMRKKVQIELISQDQIIQRFGT 99
              L  +     + C     +    +     D ++ +FGT
Sbjct: 667 TMILKTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMVKFGT 706
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna Polymerase Length = 1193 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|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|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By X-Ray Crystallography 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|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon Length = 775 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 ?
Query102
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 4e-17
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 2e-16
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 2e-15
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 3e-15
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 3e-12
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B* Length = 1193 Back     alignment and structure
 Score = 73.7 bits (180), Expect = 4e-17
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 7   KELKEAM-TLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQG 61
           K+++  +      +  +LD +Q A+K+  NSVYGFTG Q G LPC       T  G
Sbjct: 744 KQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIG 799
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query102
3iay_A 919 DNA polymerase delta catalytic subunit; protein-DN 98.84
1qht_A 775 Protein (DNA polymerase); archaea, hyperthermostab 98.79
2gv9_A 1193 DNA polymerase; polymerase alpha fold, transferase 98.75
1s5j_A 847 DNA polymerase I; replication, disulfide bonds, tr 98.59
3qex_A 903 DNA polymerase, GP43; difluorotoluene nucleoside; 98.46
3k59_A 786 POL II, DNA polymerase II; protein-DNA complex, DN 97.59
>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=98.84  E-value=3.1e-10  Score=99.00  Aligned_cols=47  Identities=66%  Similarity=0.942  Sum_probs=42.4

Q ss_pred             hhhHHHHHHHcC--cCHHHHhhcchhhhhhhccccccccccchhhccch
Q psy12449          3 KFGTKELKEAMT--LDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLP   49 (102)
Q Consensus         3 ~~~r~~~k~~~~--~~~~~~~~ld~~q~a~K~~~ns~Yg~~ga~~Er~~   49 (102)
                      -..|+++|+.|+  .||.++.+||++|+|||+.|||+||++|+...+.+
T Consensus       605 l~~R~~~K~~mk~~~d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~~r~~  653 (919)
T 3iay_A          605 ISARKRAKKDLRDEKDPFKRDVLNGRQLALKISANSVYGFTGATVGKLP  653 (919)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSSCC
T ss_pred             HHHHHHHHHHHhhcCChHHHHHHHHHHHhhcccccccccccccccCccC
Confidence            357999999997  79999999999999999999999999999886665
>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
>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
>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
>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

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 102
d1ih7a2 528 e.8.1.1 (A:376-903) Family B DNA polymerase {Bacte 3e-06
>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 = 41.9 bits (97), Expect = 3e-06
 Identities = 15/69 (21%), Positives = 24/69 (34%)

Query: 1   MVKFGTKELKEAMTLDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLPCQLWTQCQTCQ 60
           + K   K L E +   +  +      Q+  K+  NS+YG  G    +          T  
Sbjct: 155 IKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTF 214

Query: 61  GSLHEQVIC 69
           G +  Q I 
Sbjct: 215 GQMALQWIE 223

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query102
d1tgoa2 426 Family B DNA polymerase {Archaeon Thermococcus gor 98.64
d1s5ja2 415 Family B DNA polymerase {Sulfolobus solfataricus [ 98.33
d1ih7a2 528 Family B DNA polymerase {Bacteriophage RB69 [TaxId 98.05
d1q8ia2 394 Family B DNA polymerase {Escherichia coli [TaxId: 97.69
d2py5a2 388 phi29 DNA polymerase {Bacteriophage phi-29 [TaxId: 95.2
>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=98.64  E-value=1.6e-09  Score=84.68  Aligned_cols=46  Identities=39%  Similarity=0.534  Sum_probs=41.2

Q ss_pred             hhHHHHHHHcC--cCHHHHhhcchhhhhhhccccccccccchhhccch
Q psy12449          4 FGTKELKEAMT--LDEFKKKVLDGRQLALKISANSVYGFTGAQVGKLP   49 (102)
Q Consensus         4 ~~r~~~k~~~~--~~~~~~~~ld~~q~a~K~~~ns~Yg~~ga~~Er~~   49 (102)
                      ..|+.+|+.|+  .|+.++.+||.+|+|+|+.+||+||+.|+..-+.+
T Consensus       111 ~~R~~~K~~~k~~~~~~~~~~~d~~Q~a~Ki~~NS~YG~~G~~~~~~~  158 (426)
T d1tgoa2         111 EERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWY  158 (426)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHTTHHHHHHCTTCTTC
T ss_pred             HHHHHhhhhhhhccchHHHHHHHHHHHHHHHhhhHHHHHHhccchhhh
Confidence            46888888887  89999999999999999999999999999985554
>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
>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