Psyllid ID: psy14489

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-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280----
MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLMH
ccccEEEEEccHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccccccccccccccccccHHHHHcHHHHHHHHHHHcccEEEEccccHHHHHHHHHHHHHHHcccEEEEEcccccccccccccEEEEEccccccHHHHHHHHcccccHHHHHHHHcccccccccccccccHHHHHHHHHHHccHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccHHHHcc
ccccEEEEcccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHccccEEEEEEEcccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccEEEEccccHHHHHHHHHHHHHHHcccEEEEEEccHHHHHHccccEEEEEccccccHHHHHHHccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHEEEEccccccccccccHHHHccccccHHHHHHHHHHccHHHHHHHcc
MQNTLLLVDGSSCIYrafyalpdirnidnfpvgaLYGTIKMLRKLYKNYRATYIACIFdakgknfrnilypsykatrkkmpynLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALinnnkihdrttiisrfgvspekIVDYFSLIgdmsdnlpgvkkigpKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIktdcdltknivsipeslilqpkDEKLLMQLFNKYKLNKLNFLMH
MQNTLLLVDGSSCIYRAFYAlpdirnidnfPVGALYGTIKMLRKLYKNYRATYIACifdakgknfrNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIalinnnkihdrttiisrfgvsPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSipeslilqpkDEKLLMQLFNKYklnklnflmh
MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLEniinnannikgvigknLRFALNWLPklkkiltiktDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLMH
****LLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFL**
*QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNF*M*
MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLMH
*QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLMH
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MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTxxxxxxxxxxxxxxxxxxxxxKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLMH
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 ?
Query284 2.2.26 [Sep-21-2011]
P00582 928 DNA polymerase I OS=Esche N/A N/A 0.947 0.289 0.439 6e-57
P43741 930 DNA polymerase I OS=Haemo yes N/A 0.975 0.297 0.428 4e-56
Q9F173 928 DNA polymerase I OS=Salmo yes N/A 0.957 0.293 0.433 7e-56
O67550289 5'-3' exonuclease OS=Aqui yes N/A 0.876 0.861 0.395 4e-47
Q9HT80 913 DNA polymerase I OS=Pseud yes N/A 0.904 0.281 0.409 2e-45
Q9RLB6 921 DNA polymerase I OS=Ricke N/A N/A 0.764 0.235 0.414 3e-44
Q9RLA0 872 DNA polymerase I OS=Ricke yes N/A 0.904 0.294 0.386 1e-43
Q92GB7 875 DNA polymerase I OS=Ricke yes N/A 0.760 0.246 0.403 2e-43
Q1RH76 871 DNA polymerase I OS=Ricke yes N/A 0.764 0.249 0.395 5e-43
O05949 867 DNA polymerase I OS=Ricke yes N/A 0.764 0.250 0.409 7e-43
>sp|P00582|DPO1_ECOLI DNA polymerase I OS=Escherichia coli (strain K12) GN=polA PE=1 SV=1 Back     alignment and function desciption
 Score =  221 bits (562), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 127/289 (43%), Positives = 175/289 (60%), Gaps = 20/289 (6%)

Query: 2   QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
           QN L+LVDGSS +YRA++A P + N    P GA+YG + MLR L   Y+ T+ A +FDAK
Sbjct: 6   QNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAK 65

Query: 62  GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
           GK FR+ L+  YK+ R  MP +L  QI  +H MVKA+G P+L + GVEADDVIGTLA++A
Sbjct: 66  GKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREA 125

Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSPEKIVDYFSLIG 179
             K    V+IST DKDMAQLV+  I LIN   N I     +++++GV PE I+D+ +L+G
Sbjct: 126 -EKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMG 184

Query: 180 DMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLK---- 235
           D SDN+PGV  +G KTA  LL     L+ +      I G+   + R A     KL+    
Sbjct: 185 DSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGL---SFRGAKTMAAKLEQNKE 241

Query: 236 ------KILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNK 278
                 ++ TIKTD +L    ++  +  + QP  E+LL  LF KY+  +
Sbjct: 242 VAYLSYQLATIKTDVELE---LTCEQLEVQQPAAEELL-GLFKKYEFKR 286
In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.
Escherichia coli (strain K12) (taxid: 83333)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 7
>sp|P43741|DPO1_HAEIN DNA polymerase I OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|Q9F173|DPO1_SALTY DNA polymerase I OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=polA PE=3 SV=2 Back     alignment and function description
>sp|O67550|EX53_AQUAE 5'-3' exonuclease OS=Aquifex aeolicus (strain VF5) GN=aq_1628 PE=3 SV=1 Back     alignment and function description
>sp|Q9HT80|DPO1_PSEAE DNA polymerase I OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|Q9RLB6|DPO1_RICHE DNA polymerase I OS=Rickettsia helvetica GN=polA PE=3 SV=1 Back     alignment and function description
>sp|Q9RLA0|DPO1_RICTY DNA polymerase I OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|Q92GB7|DPO1_RICCN DNA polymerase I OS=Rickettsia conorii (strain ATCC VR-613 / Malish 7) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|Q1RH76|DPO1_RICBR DNA polymerase I OS=Rickettsia bellii (strain RML369-C) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|O05949|DPO1_RICPR DNA polymerase I OS=Rickettsia prowazekii (strain Madrid E) GN=polA PE=3 SV=1 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 ?
Query284
399018904293 5'-3' exonuclease (including N-terminal 0.961 0.931 0.586 2e-93
300309795 920 DNA polymerase I protein [Herbaspirillum 0.968 0.298 0.579 6e-93
409409025 920 DNA polymerase I protein [Herbaspirillum 0.968 0.298 0.579 9e-93
340785918 1165 DNA polymerase I [Collimonas fungivorans 0.968 0.236 0.571 1e-92
329912725 914 DNA polymerase I [Oxalobacteraceae bacte 0.961 0.298 0.568 3e-91
398835989 917 DNA polymerase I [Herbaspirillum sp. YR5 0.968 0.299 0.579 4e-91
395760857 916 DNA polymerase I [Janthinobacterium livi 0.978 0.303 0.544 1e-89
445494914 924 DNA polymerase I [Janthinobacterium sp. 0.978 0.300 0.540 1e-88
427402574 944 DNA polymerase I [Massilia timonae CCUG 0.978 0.294 0.537 1e-87
300703485 960 DNA polymerase i (pol i) [Ralstonia sola 0.954 0.282 0.549 4e-85
>gi|399018904|ref|ZP_10721060.1| 5'-3' exonuclease (including N-terminal domain of PolI), partial [Herbaspirillum sp. CF444] gi|398099216|gb|EJL89485.1| 5'-3' exonuclease (including N-terminal domain of PolI), partial [Herbaspirillum sp. CF444] Back     alignment and taxonomy information
 Score =  348 bits (892), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 162/276 (58%), Positives = 213/276 (77%), Gaps = 3/276 (1%)

Query: 1   MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDA 60
           MQ TLLLVDGSS +YRAF+ALPD+RN +  P GALYG I MLR+L  +Y A+YIACIFDA
Sbjct: 1   MQKTLLLVDGSSYLYRAFHALPDMRNAEGAPTGALYGIINMLRRLRNDYPASYIACIFDA 60

Query: 61  KGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120
           KGK FR+ LY  YKATRK MP +L LQI  IH  V+A+GWPIL+++G+EADDVIGTL  +
Sbjct: 61  KGKTFRDDLYTEYKATRKSMPEDLALQIEPIHAAVRALGWPILMVEGIEADDVIGTLGVR 120

Query: 121 AVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSPEKIVDYFSLI 178
           A  +  LK I+ST DKDMAQLV++ + L+N  +N+  DR  +I++FGV PE+IVDY SLI
Sbjct: 121 AA-EEGLKTIVSTGDKDMAQLVNDHVTLVNTMSNETMDRAGVIAKFGVPPERIVDYLSLI 179

Query: 179 GDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKIL 238
           GD  DN+PGV+K GPKTAVK L QY+SL+ ++ NA+ I GV+G+NLR AL WLP+ + ++
Sbjct: 180 GDTVDNVPGVEKCGPKTAVKWLTQYDSLDGVMANADKITGVVGENLRKALPWLPQARVLV 239

Query: 239 TIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKY 274
           T+KTDCDL+ ++ +I +SL +QP D   L ++F +Y
Sbjct: 240 TVKTDCDLSAHMSTILDSLTVQPNDNVALREIFTRY 275

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria
>gi|300309795|ref|YP_003773887.1| DNA polymerase I protein [Herbaspirillum seropedicae SmR1] gi|300072580|gb|ADJ61979.1| DNA polymerase I protein [Herbaspirillum seropedicae SmR1] Back     alignment and taxonomy information
>gi|409409025|ref|ZP_11257460.1| DNA polymerase I protein [Herbaspirillum sp. GW103] gi|386432347|gb|EIJ45175.1| DNA polymerase I protein [Herbaspirillum sp. GW103] Back     alignment and taxonomy information
>gi|340785918|ref|YP_004751383.1| DNA polymerase I [Collimonas fungivorans Ter331] gi|340551185|gb|AEK60560.1| DNA polymerase I [Collimonas fungivorans Ter331] Back     alignment and taxonomy information
>gi|329912725|ref|ZP_08275792.1| DNA polymerase I [Oxalobacteraceae bacterium IMCC9480] gi|327545555|gb|EGF30735.1| DNA polymerase I [Oxalobacteraceae bacterium IMCC9480] Back     alignment and taxonomy information
>gi|398835989|ref|ZP_10593339.1| DNA polymerase I [Herbaspirillum sp. YR522] gi|398214311|gb|EJN00893.1| DNA polymerase I [Herbaspirillum sp. YR522] Back     alignment and taxonomy information
>gi|395760857|ref|ZP_10441526.1| DNA polymerase I [Janthinobacterium lividum PAMC 25724] Back     alignment and taxonomy information
>gi|445494914|ref|ZP_21461958.1| DNA polymerase I [Janthinobacterium sp. HH01] gi|444791075|gb|ELX12622.1| DNA polymerase I [Janthinobacterium sp. HH01] Back     alignment and taxonomy information
>gi|427402574|ref|ZP_18893571.1| DNA polymerase I [Massilia timonae CCUG 45783] gi|425718380|gb|EKU81327.1| DNA polymerase I [Massilia timonae CCUG 45783] Back     alignment and taxonomy information
>gi|300703485|ref|YP_003745087.1| DNA polymerase i (pol i) [Ralstonia solanacearum CFBP2957] gi|299071148|emb|CBJ42461.1| DNA polymerase I (POL I) [Ralstonia solanacearum CFBP2957] 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 ?
Query284
TIGR_CMR|CBU_1795 902 CBU_1795 "DNA polymerase I" [C 0.936 0.294 0.432 1.5e-55
TIGR_CMR|CPS_4978 936 CPS_4978 "DNA polymerase I" [C 0.961 0.291 0.421 9e-50
UNIPROTKB|Q9KVN3 934 VC_0108 "DNA polymerase I" [Vi 0.950 0.289 0.409 4e-49
TIGR_CMR|VC_0108 934 VC_0108 "DNA polymerase I" [Vi 0.950 0.289 0.409 4e-49
UNIPROTKB|P00582 928 polA [Escherichia coli K-12 (t 0.968 0.296 0.424 1.1e-48
TIGR_CMR|SO_4669 922 SO_4669 "DNA polymerase I" [Sh 0.714 0.220 0.480 4.4e-47
UNIPROTKB|Q48PV5 921 polA "DNA polymerase I" [Pseud 0.697 0.214 0.492 3e-45
TIGR_CMR|GSU_0541 891 GSU_0541 "DNA polymerase I" [G 0.947 0.301 0.365 2.2e-42
TIGR_CMR|ECH_0080 944 ECH_0080 "DNA polymerase I" [E 0.707 0.212 0.394 2.4e-37
UNIPROTKB|Q0C2B4 929 polA "DNA polymerase I" [Hypho 0.711 0.217 0.428 2.1e-36
TIGR_CMR|CBU_1795 CBU_1795 "DNA polymerase I" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
 Score = 578 (208.5 bits), Expect = 1.5e-55, P = 1.5e-55
 Identities = 118/273 (43%), Positives = 174/273 (63%)

Query:     5 LLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKN 64
             L+L+DGSS ++RA+YALP + N    P GA+YG I MLRKL   Y+  Y+A +FD KGK 
Sbjct:    16 LILIDGSSYLFRAYYALPPLTNRKGQPTGAMYGVINMLRKLMVEYQPDYVAVVFDPKGKT 75

Query:    65 FRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTK 124
             FR+ LY +YKA R +MP  L  QI  + ++++A+G+P++I +G EADDVI TLAK+A  K
Sbjct:    76 FRHDLYHTYKANRIEMPNELRSQIKPLFEIIRALGFPLIIKEGYEADDVIATLAKKAKEK 135

Query:   125 HNLKVIISTNDKDMAQLVSNKIALINN--NKIHDRTTIISRFGVSPEKIVDYFSLIGDMS 182
               + V++ST DKD+AQ+V+  + L+N   +++ +   ++ +FGV PEKI+DY +L GD +
Sbjct:   136 -GMPVLVSTGDKDLAQIVNEHVTLVNTMTDRLLNSKGVLEKFGVPPEKIIDYLTLTGDTT 194

Query:   183 DNLPGVKKIGPKTAVKLLNQYNSLEXXXXXXXXXXXXXXXXLRFALNWLPXXXXXXXXXX 242
             DN+PGV K+GPKTAVK L+QY+S+E                LR  ++ LP          
Sbjct:   195 DNIPGVPKVGPKTAVKWLSQYDSVENLIKHANEIKGKVGENLRACIDDLPLMRRLVTVIS 254

Query:   243 DCDLTKNIVSIPESLILQPKDEKLLMQLFNKYK 275
             D  L +N    P  LI   K+ + L++LF +Y+
Sbjct:   255 DLPLEEN----PTDLIQTEKNREKLIELFTEYE 283
GO:0003887 "DNA-directed DNA polymerase activity" evidence=ISS
GO:0006260 "DNA replication" evidence=ISS
GO:0008409 "5'-3' exonuclease activity" evidence=ISS
TIGR_CMR|CPS_4978 CPS_4978 "DNA polymerase I" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KVN3 VC_0108 "DNA polymerase I" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0108 VC_0108 "DNA polymerase I" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
UNIPROTKB|P00582 polA [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TIGR_CMR|SO_4669 SO_4669 "DNA polymerase I" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
UNIPROTKB|Q48PV5 polA "DNA polymerase I" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_0541 GSU_0541 "DNA polymerase I" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0080 ECH_0080 "DNA polymerase I" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
UNIPROTKB|Q0C2B4 polA "DNA polymerase I" [Hyphomonas neptunium ATCC 15444 (taxid:228405)] 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) ?
P57506EX53_BUCAI3, ., 1, ., 1, 1, ., -0.39820.78160.7762yesN/A
Q9PQ75EX53_UREPA3, ., 1, ., 1, 1, ., -0.31920.94710.9307yesN/A
P75403EX53_MYCPN3, ., 1, ., 1, 1, ., -0.31220.94710.9243yesN/A
O67550EX53_AQUAE3, ., 1, ., 1, 1, ., -0.39520.87670.8615yesN/A
Q49406EX53_MYCGE3, ., 1, ., 1, 1, ., -0.34380.94710.9243yesN/A
Q89AD1EX53_BUCBP3, ., 1, ., 1, 1, ., -0.43290.87320.8211yesN/A
Q8K9D0EX53_BUCAP3, ., 1, ., 1, 1, ., -0.36170.95420.9442yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.1.11LOW CONFIDENCE prediction!
4th Layer2.7.7.7LOW 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 ?
Query284
PRK05755 880 PRK05755, PRK05755, DNA polymerase I; Provisional 1e-115
smart00475259 smart00475, 53EXOc, 5'-3' exonuclease 4e-92
TIGR00593 887 TIGR00593, pola, DNA polymerase I 2e-80
COG0258310 COG0258, Exo, 5'-3' exonuclease (including N-termi 3e-76
cd09859174 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc 2e-67
PRK14976281 PRK14976, PRK14976, 5'-3' exonuclease; Provisional 7e-66
pfam02739169 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-term 2e-59
PRK09482256 PRK09482, PRK09482, flap endonuclease-like protein 5e-41
cd0989873 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon 1e-24
pfam01367100 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin 3e-24
cd00008160 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' 4e-19
cd09860170 cd09860, PIN_T4-like, PIN domain of bacteriophage 7e-13
cd0008071 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain 4e-11
smart0027936 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol 1e-10
PHA00439286 PHA00439, PHA00439, exonuclease 8e-10
PHA02567304 PHA02567, rnh, RnaseH; Provisional 2e-07
cd0990173 cd09901, H3TH_FEN1-like, H3TH domains of Flap endo 9e-06
cd0990770 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonu 1e-05
PRK03980292 PRK03980, PRK03980, flap endonuclease-1; Provision 2e-05
cd0989768 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap 2e-05
TIGR03674338 TIGR03674, fen_arch, flap structure-specific endon 4e-05
PTZ00217393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 9e-05
cd09853163 cd09853, PIN_StructSpec-5'-nucleases, PIN domains 1e-04
cd0990365 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu 0.002
cd0990052 cd09900, H3TH_XPG-like, H3TH domains of Flap endon 0.003
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional Back     alignment and domain information 
 Score =  352 bits (906), Expect = e-115
 Identities = 133/284 (46%), Positives = 181/284 (63%), Gaps = 11/284 (3%)

Query: 2   QNTLLLVDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDA 60
             TLLL+DGSS ++RAFYAL P +RN D  P GA+YG + ML KL K  + T++A  FDA
Sbjct: 1   MKTLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDA 60

Query: 61  KGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120
           KGK FR+ LYP YKA R  MP +L  QI LI ++++A+G P+L ++G EADDVIGTLAKQ
Sbjct: 61  KGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQ 120

Query: 121 AVTKHNLKVIISTNDKDMAQLVSNKIALIN-----NNKIHDRTTIISRFGVSPEKIVDYF 175
           A      +V+I T DKD+ QLV + + L++      N+  D   ++ ++GV+PE+I+DY 
Sbjct: 121 A-EAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQIIDYL 179

Query: 176 SLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLK 235
           +L+GD SDN+PGV  IG KTA KLL +Y SLE +  N + IKG   + LR         +
Sbjct: 180 ALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAFLSR 239

Query: 236 KILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
           K+ TIKTD  L  +     E L LQP D + L+ LF + +   L
Sbjct: 240 KLATIKTDVPLEVD----LEDLELQPPDREKLIALFKELEFKSL 279

Length = 880
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease Back     alignment and domain information
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I Back     alignment and domain information
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs Back     alignment and domain information
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional Back     alignment and domain information
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal resolvase-like domain Back     alignment and domain information
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional Back     alignment and domain information
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs Back     alignment and domain information
>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold Back     alignment and domain information
>gnl|CDD|189019 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs Back     alignment and domain information
>gnl|CDD|189030 cd09860, PIN_T4-like, PIN domain of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs Back     alignment and domain information
>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination Back     alignment and domain information
>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease Back     alignment and domain information
>gnl|CDD|222882 PHA02567, rnh, RnaseH; Provisional Back     alignment and domain information
>gnl|CDD|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1 Back     alignment and domain information
>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs Back     alignment and domain information
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases Back     alignment and domain information
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease Back     alignment and domain information
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|189023 cd09853, PIN_StructSpec-5'-nucleases, PIN domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination Back     alignment and domain information
>gnl|CDD|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs Back     alignment and domain information
>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 284
PRK14976281 5'-3' exonuclease; Provisional 100.0
PRK09482256 flap endonuclease-like protein; Provisional 100.0
smart00475259 53EXOc 5'-3' exonuclease. 100.0
TIGR00593 887 pola DNA polymerase I. This family is based on the 100.0
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 100.0
PRK05755 880 DNA polymerase I; Provisional 100.0
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain 100.0
PHA00439286 exonuclease 100.0
PHA02567304 rnh RnaseH; Provisional 100.0
PTZ00217393 flap endonuclease-1; Provisional 100.0
PF02739169 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv 100.0
TIGR03674338 fen_arch flap structure-specific endonuclease. End 100.0
cd00128316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 100.0
PRK03980292 flap endonuclease-1; Provisional 100.0
PF01367101 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold 99.96
KOG2519|consensus 449 99.93
KOG2518|consensus 556 99.87
TIGR006001034 rad2 DNA excision repair protein (rad2). All prote 99.86
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 99.85
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 99.65
KOG2520|consensus 815 99.53
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 99.03
PF05991166 NYN_YacP: YacP-like NYN domain; InterPro: IPR01029 98.25
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 98.08
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 97.92
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 97.85
PF12813246 XPG_I_2: XPG domain containing 97.56
COG3688173 Predicted RNA-binding protein containing a PIN dom 97.34
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 97.11
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 97.07
PF09293122 RNaseH_C: T4 RNase H, C terminal; InterPro: IPR020 96.81
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 95.63
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 95.33
PF11977155 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domai 95.04
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 94.97
cd06167149 LabA_like LabA_like proteins. A well conserved gro 94.86
PF04599425 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P 94.27
PHA03065438 Hypothetical protein; Provisional 94.14
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 94.02
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 93.74
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 93.52
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 93.5
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 93.38
PRK12766 232 50S ribosomal protein L32e; Provisional 93.33
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 93.26
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 93.1
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 93.1
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 93.07
TIGR00194574 uvrC excinuclease ABC, C subunit. This family cons 92.83
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 92.82
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 92.64
PRK14671621 uvrC excinuclease ABC subunit C; Provisional 91.89
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 91.58
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 91.27
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 91.13
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 91.07
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 90.88
PRK00558598 uvrC excinuclease ABC subunit C; Validated 90.6
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 90.17
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 89.72
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 89.18
PRK02515132 psbU photosystem II complex extrinsic protein prec 88.93
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 88.09
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 87.06
PF03159237 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: 85.49
COG0322581 UvrC Nuclease subunit of the excinuclease complex 84.9
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 84.88
PF0237187 Transposase_20: Transposase IS116/IS110/IS902 fami 84.22
cd00141 307 NT_POLXc Nucleotidyltransferase (NT) domain of fam 83.68
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 83.15
TIGR01259120 comE comEA protein. This model describes the ComEA 81.85
PF01936146 NYN: NYN domain; InterPro: IPR021139 This highly c 81.11
PF1179832 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 80.44
>PRK14976 5'-3' exonuclease; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.6e-76  Score=541.08  Aligned_cols=272  Identities=40%  Similarity=0.613  Sum_probs=261.0

Q ss_pred             CCCcEEEEecchHHHHHhccC----CCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhC
Q psy14489          1 MQNTLLLVDGSSCIYRAFYAL----PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKAT   76 (284)
Q Consensus         1 m~~~~llIDg~~l~~r~~~a~----~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~   76 (284)
                      |.++++||||++++||+||+.    +.+++++|.+|+|++||++++.++++.++|+|+++|||+++++||+++||+||+|
T Consensus         1 m~~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKan   80 (281)
T PRK14976          1 MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQG   80 (281)
T ss_pred             CCCcEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcC
Confidence            777899999999999999996    4577899999999999999999999999999999999998899999999999999


Q ss_pred             CCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--Cc--
Q psy14489         77 RKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NN--  152 (284)
Q Consensus        77 R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~~--  152 (284)
                      |+++|++|.+|++.++++++.+||+++.++|+||||+||++|+++.. .|..++|+|+|||++||++++|.+|+  +.  
T Consensus        81 R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~-~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~  159 (281)
T PRK14976         81 RKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSK-QNITVLIYSSDKDLLQLVNENTDVLLKKKGTS  159 (281)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH-CCCeEEEEeCCCCcCccCCCCeEEEEecCCCC
Confidence            99999999999999999999999999999999999999999999887 88899999999999999999999887  33  


Q ss_pred             -EeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhc
Q psy14489        153 -KIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWL  231 (284)
Q Consensus       153 -~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~  231 (284)
                       +.++.+.|.++||++|+||+|+++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|.++++++
T Consensus       160 ~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~  239 (281)
T PRK14976        160 HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKA  239 (281)
T ss_pred             cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHH
Confidence             6899999999999999999999999999999999999999999999999999999999999999888999999999999


Q ss_pred             hhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHHHHcCch
Q psy14489        232 PKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLN  277 (284)
Q Consensus       232 ~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~  277 (284)
                      ++|++|++|++|+|++.+    ++++.+.+++.+++.++|+++||+
T Consensus       240 ~~s~~L~~l~~d~~l~~~----l~~~~~~~~~~~~l~~~~~~~e~~  281 (281)
T PRK14976        240 LLSKKLATIKTDVPLDFQ----IEDIKLKKLDQPELKKIFEELELK  281 (281)
T ss_pred             HHhhhhhEEeecCCCCCC----HHHhccCCCCHHHHHHHHHHcCCC
Confidence            999999999999999998    899999999999999999999984

>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>PHA00439 exonuclease Back     alignment and domain information
>PHA02567 rnh RnaseH; Provisional Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases Back     alignment and domain information
>KOG2519|consensus Back     alignment and domain information
>KOG2518|consensus Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>KOG2520|consensus Back     alignment and domain information
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment Back     alignment and domain information
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana Back     alignment and domain information
>smart00484 XPGI Xeroderma pigmentosum G I-region Back     alignment and domain information
>smart00485 XPGN Xeroderma pigmentosum G N-region Back     alignment and domain information
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer Back     alignment and domain information
>PF12813 XPG_I_2: XPG domain containing Back     alignment and domain information
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only] Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PF09293 RNaseH_C: T4 RNase H, C terminal; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [] Back     alignment and domain information
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A Back     alignment and domain information
>cd06167 LabA_like LabA_like proteins Back     alignment and domain information
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses Back     alignment and domain information
>PHA03065 Hypothetical protein; Provisional Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ] Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains Back     alignment and domain information
>TIGR00194 uvrC excinuclease ABC, C subunit Back     alignment and domain information
>PRK14667 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14671 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function Back     alignment and domain information
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases [] 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 ?
Query284
1bgx_T 832 Taq Polymerase In Complex With Tp7, An Inhibitory F 1e-35
1taq_A 832 Structure Of Taq Dna Polymerase Length = 832 1e-35
1ut5_A291 Divalent Metal Ions (Manganese) Bound To T5 5'-Exon 8e-07
1xo1_A291 T5 5'-Exonuclease Mutant K83a Length = 291 3e-06
1exn_A290 T5 5'-Exonuclease Length = 290 4e-06
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab Length = 832 Back     alignment and structure 
Iteration: 1

 Score =  146 bits (369), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 84/207 (40%), Positives = 120/207 (57%), Gaps = 3/207 (1%)
Query: 2   QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
           +  +LLVDG    YR F+AL  +      PV A+YG  K L K  K      +  +FDAK
Sbjct: 11  KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKE-DGDAVIVVFDAK 69
Query: 62  GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
             +FR+  Y  YKA R   P +   Q+ LI ++V  +G   L + G EADDV+ +LAK+A
Sbjct: 70  APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 129
Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGD 180
             K   +V I T DKD+ QL+S++I +++    +     +  ++G+ P++  DY +L GD
Sbjct: 130 -EKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGD 188
Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLE 207
            SDNLPGVK IG KTA KLL ++ SLE
Sbjct: 189 ESDNLPGVKGIGEKTARKLLEEWGSLE 215
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase Length = 832 Back     alignment and structure
>pdb|1UT5|A Chain A, Divalent Metal Ions (Manganese) Bound To T5 5'-Exonuclease Length = 291 Back     alignment and structure
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a Length = 291 Back     alignment and structure
>pdb|1EXN|A Chain A, T5 5'-Exonuclease Length = 290 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 ?
Query284
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 1e-117
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 2e-96
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 2e-33
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-07
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 1e-07
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 1e-07
1rxw_A336 Flap structure-specific endonuclease; helical clam 2e-07
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 6e-06
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 2e-05
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 2e-05
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 2e-04
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Length = 832 Back     alignment and structure
 Score =  354 bits (912), Expect = e-117
 Identities = 94/279 (33%), Positives = 146/279 (52%), Gaps = 9/279 (3%)

Query: 2   QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
           +  +LLVDG    YR F+AL  +      PV A+YG  K L K  K      +  +FDAK
Sbjct: 11  KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALK-EDGDAVIVVFDAK 69

Query: 62  GKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQA 121
             +FR+  Y  YKA R   P +   Q+ LI ++V  +G   L + G EADDV+ +LAK+A
Sbjct: 70  APSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKA 129

Query: 122 VTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTIISRFGVSPEKIVDYFSLIGD 180
             K   +V I T DKD+ QL+S++I +++    +     +  ++G+ P++  DY +L GD
Sbjct: 130 -EKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWADYRALTGD 188

Query: 181 MSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTI 240
            SDNLPGVK IG KTA KLL ++ SLE ++ N + +K  I + +   ++ L     +  +
Sbjct: 189 ESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKLSWDLAKV 248

Query: 241 KTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKL 279
           +TD  L        +    +  D + L     + +   L
Sbjct: 249 RTDLPLE------VDFAKRREPDRERLRAFLERLEFGSL 281
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Length = 290 Back     alignment and structure
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A Length = 305 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
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A* Length = 341 Back     alignment and structure
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Length = 379 Back     alignment and structure
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Length = 336 Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Length = 346 Back     alignment and structure
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Length = 326 Back     alignment and structure
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363 Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Length = 340 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query284
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 100.0
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 100.0
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 100.0
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 100.0
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 100.0
1rxw_A336 Flap structure-specific endonuclease; helical clam 100.0
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 100.0
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 100.0
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 100.0
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 100.0
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 100.0
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 96.95
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 96.57
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 96.57
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 96.37
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 96.35
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 96.25
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 96.03
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 95.88
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 95.55
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 95.34
3fqd_A 899 Protein DHP1, 5'-3' exoribonuclease 2; protein-pro 95.25
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 94.21
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 93.23
3v32_B185 Ribonuclease ZC3H12A; rossmann-like sandwich fold, 92.91
2qip_A165 Protein of unknown function VPA0982; APC85975, vib 92.31
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 92.01
4gfj_A 685 Topoisomerase V; helix-hairpin-helix, DNA repair e 91.82
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 90.33
3v33_A223 Ribonuclease ZC3H12A; rossmann-like sandwich fold, 89.49
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 88.34
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein- 87.79
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 86.64
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 85.54
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 84.99
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 84.31
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 83.94
2i5h_A205 Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s 80.74
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, trans 80.61
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 80.47
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Back     alignment and structure
Probab=100.00  E-value=3.7e-70  Score=498.79  Aligned_cols=243  Identities=22%  Similarity=0.299  Sum_probs=232.7

Q ss_pred             cEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC--
Q psy14489          4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP--   81 (284)
Q Consensus         4 ~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p--   81 (284)
                      +++||||++++||+||      +++|.|  |++||++++.++++.++|+|+++|||+++++||+++||+||+||+++|  
T Consensus        20 ~lllIDg~~llyRa~~------~~~G~p--av~Gf~~~l~~ll~~~~p~~~vvvFD~~~~tfR~~~~~~YKa~R~~~p~~   91 (290)
T 1exn_A           20 NLMIVDGTNLGFRFKH------NNSKKP--FASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQ   91 (290)
T ss_dssp             EEEEEEHHHHHHHHHH------HCSSSC--CHHHHHHHHHHHHHHTTEEEEEEECCBSCCHHHHHHCTTTTHHHHHHHHT
T ss_pred             CEEEEECcHHHHHHHh------CCCCch--HHHHHHHHHHHHHHHcCCCeEEEEEcCCCchhhhhCcHHHHcCCCCCCcc
Confidence            6999999999999998      467888  999999999999999999999999998889999999999999999999  


Q ss_pred             -----hhHHHH-HHHHHHHHHh--cCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--C
Q psy14489         82 -----YNLILQ-INLIHQMVKA--IGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--N  151 (284)
Q Consensus        82 -----~~l~~q-~~~i~~~l~~--~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~  151 (284)
                           ++|.+| ++.++++|+.  +|||++.++||||||+||+||+++.+ .|.+|+|+|+|||++||++++|++|+  +
T Consensus        92 ~~~~~e~L~~q~~~~ikell~~~~~gip~i~~~g~EADDviatLa~~~~~-~G~~v~IvS~DkDl~Qlv~~~v~v~~~~~  170 (290)
T 1exn_A           92 RTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGH-LYDHVWLISTDGDWDTLLTDKVSRFSFTT  170 (290)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHTTTSCEECCTTBCHHHHHHHHHHHHGG-GSSCEEEECSCGGGGGGCCSSEEEEETTT
T ss_pred             ccccchhHHHhhHHHHHHHHHhhCCCCcEEEECCcCHHHHHHHHHHHHHH-CCCcEEEEeCCCChhhcCCCCEEEEECCC
Confidence                 999999 9999999999  99999999999999999999999887 78899999999999999999999998  5


Q ss_pred             cEeeeHhHHHHHhCCCh-hHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhh-hhhhhccHHHhHh
Q psy14489        152 NKIHDRTTIISRFGVSP-EKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNI-KGVIGKNLRFALN  229 (284)
Q Consensus       152 ~~~~~~~~~~~~~G~~p-~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~-~~~~~~~l~~~~~  229 (284)
                      .+.++.+.+.++||++| +|++|+++|+||+|||||||||||||||.+||++|||+|+|+++++++ +++++++|.++++
T Consensus       171 ~~~~~~~~v~ek~Gv~p~~q~iD~~~L~GD~sDniPGVpGIG~KTA~kLL~~~gsle~i~~~~~~~~~~~~~~~L~~~~~  250 (290)
T 1exn_A          171 RREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEE  250 (290)
T ss_dssp             TEEECGGGHHHHHSSSSHHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSCSCCCHHHHHHHTCHH
T ss_pred             CEEEcHHHHHHHcCCCHHHHHHHHHHhcCCCcCCCCCCCcCCHhHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHH
Confidence            67899999999999999 999999999999999999999999999999999999999999999999 8899999999999


Q ss_pred             hchhhhhhhhhccccCCCCCcCCCcccccc
Q psy14489        230 WLPKLKKILTIKTDCDLTKNIVSIPESLIL  259 (284)
Q Consensus       230 ~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~  259 (284)
                      ++++||+|++|++|+|++.+    ++++++
T Consensus       251 ~~~ls~~L~~i~~d~~~~~~----~~~l~~  276 (290)
T 1exn_A          251 LLFRNLILVDLPTYCVDAIA----AVGQDV  276 (290)
T ss_dssp             HHHHHHHHHCHHHHHHHHHH----TTCHHH
T ss_pred             HHHHHHHhceeeeCCCCCCC----hhhhhh
Confidence            99999999999999998887    666654
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Back     alignment and structure
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A* Back     alignment and structure
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Back     alignment and structure
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Back     alignment and structure
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Back     alignment and structure
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Back     alignment and structure
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster} Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo domain, mRNA turnover, RRN processing, RNA binding, DNA binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A Back     alignment and structure
>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex, exonuclease, hydrolase, mRNA proces nuclease, nucleus, rRNA processing, transcription; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>3v32_B Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens} PDB: 3v34_A Back     alignment and structure
>2qip_A Protein of unknown function VPA0982; APC85975, vibrio parahaemolyticus RIMD 2210633, STR genomics, PSI-2, protein structure initiative; 1.48A {Vibrio parahaemolyticus} Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} Back     alignment and structure
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens} Back     alignment and structure
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Back     alignment and structure
>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_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 284
d1xo1a2167 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacterioph 2e-30
d1cmwa2164 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain o 3e-28
d1tfra2169 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 3e-25
d1cmwa1116 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain o 6e-16
d1ul1x1140 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu 8e-15
d1xo1a1105 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph 3e-13
d1rxwa1105 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu 2e-09
d1a77a1108 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu 6e-08
d1b43a1120 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu 2e-04
>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 167 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score =  110 bits (275), Expect = 2e-30
 Identities = 32/175 (18%), Positives = 61/175 (34%), Gaps = 21/175 (12%)

Query: 2   QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61
           +  L++VDG++  +R  +         N         +  ++ L K+Y A     + D  
Sbjct: 1   RRNLMIVDGTNLGFRFKHN--------NSKKPFASSYVSTIQSLAKSYSARTTIVLGDKG 52

Query: 62  GKNFRNILYPSYKATRKKMPYNL-----ILQINLIHQMVKAIG-----WPILIIKGVEAD 111
              FR    P Y   R +           L       +  A       +P   I+GVEAD
Sbjct: 53  KSVFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEAD 112

Query: 112 DVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRF 164
           D+   + K         V + + D D   L+++K++  +    + +    +    
Sbjct: 113 DMAAYIVKLIGHL-YDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRDMYEHH 166
>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Length = 164 Back     information, alignment and structure
>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]} Length = 169 Back     information, alignment and structure
>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Length = 116 Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140 Back     information, alignment and structure
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105 Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105 Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108 Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120 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 ?
Query284
d1cmwa2164 5' to 3' exonuclease domain of DNA polymerase Taq 100.0
d1xo1a2167 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 100.0
d1tfra2169 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 100.0
d1cmwa1116 5' to 3' exonuclease domain of DNA polymerase Taq 99.97
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 99.88
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.85
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.79
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.79
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.64
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.63
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.61
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.6
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.59
d1tfra1123 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 98.03
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 97.61
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 97.35
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 97.19
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 96.89
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 96.66
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 96.14
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 95.7
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 94.84
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 94.8
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 94.59
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 94.32
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 93.85
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 93.38
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 93.01
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 90.62
d2csba355 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 88.97
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 88.49
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 88.02
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 82.58
>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=1.2e-43  Score=297.71  Aligned_cols=162  Identities=36%  Similarity=0.547  Sum_probs=154.2

Q ss_pred             CCcEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC
Q psy14489          2 QNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP   81 (284)
Q Consensus         2 ~~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p   81 (284)
                      +++++||||++++||+|||.+.+.+++|.++++++||++++.++++. .+++++++||+++++||++++|+||+||+++|
T Consensus         2 ~~~~lLIDg~~l~~R~~~a~~~~~~~~g~~~~~i~gf~~~l~~~~~~-~~~~~~v~~d~~~~~~R~~l~p~YK~~R~~~~   80 (164)
T d1cmwa2           2 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKE-DGDAVIVVFDAKAPSFRHEAYGGYKAGRAPTP   80 (164)
T ss_dssp             CEEEEEEETTHHHHHHHTSSTTCBCTTSCBCHHHHHHHHHHHHHHHH-CCSEEEEECCCSSSCTTGGGGSTTTSCCCCCC
T ss_pred             CCeEEEEeChHHHHHHHHcCCcccCCCCCeeHHHHHHHHHHHHHHhc-CCceEEEEEecccccchhhhhhhhhhccccCc
Confidence            35899999999999999999988899999999999999999999976 57899999999889999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe-CcEeeeHhHH
Q psy14489         82 YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN-NNKIHDRTTI  160 (284)
Q Consensus        82 ~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~-~~~~~~~~~~  160 (284)
                      +++..|++.+.+++..+|++++..+|+||||+||++|++..+ .+.+|+|+|+|||++||++++|.+|+ +.+.++.++|
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~~~~~~EADDvIa~la~~~~~-~~~~v~IvS~DkD~~QLv~~~v~i~~~~~~~~~~~~v  159 (164)
T d1cmwa2          81 EDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEK-EGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWL  159 (164)
T ss_dssp             SSHHHHHHHHHHHHHHTTCEEECCTTSCHHHHHHHHHHHHHH-TTEEEEEECSSGGGGGSCCSSCEEECSSSSEECHHHH
T ss_pred             hhHHHHHHHHHHHHhhcCceEEEecCcchHHHHHHHHHHhcc-ccceEEEecCCCChHHheeCCEEEEeCCCEEECHHHH
Confidence            999999999999999999999999999999999999999888 78899999999999999999999999 7788999999


Q ss_pred             HHHhC
Q psy14489        161 ISRFG  165 (284)
Q Consensus       161 ~~~~G  165 (284)
                      .|+||
T Consensus       160 ~ek~G  164 (164)
T d1cmwa2         160 WEKYG  164 (164)
T ss_dssp             HHSSC
T ss_pred             HhhhC
Confidence            99998
>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Back     information, alignment and structure
>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1tfra1 a.60.7.1 (A:183-305) T4 RNase H {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure