Citrus Sinensis ID: 020010

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-------290-------300-------310-------320-------330--
MMINTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMTKTEVVEAKTTVISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
cccccEEEcccccEEEccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccHHHHHHHHHHHHHccccEEEEEEcccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHccccEEEEcccccccccccccEEEEEEcccccccEEccHHHHHHHHccccccHHHHHHHcccccccccccccccccccHHHHHHHHHHHccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHccc
ccccEEEEEccccccccccccccccccccEEccccccccEEEEEEEEEEEEEcHcccccEEEccccEEEEcccccccccccEEEEcccHHHHHcccccHHHHHHHHHHHHHHHHcccEEEEEEEccccccccHHHHHHHHcccccccHHHHHHHHHcccccccccHHHHHHHHHHcccEEEEccccHHHHHHHHHHHHHHcccEEEEEEccHHHHHHccccEEEEEccccccEEEEccHHHHHHHHcccHHHHHHHHHHHccccccccccEEEcccccHHHHHHHHHHcccHHHHHHHcccHcccccHHHHHHHHHHHHHHHHHHHHHHccc
MMINTIEVAVPihvnikpclpinpfksisiikpgkrmtkTEVVEAKTTVIsgsfdrtvgrqllgkadfcgnglektkskkrvffldvnplcyegsrpslqSFGRWLSLFFdqvshadpviavfdgeggtehrrQLLPSYKAHRRKFLRQLTASqrfsrgrvgrsHQFILDVLgkcnvpvvkiegheADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVqlvmplqdldrwsfYTLKHYIAqyncdphselslrcivgddvdgvpgiqhvvpgfGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
MMINTIEVAVPIhvnikpclpinpfksisiikpgkrmtkTEVVeakttvisgsfdrtvgrqLLGKADfcgnglektkskkrvFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLtasqrfsrgrvgrSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALtkhadylrrnYEVLALRRY
MMINTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMtktevveakttvISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
**INTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMTKTEVVEAKTTVISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLAL***
****TIEVAVPIHVNIKPCLPINP**********************************************************FFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAV**********ALTKHADYLRRNYEVLALRR*
MMINTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMTKTEVVEAKTTVISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
*MINTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMTKTEVVEAKTTVISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MMINTIEVAVPIHVNIKPCLPINPFKSISIIKPGKRMTKTEVVEAKTTVISGSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY
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 ?
Query332 2.2.26 [Sep-21-2011]
O67550289 5'-3' exonuclease OS=Aqui yes no 0.578 0.664 0.325 3e-23
Q04957 877 DNA polymerase I OS=Bacil N/A no 0.581 0.220 0.297 3e-18
P46835 911 DNA polymerase I OS=Mycob yes no 0.551 0.200 0.333 5e-18
P0A550 904 DNA polymerase I OS=Mycob yes no 0.578 0.212 0.325 6e-18
P0A551 904 DNA polymerase I OS=Mycob yes no 0.578 0.212 0.325 6e-18
Q92GB7 875 DNA polymerase I OS=Ricke yes no 0.569 0.216 0.297 4e-17
P52028 834 DNA polymerase I, thermos yes no 0.557 0.221 0.319 4e-17
Q9RLB6 921 DNA polymerase I OS=Ricke N/A no 0.569 0.205 0.301 4e-17
P52026 876 DNA polymerase I OS=Geoba N/A no 0.542 0.205 0.292 5e-17
Q9S1G2 1016 DNA polymerase I OS=Rhizo yes no 0.560 0.183 0.304 6e-17
>sp|O67550|EX53_AQUAE 5'-3' exonuclease OS=Aquifex aeolicus (strain VF5) GN=aq_1628 PE=3 SV=1 Back     alignment and function desciption
 Score =  109 bits (272), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 70/215 (32%), Positives = 110/215 (51%), Gaps = 23/215 (10%)

Query: 84  FLDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADP--VIAVFDGEGGTEHRRQLLPSYKA 141
           F  + PL      P+   +G +L + F  +    P  ++ VFD    T+ R ++   YK 
Sbjct: 17  FFALPPLSTSKGFPTNAIYG-FLRMLFSLIKKERPQYLVVVFDAPAKTK-REKIYADYKK 74

Query: 142 HRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQK 201
            R K    L                 I ++L    +P++++ G+EADDVIA L  +  QK
Sbjct: 75  QRPKAPDPLKVQ-----------IPVIKEILKLAGIPLLELPGYEADDVIAYLAEKFSQK 123

Query: 202 GYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVG 261
           G++  + SPDKD  QL+SE+V ++ P+ D      +T +  I ++  +P        +VG
Sbjct: 124 GFKVKIYSPDKDLLQLVSENVLVINPMND----EVFTKERVIKKFGVEPQKIPDYLALVG 179

Query: 262 DDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLL 296
           D VD VPGI+    G G KTA+ +LKK+GS+EN+L
Sbjct: 180 DKVDNVPGIE----GVGPKTAINILKKYGSVENIL 210
5'-3' exonuclease acting preferentially on double-stranded DNA.
Aquifex aeolicus (strain VF5) (taxid: 224324)
EC: 3EC: .EC: 1EC: .EC: 1EC: 1EC: .EC: -
>sp|Q04957|DPO1_BACCA DNA polymerase I OS=Bacillus caldotenax GN=polA PE=1 SV=1 Back     alignment and function description
>sp|P46835|DPO1_MYCLE DNA polymerase I OS=Mycobacterium leprae (strain TN) GN=polA PE=3 SV=1 Back     alignment and function description
>sp|P0A550|DPO1_MYCTU DNA polymerase I OS=Mycobacterium tuberculosis GN=polA PE=3 SV=1 Back     alignment and function description
>sp|P0A551|DPO1_MYCBO DNA polymerase I OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) 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|P52028|DPO1T_THET8 DNA polymerase I, thermostable OS=Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) GN=polA PE=3 SV=2 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|P52026|DPO1_GEOSE DNA polymerase I OS=Geobacillus stearothermophilus GN=polA PE=1 SV=2 Back     alignment and function description
>sp|Q9S1G2|DPO1_RHILE DNA polymerase I OS=Rhizobium leguminosarum 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 ?
Query332
255571798411 DNA polymerase I, putative [Ricinus comm 0.993 0.802 0.662 1e-128
118483131375 unknown [Populus trichocarpa] 0.981 0.869 0.668 1e-127
224135903368 predicted protein [Populus trichocarpa] 0.960 0.866 0.670 1e-124
356561357368 PREDICTED: 5'-3' exonuclease-like [Glyci 0.954 0.861 0.651 1e-122
296081158380 unnamed protein product [Vitis vinifera] 0.957 0.836 0.688 1e-119
225460702366 PREDICTED: 5'-3' exonuclease-like [Vitis 0.900 0.816 0.707 1e-118
449441764377 PREDICTED: 5'-3' exonuclease-like [Cucum 0.915 0.806 0.637 1e-114
186488278347 5'-3' exonuclease-like protein [Arabidop 0.813 0.778 0.698 1e-110
297851880335 At1g34380 [Arabidopsis lyrata subsp. lyr 0.870 0.862 0.644 1e-107
12323855343 DNA polymerase type I, putative; 54894-5 0.801 0.775 0.688 1e-107
>gi|255571798|ref|XP_002526842.1| DNA polymerase I, putative [Ricinus communis] gi|223533846|gb|EEF35577.1| DNA polymerase I, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 236/356 (66%), Positives = 274/356 (76%), Gaps = 26/356 (7%)

Query: 2   MINTIEVAVPIHVNIKPCLPINPFKSISI--IKPGKRMTKT---------EVVEAKTTVI 50
           M+ TIEVA+P HV   P L  +P   IS   ++  KR TKT           V A TT  
Sbjct: 1   MLKTIEVAMPTHVQPNPSLSPSPCLPISTRNLRNKKRKTKTAYTYKTWKITAVSACTTSS 60

Query: 51  S-----GSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFFLDVNPLCYEGSRPSLQSFGRW 105
           S     G F++TVG Q L   +   +G E+++ KKRVFFLDVNPLCY GS PSL SFG W
Sbjct: 61  SSSSSSGPFNQTVGGQFLSGCEISRSGEERSRRKKRVFFLDVNPLCYAGSTPSLHSFGYW 120

Query: 106 LSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRG------ 159
           +SLFF QVS +DPVIAV DGEGG EHRR+LLPSYKAHRRKFL Q +A Q+FS+G      
Sbjct: 121 ISLFFSQVSLSDPVIAVLDGEGGHEHRRKLLPSYKAHRRKFLSQSSAFQKFSKGQSSAFK 180

Query: 160 RVGRSH----QFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFK 215
           R  + H    + ++DVL KCNVPVVKIEGHEADDV+ATLV QVLQ+GY+AVVASPDKDFK
Sbjct: 181 RSSKGHVTRSEVVMDVLTKCNVPVVKIEGHEADDVVATLVEQVLQRGYKAVVASPDKDFK 240

Query: 216 QLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVP 275
           QL+SEDVQ+V+P+ +L RWSFYT+KHYIAQYNCDP S+LSLRCI+GD+VDG+PGIQ V P
Sbjct: 241 QLVSEDVQIVLPVTELKRWSFYTIKHYIAQYNCDPCSDLSLRCIMGDEVDGIPGIQSVAP 300

Query: 276 GFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRR 331
           GFGRKTALKLLKKHGSLENLLN AA+RTVG+ YAQ+ALTKHADYLRRNYEVLALRR
Sbjct: 301 GFGRKTALKLLKKHGSLENLLNVAAIRTVGKPYAQDALTKHADYLRRNYEVLALRR 356

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|118483131|gb|ABK93472.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224135903|ref|XP_002327332.1| predicted protein [Populus trichocarpa] gi|222835702|gb|EEE74137.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356561357|ref|XP_003548949.1| PREDICTED: 5'-3' exonuclease-like [Glycine max] Back     alignment and taxonomy information
>gi|296081158|emb|CBI18184.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225460702|ref|XP_002267236.1| PREDICTED: 5'-3' exonuclease-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|449441764|ref|XP_004138652.1| PREDICTED: 5'-3' exonuclease-like [Cucumis sativus] gi|449490129|ref|XP_004158516.1| PREDICTED: 5'-3' exonuclease-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|186488278|ref|NP_001117409.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|51536440|gb|AAU05458.1| At1g34380 [Arabidopsis thaliana] gi|52421279|gb|AAU45209.1| At1g34380 [Arabidopsis thaliana] gi|332193586|gb|AEE31707.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297851880|ref|XP_002893821.1| At1g34380 [Arabidopsis lyrata subsp. lyrata] gi|297339663|gb|EFH70080.1| At1g34380 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|12323855|gb|AAG51896.1|AC023913_4 DNA polymerase type I, putative; 54894-56354 [Arabidopsis thaliana] 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 ?
Query332
TAIR|locus:2036293347 AT1G34380 [Arabidopsis thalian 0.894 0.855 0.651 6.9e-102
UNIPROTKB|P0A550 904 polA "DNA polymerase I" [Mycob 0.581 0.213 0.331 1.1e-17
TIGR_CMR|GSU_0541 891 GSU_0541 "DNA polymerase I" [G 0.536 0.199 0.315 4.3e-17
TIGR_CMR|BA_4831 877 BA_4831 "DNA polymerase I" [Ba 0.484 0.183 0.316 2.7e-16
TIGR_CMR|SO_4669 922 SO_4669 "DNA polymerase I" [Sh 0.590 0.212 0.300 7.8e-16
UNIPROTKB|Q9KVN3 934 VC_0108 "DNA polymerase I" [Vi 0.581 0.206 0.307 2.7e-15
TIGR_CMR|VC_0108 934 VC_0108 "DNA polymerase I" [Vi 0.581 0.206 0.307 2.7e-15
UNIPROTKB|Q3ABL3 831 polA "DNA polymerase" [Carboxy 0.692 0.276 0.268 1e-14
TIGR_CMR|CHY_1650 831 CHY_1650 "DNA polymerase I" [C 0.692 0.276 0.268 1e-14
TIGR_CMR|CBU_1795 902 CBU_1795 "DNA polymerase I" [C 0.490 0.180 0.338 2.7e-14
TAIR|locus:2036293 AT1G34380 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1010 (360.6 bits), Expect = 6.9e-102, P = 6.9e-102
 Identities = 200/307 (65%), Positives = 236/307 (76%)

Query:    26 KSISIIKPGKRMXXXXXXXXXXXXIS-GSFDRTVGRQLLGKADFCGNGLEKTKSKKRVFF 84
             KSI   +P +               S  +F RT   Q+L K   CGN  E  K  KRVFF
Sbjct:    18 KSIDKTQPSRTKWVSSSSSSFSSHSSVETFHRTGNVQVLQKDVLCGNNEEIRKKNKRVFF 77

Query:    85 LDVNPLCYEGSRPSLQSFGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRR 144
             LDV+PLCYEG++PS Q+FG W+SLFF QVS  DPVIAV DGE G + RR+LLPSYKAHR+
Sbjct:    78 LDVSPLCYEGNKPSSQAFGHWISLFFSQVSLTDPVIAVIDGEEGNQRRRELLPSYKAHRK 137

Query:   145 KFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYR 204
                       R+S+    R HQF+ +VL KCNVPVV+IEGHEADDV+ATL+ Q +Q+GYR
Sbjct:   138 S-----PNHGRYSK----RPHQFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAVQRGYR 188

Query:   205 AVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDV 264
             AV+ASPDKDFKQLISE+VQ+V+PL DL RWSFYTLKHY AQYNCDP S+LS RCI+GD+V
Sbjct:   189 AVIASPDKDFKQLISENVQIVIPLADLRRWSFYTLKHYHAQYNCDPQSDLSFRCIMGDEV 248

Query:   265 DGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDYAQEALTKHADYLRRNY 324
             DGVPGIQH+VP FGRKTA+KL++KHGSLE+LL+AAAVRTVGR YAQEALTK+ADYLRRNY
Sbjct:   249 DGVPGIQHMVPAFGRKTAMKLVRKHGSLESLLSAAAVRTVGRPYAQEALTKYADYLRRNY 308

Query:   325 EVLALRR 331
             +VLAL R
Sbjct:   309 QVLALNR 315
GO:0003677 "DNA binding" evidence=IEA
GO:0003824 "catalytic activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0008409 "5'-3' exonuclease activity" evidence=IEA
UNIPROTKB|P0A550 polA "DNA polymerase I" [Mycobacterium tuberculosis (taxid:1773)] 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|BA_4831 BA_4831 "DNA polymerase I" [Bacillus anthracis str. Ames (taxid:198094)] 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|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|Q3ABL3 polA "DNA polymerase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1650 CHY_1650 "DNA polymerase I" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1795 CBU_1795 "DNA polymerase I" [Coxiella burnetii RSA 493 (taxid:227377)] 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.1.11LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00031798001
SubName- Full=Chromosome chr18 scaffold_59, whole genome shotgun sequence; (380 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00032487001
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (436 aa)
 •      0.814

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query332
smart00475259 smart00475, 53EXOc, 5'-3' exonuclease 1e-37
PRK05755 880 PRK05755, PRK05755, DNA polymerase I; Provisional 3e-35
TIGR00593 887 TIGR00593, pola, DNA polymerase I 5e-33
COG0258310 COG0258, Exo, 5'-3' exonuclease (including N-termi 1e-28
cd09859174 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc 4e-26
PRK09482256 PRK09482, PRK09482, flap endonuclease-like protein 8e-20
PRK14976281 PRK14976, PRK14976, 5'-3' exonuclease; Provisional 2e-19
pfam02739169 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-term 9e-19
cd0989873 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon 9e-15
cd09860170 cd09860, PIN_T4-like, PIN domain of bacteriophage 5e-12
PHA02567304 PHA02567, rnh, RnaseH; Provisional 2e-11
PHA00439286 PHA00439, PHA00439, exonuclease 9e-11
pfam01367100 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin 1e-10
cd00008160 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' 9e-10
cd0989974 cd09899, H3TH_T4-like, H3TH domain of bacteriophag 4e-06
cd09853163 cd09853, PIN_StructSpec-5'-nucleases, PIN domains 1e-05
cd0008071 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain 2e-05
cd0989768 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap 4e-04
PRK03980292 PRK03980, PRK03980, flap endonuclease-1; Provision 9e-04
cd0990770 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonu 0.001
cd0990173 cd09901, H3TH_FEN1-like, H3TH domains of Flap endo 0.002
TIGR03674338 TIGR03674, fen_arch, flap structure-specific endon 0.002
PTZ00217393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 0.003
smart0027936 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol 0.004
cd0990365 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu 0.004
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease Back     alignment and domain information 
 Score =  135 bits (341), Expect = 1e-37
 Identities = 76/235 (32%), Positives = 117/235 (49%), Gaps = 30/235 (12%)

Query: 102 FGRWLSLFFDQVSHADPVIAVFDGEGGTEHRRQLLPSYKAHRRK----FLRQLTASQRFS 157
           F R L     +      V  VFD +G T  R +L P YKA+R K     L Q+       
Sbjct: 36  FLRMLLKLIKEEK-PTYVAVVFDAKGKT-FRHELYPEYKANRPKTPDELLEQI------- 86

Query: 158 RGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQL 217
                     I ++L    +PV+++EG+EADDVIATL  +   +GY   + S DKD  QL
Sbjct: 87  --------PLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQL 138

Query: 218 ISEDVQLVMPLQDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGF 277
           +S+ V ++ P + +  +  YT ++ I +Y   P   +  + ++GD  D +PG    VPG 
Sbjct: 139 VSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPG----VPGI 194

Query: 278 GRKTALKLLKKHGSLENLL-NAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRR 331
           G KTA KLLK+ GSLEN+L N   ++       +E L  H +  + + ++  +  
Sbjct: 195 GEKTAAKLLKEFGSLENILENLDKLKKK----LREKLLAHKEDAKLSRKLATIET 245

Length = 259
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional 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|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional 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|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|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|222882 PHA02567, rnh, RnaseH; Provisional Back     alignment and domain information
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease 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|188619 cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs 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|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|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|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional 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|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|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|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 332
PRK09482256 flap endonuclease-like protein; Provisional 100.0
smart00475259 53EXOc 5'-3' exonuclease. 100.0
PRK14976281 5'-3' exonuclease; Provisional 100.0
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 100.0
TIGR00593 887 pola DNA polymerase I. This family is based on the 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 99.89
KOG2519 449 consensus 5'-3' exonuclease [Replication, recombin 99.85
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 99.8
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.77
KOG2518 556 consensus 5'-3' exonuclease [Replication, recombin 99.74
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 99.54
KOG2520 815 consensus 5'-3' exonuclease [Replication, recombin 99.28
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 98.96
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 98.23
PF05991166 NYN_YacP: YacP-like NYN domain; InterPro: IPR01029 97.49
PF12813246 XPG_I_2: XPG domain containing 97.03
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 96.42
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 96.28
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 95.88
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 94.31
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 94.07
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 94.05
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 94.0
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 93.56
PF11977155 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domai 93.39
COG3688173 Predicted RNA-binding protein containing a PIN dom 93.36
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 93.28
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 92.54
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 92.37
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 91.8
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 91.69
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 91.2
TIGR00194574 uvrC excinuclease ABC, C subunit. This family cons 90.93
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 90.75
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 89.68
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 89.2
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 88.57
PRK02515132 psbU photosystem II complex extrinsic protein prec 88.12
PRK14671621 uvrC excinuclease ABC subunit C; Provisional 88.06
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 87.86
PHA03065 438 Hypothetical protein; Provisional 87.84
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 87.14
PRK00558598 uvrC excinuclease ABC subunit C; Validated 87.13
PRK12766 232 50S ribosomal protein L32e; Provisional 87.05
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 86.99
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 86.51
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 86.2
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 84.53
PF03159237 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: 84.38
PF09293122 RNaseH_C: T4 RNase H, C terminal; InterPro: IPR020 83.74
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 82.54
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 81.82
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 80.08
>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.2e-62  Score=460.11  Aligned_cols=230  Identities=25%  Similarity=0.380  Sum_probs=206.2

Q ss_pred             CCcEEEEeCcchhhhhc--Cc--h--hhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCch--hhhhhchhHHhcchhhhh
Q 020010           79 KKRVFFLDVNPLCYEGS--RP--S--LQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTE--HRRQLLPSYKAHRRKFLR  148 (332)
Q Consensus        79 ~~~vllIDg~~l~yra~--~p--~--~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~--fR~el~p~YKanR~~~p~  148 (332)
                      +++++||||++++||+|  .|  .  .+++.+|++++++.++.  ++++++|||++ +++  ||+++||+||+||+++| 
T Consensus         2 ~~~llLiDg~~l~~R~~~a~~~~~g~t~av~gf~~~l~~ll~~~~p~~i~v~fD~~-~~~~~fR~~l~p~YKa~R~~~P-   79 (256)
T PRK09482          2 MNHLLIIDALNLIRRIHAVQPSPNDINACVETCQHALDKLIRHSQPTHAVAVFDGD-ARSSGWRHQLLPDYKAGRKPMP-   79 (256)
T ss_pred             CCeEEEEeCcHHHHHHHhCCCCCCCcchHHHHHHHHHHHHHHHcCCCEEEEEEeCC-CCCcccHHHHhHHHhcCCCCCc-
Confidence            56799999999999986  22  1  24566777777766643  66799999995 555  99999999999999885 


Q ss_pred             hhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecC
Q 020010          149 QLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPL  228 (332)
Q Consensus       149 p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~  228 (332)
                                ++|..|++.++++++++||+++..+||||||+|||+|+++...|..|+|+|+|||++||++++|++|++.
T Consensus        80 ----------e~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~  149 (256)
T PRK09482         80 ----------EALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF  149 (256)
T ss_pred             ----------HHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc
Confidence                      6799999999999999999999999999999999999999989999999999999999999999999875


Q ss_pred             CCCCccEEeeHHHHHHHhCCChhHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCchH
Q 020010          229 QDLDRWSFYTLKHYIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRDY  308 (332)
Q Consensus       229 ~~~~~~~~~~~~~v~e~~Gv~P~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~~  308 (332)
                      +    ...++.+.+.++||++|+|++||++|+||+|||||||    ||||||||.+||++|||+|+|+++++.  . +++
T Consensus       150 ~----~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGV----pGIG~KtA~~LL~~~gsle~i~~~~~~--~-~~~  218 (256)
T PRK09482        150 Q----KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGV----AGIGPKSAAELLNQFRSLENIYESLDA--L-PEK  218 (256)
T ss_pred             c----cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCC----CCcChHHHHHHHHHhCCHHHHHHhHHH--h-hHH
Confidence            3    2458999999999999999999999999999999999    999999999999999999999999984  3 246


Q ss_pred             HHHHHHHhHHHHHhhcccceecc
Q 020010          309 AQEALTKHADYLRRNYEVLALRR  331 (332)
Q Consensus       309 ~~~~L~~~~~~~~~s~~L~~L~~  331 (332)
                      ++++|.++++++++||+|++|++
T Consensus       219 ~~~~L~~~~~~a~lsr~L~~l~~  241 (256)
T PRK09482        219 WRKKLEEHKEMARLCRKLAQLQT  241 (256)
T ss_pred             HHHHHHHhHHHHHHHHhhheEee
Confidence            89999999999999999999986

>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>PRK14976 5'-3' exonuclease; Provisional 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
>TIGR00593 pola DNA polymerase I 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 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair] 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
>smart00484 XPGI Xeroderma pigmentosum G I-region 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
>PF12813 XPG_I_2: XPG domain containing 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
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>smart00485 XPGN Xeroderma pigmentosum G N-region 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
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional 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
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only] 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
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional 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
>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
>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
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>PRK14671 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PHA03065 Hypothetical protein; Provisional Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14606 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
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 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
>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
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [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
>TIGR00575 dnlj DNA ligase, NAD-dependent 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 ?
Query332
1taq_A 832 Structure Of Taq Dna Polymerase Length = 832 1e-15
1bgx_T 832 Taq Polymerase In Complex With Tp7, An Inhibitory F 1e-15
1ut5_A291 Divalent Metal Ions (Manganese) Bound To T5 5'-Exon 4e-06
1exn_A290 T5 5'-Exonuclease Length = 290 1e-05
1xo1_A291 T5 5'-Exonuclease Mutant K83a Length = 291 2e-05
1tfr_A305 Rnase H From Bacteriophage T4 Length = 305 3e-04
3h8s_A305 Structure Of D19n T4 Rnase H In The Presence Of Div 3e-04
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase Length = 832 Back     alignment and structure 
Iteration: 1

 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 120/270 (44%), Gaps = 45/270 (16%)
Query: 77  KSKKRVFFLDVNPLCYEG-----------SRPSLQSFGRWLSLFFDQVSHADPVIAVFDG 125
           + K RV  +D + L Y               P    +G   SL        D VI VFD 
Sbjct: 9   EPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDA 68
Query: 126 EGGTEHRRQLLPSYKAHR----RKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVK 181
           +  +  R +    YKA R      F RQL   +             ++D+LG   +   +
Sbjct: 69  KAPS-FRHEAYGGYKAGRAPTPEDFPRQLALIKE------------LVDLLGLARL---E 112
Query: 182 IEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTLKH 241
           + G+EADDV+A+L  +  ++GY   + + DKD  QL+S+ + ++ P   L      T   
Sbjct: 113 VPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYL-----ITPAW 167
Query: 242 YIAQYNCDPHSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLL-NAAA 300
              +Y   P      R + GD+ D +PG++    G G KTA KLL++ GSLE LL N   
Sbjct: 168 LWEKYGLRPDQWADYRALTGDESDNLPGVK----GIGEKTARKLLEEWGSLEALLKNLDR 223
Query: 301 VRTVGRDYAQEALTKHADYLRRNYEVLALR 330
           ++   R    E +  H D L+ ++++  +R
Sbjct: 224 LKPAIR----EKILAHMDDLKLSWDLAKVR 249
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab 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|1EXN|A Chain A, T5 5'-Exonuclease Length = 290 Back     alignment and structure
>pdb|1XO1|A Chain A, T5 5'-Exonuclease Mutant K83a Length = 291 Back     alignment and structure
>pdb|1TFR|A Chain A, Rnase H From Bacteriophage T4 Length = 305 Back     alignment and structure
>pdb|3H8S|A Chain A, Structure Of D19n T4 Rnase H In The Presence Of Divalent Mag Length = 305 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 ?
Query332
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 3e-38
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 5e-38
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 5e-22
1rxw_A336 Flap structure-specific endonuclease; helical clam 4e-06
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 6e-06
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 7e-06
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 1e-05
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 7e-05
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 8e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-04
>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
 Score =  136 bits (345), Expect = 3e-38
 Identities = 49/219 (22%), Positives = 86/219 (39%), Gaps = 13/219 (5%)

Query: 115 HADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGK 174
            A   I + D       R + LP YK +R +   Q T  +  +       +      L K
Sbjct: 58  SARTTIVLGDKGKSVF-RLEHLPEYKGNRDEKYAQRT-EEEKALDEQFFEYLKDAFELCK 115

Query: 175 CNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRW 234
              P   I G EADD+ A +V  +        + S D D+  L+++ V            
Sbjct: 116 TTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTR---- 171

Query: 235 SFYTLKHYIAQYNCDPHSEL-SLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLE 293
             Y L+     +N D   +  SL+ I+GD  D + G    V G G K    ++++ G++ 
Sbjct: 172 REYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRG----VEGIGAKRGYNIIREFGNVL 227

Query: 294 NLLNAAAVRTVGRDYAQEALTKHADYLRRNYEVLALRRY 332
           ++++   +    +    + L    + L RN  ++ L  Y
Sbjct: 228 DIIDQLPLPGKQK--YIQNLNASEELLFRNLILVDLPTY 264
>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
>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
>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
>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
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363 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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query332
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 100.0
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 100.0
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 100.0
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 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
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 100.0
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 100.0
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 100.0
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 100.0
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 96.47
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 95.94
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 95.72
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 95.67
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 95.53
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 95.2
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 94.93
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 94.27
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 92.03
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 91.56
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 91.26
3v32_B185 Ribonuclease ZC3H12A; rossmann-like sandwich fold, 90.69
4gfj_A 685 Topoisomerase V; helix-hairpin-helix, DNA repair e 88.68
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 88.59
3fqd_A 899 Protein DHP1, 5'-3' exoribonuclease 2; protein-pro 88.2
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 87.03
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 86.21
3v33_A223 Ribonuclease ZC3H12A; rossmann-like sandwich fold, 84.97
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 83.64
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 82.97
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 81.36
3b0x_A 575 DNA polymerase beta family (X family); structural 80.76
>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=2.6e-60  Score=452.37  Aligned_cols=235  Identities=22%  Similarity=0.334  Sum_probs=207.1

Q ss_pred             CCcEEEEeCcchhhhhc-----CchhhHHHHHHHHHHHHhcC--CCcEEEEEcCCCCchhhhhhchhHHhcchhhhhhhh
Q 020010           79 KKRVFFLDVNPLCYEGS-----RPSLQSFGRWLSLFFDQVSH--ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLT  151 (332)
Q Consensus        79 ~~~vllIDg~~l~yra~-----~p~~~~~~~~l~~ll~~i~~--~~pvivvFD~~~~~~fR~el~p~YKanR~~~p~p~~  151 (332)
                      ++++++|||++++||++     .|   ++.+|++++.+.+..  ++++++|||++ +++||+++||+||+||+++|+...
T Consensus        18 ~~~lllIDg~~llyRa~~~~~G~p---av~Gf~~~l~~ll~~~~p~~~vvvFD~~-~~tfR~~~~~~YKa~R~~~p~~~~   93 (290)
T 1exn_A           18 RRNLMIVDGTNLGFRFKHNNSKKP---FASSYVSTIQSLAKSYSARTTIVLGDKG-KSVFRLEHLPEYKGNRDEKYAQRT   93 (290)
T ss_dssp             -CEEEEEEHHHHHHHHHHHCSSSC---CHHHHHHHHHHHHHHTTEEEEEEECCBS-CCHHHHHHCTTTTHHHHHHHHTSC
T ss_pred             CCCEEEEECcHHHHHHHhCCCCch---HHHHHHHHHHHHHHHcCCCeEEEEEcCC-CchhhhhCcHHHHcCCCCCCcccc
Confidence            56899999999999984     45   455666666655543  45589999985 789999999999999999863211


Q ss_pred             hhhhcchhhHHHh-HHHHHHHHhc--CCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEecC
Q 020010          152 ASQRFSRGRVGRS-HQFILDVLGK--CNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPL  228 (332)
Q Consensus       152 ~~~~~~~~~L~~q-l~~i~elL~~--~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~~  228 (332)
                          +..++|..| ++.++++|++  +|||++.++||||||+||+||+++.+.|..|+|+|+|||++||++++|+++++.
T Consensus        94 ----~~~e~L~~q~~~~ikell~~~~~gip~i~~~g~EADDviatLa~~~~~~G~~v~IvS~DkDl~Qlv~~~v~v~~~~  169 (290)
T 1exn_A           94 ----EEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFT  169 (290)
T ss_dssp             ----HHHHHHHHHHHHHHHHHHHHHTTTSCEECCTTBCHHHHHHHHHHHHGGGSSCEEEECSCGGGGGGCCSSEEEEETT
T ss_pred             ----ccchhHHHhhHHHHHHHHHhhCCCCcEEEECCcCHHHHHHHHHHHHHHCCCcEEEEeCCCChhhcCCCCEEEEECC
Confidence                112679999 9999999999  999999999999999999999999988999999999999999999999999875


Q ss_pred             CCCCccEEeeHHHHHHHhCCCh-hHHHHhhhcccCCCCCCCCcccCCCCccHHHHHHHHHhcCCHHHHHHHhhhcccCch
Q 020010          229 QDLDRWSFYTLKHYIAQYNCDP-HSELSLRCIVGDDVDGVPGIQHVVPGFGRKTALKLLKKHGSLENLLNAAAVRTVGRD  307 (332)
Q Consensus       229 ~~~~~~~~~~~~~v~e~~Gv~P-~q~~d~~aL~GD~sDNIPGI~~~~~GIG~KTA~kLL~~ygsle~il~~~~~~~~~~~  307 (332)
                          .++.++.+.+.++||++| +||+|+++|+||+|||||||    ||||||||.+||++|||+|+|+++++.  .+++
T Consensus       170 ----~~~~~~~~~v~ek~Gv~p~~q~iD~~~L~GD~sDniPGV----pGIG~KTA~kLL~~~gsle~i~~~~~~--~~~~  239 (290)
T 1exn_A          170 ----TRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGV----EGIGAKRGYNIIREFGNVLDIIDQLPL--PGKQ  239 (290)
T ss_dssp             ----TTEEECGGGHHHHHSSSSHHHHHHHHHHHCBGGGTBCCC----TTCCHHHHHHHHHHHCSHHHHHHHCSC--SCCC
T ss_pred             ----CCEEEcHHHHHHHcCCCHHHHHHHHHHhcCCCcCCCCCC----CcCCHhHHHHHHHHcCCHHHHHHHHHH--hccH
Confidence                457899999999999999 99999999999999999999    999999999999999999999999984  2133


Q ss_pred             HHHHHHHHhHHHHHhhcccceecc
Q 020010          308 YAQEALTKHADYLRRNYEVLALRR  331 (332)
Q Consensus       308 ~~~~~L~~~~~~~~~s~~L~~L~~  331 (332)
                      +++++|++++|++++||+|++|++
T Consensus       240 ~~~~~L~~~~~~~~ls~~L~~i~~  263 (290)
T 1exn_A          240 KYIQNLNASEELLFRNLILVDLPT  263 (290)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHhHHHHHHHHHhceeee
Confidence            689999999999999999999986
>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
>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
>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
>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
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} 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
>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
>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
>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
>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
>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
>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
>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
>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
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster} 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
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} 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
>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
>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
>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
>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens} Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} 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
>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
>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_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 332
d1xo1a2167 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacterioph 1e-14
d1tfra2169 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 2e-13
d1cmwa2164 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain o 1e-07
d1xo1a1105 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph 6e-05
d1ul1x1140 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu 0.001
>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 = 68.6 bits (167), Expect = 1e-14
 Identities = 28/128 (21%), Positives = 48/128 (37%), Gaps = 5/128 (3%)

Query: 120 IAVFDGEGGTEHRRQLLPSYKAHRRKFLRQLTASQRFSRGRVGRSHQFILDVLGKCNVPV 179
             V   +G +  R + LP Y  +R +   Q T  ++    +     +   + L K   P 
Sbjct: 45  TIVLGDKGKSVFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFE-LCKTTFPT 103

Query: 180 VKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMPLQDLDRWSFYTL 239
             I G EADD+ A +V  +        + S D D+  L+++ V              Y L
Sbjct: 104 FTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTR----REYHL 159

Query: 240 KHYIAQYN 247
           +     +N
Sbjct: 160 RDMYEHHN 167
>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]} Length = 169 Back     information, alignment and structure
>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
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query332
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]} 99.97
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 99.87
d1cmwa1116 5' to 3' exonuclease domain of DNA polymerase Taq 99.85
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.65
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.59
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.55
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.27
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.27
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.24
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.23
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.12
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 96.97
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 96.64
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 96.38
d1tfra1123 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 96.34
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 96.28
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 95.57
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 95.47
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 94.89
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 93.5
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 92.92
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 91.99
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 91.77
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 91.13
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 90.24
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 89.41
d2csba355 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 85.3
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 82.65
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 80.07
>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=8.6e-35  Score=252.96  Aligned_cols=152  Identities=26%  Similarity=0.407  Sum_probs=130.7

Q ss_pred             CCcEEEEeCcchhhhhc--Cch--------hhHHHHHHHHHHHHhcC-CCcEEEEEcCCCCchhhhhhchhHHhcchhhh
Q 020010           79 KKRVFFLDVNPLCYEGS--RPS--------LQSFGRWLSLFFDQVSH-ADPVIAVFDGEGGTEHRRQLLPSYKAHRRKFL  147 (332)
Q Consensus        79 ~~~vllIDg~~l~yra~--~p~--------~~~~~~~l~~ll~~i~~-~~pvivvFD~~~~~~fR~el~p~YKanR~~~p  147 (332)
                      +++++||||++++||++  .+.        ..++.+|++++.+.++. ++.++++||+. +++||+++||+||+||.++|
T Consensus         2 ~~~~lLIDg~~l~~R~~~a~~~~~~~~g~~~~~i~gf~~~l~~~~~~~~~~~~v~~d~~-~~~~R~~l~p~YK~~R~~~~   80 (164)
T d1cmwa2           2 KGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAK-APSFRHEAYGGYKAGRAPTP   80 (164)
T ss_dssp             CEEEEEEETTHHHHHHHTSSTTCBCTTSCBCHHHHHHHHHHHHHHHHCCSEEEEECCCS-SSCTTGGGGSTTTSCCCCCC
T ss_pred             CCeEEEEeChHHHHHHHHcCCcccCCCCCeeHHHHHHHHHHHHHHhcCCceEEEEEecc-cccchhhhhhhhhhccccCc
Confidence            57899999999999985  121        24566777777666543 44578888874 78999999999999999885


Q ss_pred             hhhhhhhhcchhhHHHhHHHHHHHHhcCCCcEEecCCchHHHHHHHHHHHHHhCCCeEEEEcCCCCcCccCCCCeEEEec
Q 020010          148 RQLTASQRFSRGRVGRSHQFILDVLGKCNVPVVKIEGHEADDVIATLVGQVLQKGYRAVVASPDKDFKQLISEDVQLVMP  227 (332)
Q Consensus       148 ~p~~~~~~~~~~~L~~ql~~i~elL~~~gi~~i~~~g~EADDvIAtLa~~~~~~g~~v~IvS~DKDl~QLv~~~v~v~~~  227 (332)
                                 +++..|++.++++++.+|++++..+|+||||+||+||+++...+.+|+|+|+|||++||++++|.+|+|
T Consensus        81 -----------~~~~~~~~~~~~~~~~~g~~~~~~~~~EADDvIa~la~~~~~~~~~v~IvS~DkD~~QLv~~~v~i~~~  149 (164)
T d1cmwa2          81 -----------EDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHP  149 (164)
T ss_dssp             -----------SSHHHHHHHHHHHHHHTTCEEECCTTSCHHHHHHHHHHHHHHTTEEEEEECSSGGGGGSCCSSCEEECS
T ss_pred             -----------hhHHHHHHHHHHHHhhcCceEEEecCcchHHHHHHHHHHhccccceEEEecCCCChHHheeCCEEEEeC
Confidence                       568889999999999999999999999999999999999998899999999999999999999999998


Q ss_pred             CCCCCccEEeeHHHHHHHhC
Q 020010          228 LQDLDRWSFYTLKHYIAQYN  247 (332)
Q Consensus       228 ~~~~~~~~~~~~~~v~e~~G  247 (332)
                      .+     ..++.+.|.|+||
T Consensus       150 ~~-----~~~~~~~v~ek~G  164 (164)
T d1cmwa2         150 EG-----YLITPAWLWEKYG  164 (164)
T ss_dssp             SS-----SEECHHHHHHSSC
T ss_pred             CC-----EEECHHHHHhhhC
Confidence            43     3589999999998
>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
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} 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
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 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
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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
>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} 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
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} 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
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {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
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} 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
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} 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
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure