Psyllid ID: psy11328

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410
MFAQDLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRPEVSSGSL
cccHHHHHHHHHHcccEEEEEEccccEEEEEHHHHHcccccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHcccEEEEEEEccEEEEEEccEEEEEccHHHHHHHHccccHHHHHHHHHHHcccEEEEEEEcccccccccccccccHHHHHHHHHHHcccccccccccccccHHHHcccHHHHHHHHHHHHccccEEEEEcccHHHHHHHHHHHHcccccccHHHHHHccccccccHHHHHcHHHHHHHHccccccHHHHHHHHcHHHHHccccccHHHHHHHHHHcHHHHHHHHHccccccccccccccccHHHHHHHHccccHHHHHHHcHHHHHHHHccccHHHHHHHHHHcccccccccc
ccHHHHHHHHHHHcccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHcccEEcccccccccccccccEEEEEHHHcccHHHHHHHHcccEEEEEccccccEEccccEEEEEEEHHHHHHHHHcccHHHHHHHHHHHccEEEEEEEEcccccEEEccccHcccccccccEcccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEcccHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccHHHHHHHccccccHHHHHEEccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccHHHHHccHHHHHHHHHcHHHHHHHHHHHccccccccccc
MFAQDLSSklrslkptsvIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEktnmavpteqdgvstepeescgRVIVDMREFRSELPVLlhkrglyiepvtisvgdyilspdicvERKSISDLIgslqsgrlYTQVQQMCRHYAKpllliefdhnkpfelqgnyYLSRDIAAKFLIefdhnkpfelqgnyylsrdiaaKSSDITAKLQLLTLHFPklrliwssgpyntAQLFFELkqgrdepsaevassigqtpnedytDRYNAAIEDFISKLPGMAEWSRARTLNlevlglnpgqggnfLTELFRASSFFLLLFrikpapgresnprprvtsknkaavlnrgsslpalCKLSEQELCSLVENTTLGNALYKALhtrpevssgsl
mfaqdlssklrslkptsVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIqektnmavpteqdgvstepeeSCGRVIVDMREFRSELPvllhkrglyiepVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVassigqtpnedYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKpapgresnprprvtsknkaavlnrgsslpALCKLSEQELCSLVENTTLGNALYKalhtrpevssgsl
MFAQDLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTElfrassfflllfrIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRPEVSSGSL
***************TSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQ*********************CGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFEL**********************YTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIK****************************PALCKLSEQELCSLVENTTLGNALYKAL***********
****DLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYL**LRR**KAFEYLIQEK*********************RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYL*********DITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQ**************************AAIEDFISKLPGMAEWSRARTLNLEV****************RASSFFLLLFRIKP***************************PALCKLSEQELCSLVENTTLGNALYKALH**********
********KLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVP*************CGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQ*************GQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPG*************KAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHT*********
MFAQDLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNK****************KSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKP************************SSLPALCKLSEQELCSLVENTTLGNALYKALHT*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFAQDLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPTEQDGVSTEPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRPEVSSGSL
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 ?
Query410 2.2.26 [Sep-21-2011]
Q24087961 DNA repair endonuclease X yes N/A 0.658 0.280 0.478 6e-77
Q9QZD4917 DNA repair endonuclease X yes N/A 0.709 0.317 0.412 2e-68
Q92889916 DNA repair endonuclease X yes N/A 0.653 0.292 0.426 6e-68
Q9QYM7913 DNA repair endonuclease X yes N/A 0.648 0.291 0.430 2e-66
Q9LKI5956 DNA repair endonuclease U yes N/A 0.639 0.274 0.409 3e-57
P36617877 DNA repair protein rad16 yes N/A 0.639 0.298 0.408 8e-54
Q54PN5964 DNA repair endonuclease X yes N/A 0.643 0.273 0.361 8e-51
P067771100 DNA repair protein RAD1 O yes N/A 0.597 0.222 0.363 2e-48
Q58900778 Putative ATP-dependent RN yes N/A 0.173 0.091 0.4 5e-06
>sp|Q24087|XPF_DROME DNA repair endonuclease XPF OS=Drosophila melanogaster GN=mei-9 PE=2 SV=2 Back     alignment and function desciption
 Score =  288 bits (736), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 157/328 (47%), Positives = 202/328 (61%), Gaps = 58/328 (17%)

Query: 6   LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQS---EVKVKVFFMQYGESVEEQAYLSD 62
           L   L  L+P  V+ YN +V AIRQ+EV++  +      ++KV+F+ +  +VEEQAYL+ 
Sbjct: 573 LEHMLEQLQPHYVVMYNMNVTAIRQLEVFEARRRLPPADRMKVYFLIHARTVEEQAYLTS 632

Query: 63  LRREKKAFEYLIQEKTNMAVPTEQDGVSTE--------------------------PEES 96
           LRREK AFE++I  K+ M +P  QDG + E                          P+ +
Sbjct: 633 LRREKAAFEFIIDTKSKMVIPKYQDGKTDEAFLLLKTYDDEPTDENAKSRQAGGQAPQAT 692

Query: 97  --CGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQS 154
               +VIVDMREFRS+LP L+HKRGL + P+TI++GDYIL+PDICVERKSISDLIGSL S
Sbjct: 693 KETPKVIVDMREFRSDLPCLIHKRGLEVLPLTITIGDYILTPDICVERKSISDLIGSLNS 752

Query: 155 GRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGN 214
           GRLY Q  QM RHYAKP+LLIEFD NKPF LQG          KF+              
Sbjct: 753 GRLYNQCVQMQRHYAKPILLIEFDQNKPFHLQG----------KFM-------------- 788

Query: 215 YYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASS 274
             LS+  +  ++DI  KLQLLTLHFPKLRLIWS  PY TAQLF ELK G+ EP  + A++
Sbjct: 789 --LSQQTSMANADIVQKLQLLTLHFPKLRLIWSPSPYATAQLFEELKLGKPEPDPQTAAA 846

Query: 275 IG-QTPNEDYTDRYNAAIEDFISKLPGM 301
           +G   P       +N+ I DF+ +LPG+
Sbjct: 847 LGSDEPTAGEQLHFNSGIYDFLLRLPGV 874
Implicated in recombination events during meiosis, mostly in meiotic exchange. May directly resolve Holliday junctions within recombination intermediates leading to DNA exchange. Also required for the repair of mismatches within meiotic heteroduplex DNA and for nucleotide excision repair.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q9QZD4|XPF_MOUSE DNA repair endonuclease XPF OS=Mus musculus GN=Ercc4 PE=2 SV=3 Back     alignment and function description
>sp|Q92889|XPF_HUMAN DNA repair endonuclease XPF OS=Homo sapiens GN=ERCC4 PE=1 SV=3 Back     alignment and function description
>sp|Q9QYM7|XPF_CRIGR DNA repair endonuclease XPF OS=Cricetulus griseus GN=ERCC4 PE=2 SV=3 Back     alignment and function description
>sp|Q9LKI5|XPF_ARATH DNA repair endonuclease UVH1 OS=Arabidopsis thaliana GN=UVH1 PE=1 SV=2 Back     alignment and function description
>sp|P36617|RAD16_SCHPO DNA repair protein rad16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad16 PE=1 SV=2 Back     alignment and function description
>sp|Q54PN5|XPF_DICDI DNA repair endonuclease XPF OS=Dictyostelium discoideum GN=ercc4 PE=3 SV=1 Back     alignment and function description
>sp|P06777|RAD1_YEAST DNA repair protein RAD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD1 PE=1 SV=1 Back     alignment and function description
>sp|Q58900|Y1505_METJA Putative ATP-dependent RNA helicase MJ1505 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1505 PE=3 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query410
345489848 1022 PREDICTED: DNA repair endonuclease XPF-l 0.797 0.319 0.464 7e-85
307186525 866 DNA repair endonuclease XPF [Camponotus 0.743 0.352 0.450 2e-84
307215344 868 DNA repair endonuclease XPF [Harpegnatho 0.7 0.330 0.5 4e-83
357618962 838 hypothetical protein KGM_15729 [Danaus p 0.678 0.331 0.483 7e-83
340715119 865 PREDICTED: LOW QUALITY PROTEIN: DNA repa 0.743 0.352 0.429 2e-81
321455581 818 hypothetical protein DAPPUDRAFT_331812 [ 0.692 0.347 0.494 3e-81
383860837 865 PREDICTED: DNA repair endonuclease XPF-l 0.680 0.322 0.494 7e-81
350414750 836 PREDICTED: DNA repair endonuclease XPF-l 0.743 0.364 0.424 3e-80
350414747 865 PREDICTED: DNA repair endonuclease XPF-l 0.743 0.352 0.424 3e-80
189237991 870 PREDICTED: similar to DNA repair endonuc 0.656 0.309 0.490 3e-79
>gi|345489848|ref|XP_001600324.2| PREDICTED: DNA repair endonuclease XPF-like [Nasonia vitripennis] Back     alignment and taxonomy information
 Score =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 185/398 (46%), Positives = 235/398 (59%), Gaps = 71/398 (17%)

Query: 6    LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRR 65
            L   L  ++P+ VI Y AD++ +RQ+EVYQ     + +KVFF+ YG SVEEQAYL+ LRR
Sbjct: 652  LHRTLDEVQPSYVIMYAADISTVRQLEVYQNKYPSISLKVFFLIYGGSVEEQAYLTSLRR 711

Query: 66   EKKAFEYLIQEKTNMAVPTEQDGVSTEPEES--------------------CGRVIVDMR 105
            EK AF+ L+  KT M VP EQDG   EP  S                      ++IVDMR
Sbjct: 712  EKDAFDKLVFAKTTMVVPAEQDGKCAEPTPSDSVDEDNTRKGGLIEDQAANVNKIIVDMR 771

Query: 106  EFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMC 165
            EFRSELP LLH+R + IEPVTI +GDYILSP+ICVERKSISDLIGSL SGRLY Q   M 
Sbjct: 772  EFRSELPSLLHQRNIEIEPVTILIGDYILSPEICVERKSISDLIGSLNSGRLYNQAVAMT 831

Query: 166  RHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKS 225
            R+YAKP+LLIEFD NKPF LQGNYY+S+D+                            +S
Sbjct: 832  RYYAKPMLLIEFDQNKPFGLQGNYYVSKDM----------------------------RS 863

Query: 226  SDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNED--- 282
             DIT KLQLLT+HFP+L+L+WS  P+ TAQLF ELKQGR +P A  A+ IG   + D   
Sbjct: 864  IDITHKLQLLTMHFPRLKLVWSPSPHATAQLFEELKQGRPQPDAIKAAQIGMDDDTDDKN 923

Query: 283  -YTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNF--------LTELFRAS 333
               ++YN  I+D ++KLPG+       + NL  + LN GQ  ++        LTE+    
Sbjct: 924  IMAEKYNCHIQDLVAKLPGV------HSKNLRQI-LNKGQSLDYLITRSKIELTEMISNE 976

Query: 334  SFFLLLF---RIKPAPGRESNPRPRVTSKNKAAVLNRG 368
            S   LL+    +K  P  ES+    V +   + V +RG
Sbjct: 977  SDAELLYNALHLKHKPSFESSTNGGVKAA-ASKVKSRG 1013

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|307186525|gb|EFN72085.1| DNA repair endonuclease XPF [Camponotus floridanus] Back     alignment and taxonomy information
>gi|307215344|gb|EFN90056.1| DNA repair endonuclease XPF [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|357618962|gb|EHJ71746.1| hypothetical protein KGM_15729 [Danaus plexippus] Back     alignment and taxonomy information
>gi|340715119|ref|XP_003396067.1| PREDICTED: LOW QUALITY PROTEIN: DNA repair endonuclease XPF-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|321455581|gb|EFX66710.1| hypothetical protein DAPPUDRAFT_331812 [Daphnia pulex] Back     alignment and taxonomy information
>gi|383860837|ref|XP_003705895.1| PREDICTED: DNA repair endonuclease XPF-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|350414750|ref|XP_003490406.1| PREDICTED: DNA repair endonuclease XPF-like isoform 2 [Bombus impatiens] Back     alignment and taxonomy information
>gi|350414747|ref|XP_003490405.1| PREDICTED: DNA repair endonuclease XPF-like isoform 1 [Bombus impatiens] Back     alignment and taxonomy information
>gi|189237991|ref|XP_001812786.1| PREDICTED: similar to DNA repair endonuclease xp-f / mei-9 / rad1 [Tribolium castaneum] gi|270008119|gb|EFA04567.1| meiotic 9 [Tribolium castaneum] 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 ?
Query410
UNIPROTKB|Q6DFB2897 ercc4 "Ercc4-prov protein" [Xe 0.236 0.108 0.690 5.4e-56
ASPGD|ASPL0000070525985 AN8713 [Emericella nidulans (t 0.441 0.183 0.478 3.4e-55
UNIPROTKB|F1NAV2897 ERCC4 "Uncharacterized protein 0.314 0.143 0.548 9.2e-54
ZFIN|ZDB-GENE-030131-5533886 ercc4 "excision repair cross-c 0.297 0.137 0.617 1.8e-52
UNIPROTKB|Q7RW07957 NCU07440 "Putative uncharacter 0.475 0.203 0.387 5.3e-43
FB|FBgn0002707961 mei-9 "meiotic 9" [Drosophila 0.356 0.151 0.529 1.1e-38
DICTYBASE|DDB_G0284419964 xpf "DNA excision repair prote 0.243 0.103 0.53 7.7e-40
UNIPROTKB|F1RLR4917 ERCC4 "Uncharacterized protein 0.692 0.309 0.321 8e-40
UNIPROTKB|Q9QYM7913 ERCC4 "DNA repair endonuclease 0.695 0.312 0.332 2.6e-39
UNIPROTKB|Q92889916 ERCC4 "DNA repair endonuclease 0.702 0.314 0.322 5.5e-39
UNIPROTKB|Q6DFB2 ercc4 "Ercc4-prov protein" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
 Score = 359 (131.4 bits), Expect = 5.4e-56, Sum P(3) = 5.4e-56
 Identities = 67/97 (69%), Positives = 81/97 (83%)

Query:   100 VIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYT 159
             +IVDMREFRSELP L+H+RG+ IEPVT+ VGDYIL+PDICVERKS+SDLIGSL +GRLYT
Sbjct:   665 IIVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPDICVERKSVSDLIGSLNNGRLYT 724

Query:   160 QVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIA 196
             Q   MCR+Y KP+LLIEFD NKPF L     + ++I+
Sbjct:   725 QCVSMCRYYKKPILLIEFDPNKPFSLVSRNSIHQEIS 761
GO:0000110 "nucleotide-excision repair factor 1 complex" evidence=ISS
GO:0000724 "double-strand break repair via homologous recombination" evidence=ISS
GO:0000784 "nuclear chromosome, telomeric region" evidence=ISS
GO:0003684 "damaged DNA binding" evidence=ISS
GO:0003697 "single-stranded DNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISS
GO:0006289 "nucleotide-excision repair" evidence=ISS
GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISS
GO:0006296 "nucleotide-excision repair, DNA incision, 5'-to lesion" evidence=ISS
GO:0008022 "protein C-terminus binding" evidence=ISS
GO:0009411 "response to UV" evidence=ISS
GO:0032205 "negative regulation of telomere maintenance" evidence=ISS
GO:0033683 "nucleotide-excision repair, DNA incision" evidence=ISS
GO:0047485 "protein N-terminus binding" evidence=ISS
GO:0004520 "endodeoxyribonuclease activity" evidence=ISS
GO:0043566 "structure-specific DNA binding" evidence=ISS
ASPGD|ASPL0000070525 AN8713 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|F1NAV2 ERCC4 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-5533 ercc4 "excision repair cross-complementing rodent repair deficiency, complementation group 4" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q7RW07 NCU07440 "Putative uncharacterized protein" [Neurospora crassa OR74A (taxid:367110)] Back     alignment and assigned GO terms
FB|FBgn0002707 mei-9 "meiotic 9" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0284419 xpf "DNA excision repair protein 4" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|F1RLR4 ERCC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q9QYM7 ERCC4 "DNA repair endonuclease XPF" [Cricetulus griseus (taxid:10029)] Back     alignment and assigned GO terms
UNIPROTKB|Q92889 ERCC4 "DNA repair endonuclease XPF" [Homo sapiens (taxid:9606)] 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 EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query410
TIGR00596814 TIGR00596, rad1, DNA repair protein (rad1) 1e-103
COG1948254 COG1948, MUS81, ERCC4-type nuclease [DNA replicati 2e-30
smart0089198 smart00891, ERCC4, ERCC4 domain 8e-21
PRK13766773 PRK13766, PRK13766, Hef nuclease; Provisional 1e-20
pfam02732102 pfam02732, ERCC4, ERCC4 domain 3e-19
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1) Back     alignment and domain information 
 Score =  322 bits (828), Expect = e-103
 Identities = 143/323 (44%), Positives = 192/323 (59%), Gaps = 54/323 (16%)

Query: 6   LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRR 65
           L   L  L P  VI Y  D++ IRQ+EVY+ ++    ++V+F+ YG S+EEQ YL+ LRR
Sbjct: 468 LRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRPLRVYFLYYGGSIEEQRYLTSLRR 527

Query: 66  EKKAFEYLIQEKTNMAVPTE-----------------QDGVSTEPEESCG---------- 98
           EK AF  LI+EK NM++P E                      ++   + G          
Sbjct: 528 EKDAFTKLIREKANMSIPFETNEDLESKFLRLVNTRISKLRKSKTRNAGGQLGFANLTQP 587

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           +VIVDMREFRS LP LLH+RG+ + P  ++VGDYIL+PDICVERKSISDLIGSL +GRLY
Sbjct: 588 KVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLY 647

Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
            Q ++M R+YA P+LLIEFD NK F L+                     P        LS
Sbjct: 648 NQCEKMLRYYAYPVLLIEFDQNKSFSLE---------------------PR-----NDLS 681

Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQ- 277
           ++I++ ++DI  KL LLTLHFPKLR+IWSS PY TA++F ELK G++EP    A+++G  
Sbjct: 682 QEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSD 741

Query: 278 TPNEDYTDRYNAAIEDFISKLPG 300
                   ++N   +DF+ KLPG
Sbjct: 742 ENTTAEGLKFNDGPQDFLLKLPG 764

All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]. Length = 814
>gnl|CDD|224859 COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|214888 smart00891, ERCC4, ERCC4 domain Back     alignment and domain information
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional Back     alignment and domain information
>gnl|CDD|217207 pfam02732, ERCC4, ERCC4 domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 410
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 100.0
KOG0442|consensus892 100.0
PRK13766773 Hef nuclease; Provisional 100.0
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 100.0
PF02732143 ERCC4: ERCC4 domain; InterPro: IPR006166 This entr 99.89
KOG2379|consensus501 99.73
KOG2841|consensus254 99.67
COG1111542 MPH1 ERCC4-like helicases [DNA replication, recomb 99.47
TIGR00597112 rad10 DNA repair protein rad10. All proteins in th 98.17
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 98.11
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 97.55
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 97.37
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 97.31
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1 97.24
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 97.15
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 97.08
PRK12766 232 50S ribosomal protein L32e; Provisional 97.07
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 96.96
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 96.94
PRK13482352 DNA integrity scanning protein DisA; Provisional 96.78
PRK14671621 uvrC excinuclease ABC subunit C; Provisional 96.66
PRK00558598 uvrC excinuclease ABC subunit C; Validated 96.57
COG0322581 UvrC Nuclease subunit of the excinuclease complex 96.43
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 96.17
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 95.92
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 95.91
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain 95.47
KOG0354|consensus746 95.2
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 95.09
PRK00254720 ski2-like helicase; Provisional 94.81
PF0383469 Rad10: Binding domain of DNA repair protein Ercc1 94.33
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 94.21
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 93.76
TIGR02236 310 recomb_radA DNA repair and recombination protein R 93.21
PRK04301 317 radA DNA repair and recombination protein RadA; Va 91.38
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 90.14
COG1623349 Predicted nucleic-acid-binding protein (contains t 89.03
TIGR00194574 uvrC excinuclease ABC, C subunit. This family cons 85.91
TIGR01259120 comE comEA protein. This model describes the ComEA 85.87
PLN031421033 Probable chromatin-remodeling complex ATPase chain 84.69
smart00611312 SEC63 Domain of unknown function in Sec63p, Brr2p 84.03
PRK00024 224 hypothetical protein; Reviewed 83.96
PF02889 314 Sec63: Sec63 Brl domain; InterPro: IPR004179 This 82.54
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information 
Probab=100.00  E-value=2.5e-82  Score=690.35  Aligned_cols=315  Identities=50%  Similarity=0.823  Sum_probs=285.8

Q ss_pred             HHHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-C
Q psy11328          6 LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVP-T   84 (410)
Q Consensus         6 ~~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~Li~~k~~m~ip-~   84 (410)
                      +.++|++++|+||||||||++|||+||+|++++++.+++||||+|+||+|||+||+++||||+||++||++|++|++| .
T Consensus       468 ~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~~rVyfL~y~~S~EEq~yl~sirrEK~AFe~LIreka~m~~~~~  547 (814)
T TIGR00596       468 LRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRPLRVYFLYYGGSIEEQRYLTSLRREKDAFTKLIREKANMSIPFE  547 (814)
T ss_pred             HHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCCcEEEEEEECCcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc
Confidence            668999999999999999999999999999999999999999999999999999999999999999999999999999 3


Q ss_pred             CCCCCC-------------------------C-CCCCCCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCe
Q psy11328         85 EQDGVS-------------------------T-EPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDI  138 (410)
Q Consensus        85 ~~~~~~-------------------------~-~~~~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i  138 (410)
                      .+++..                         . .....+++||||+|||+|+||..||++|++|+|++|+||||||||+|
T Consensus       548 ~~~~~~~~~~~~~~~~~~~~~~~~tR~agg~~~~~~~~~~~IiVD~REfrS~lp~~L~~~G~~v~p~tL~VGDYilS~~i  627 (814)
T TIGR00596       548 TNEDLESKFLRLVNTRISKLRKSKTRNAGGQLGFANLTQPKVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDI  627 (814)
T ss_pred             cccccchhhhhcccccccccccccchhhccccccccCCCceEEEecCcccchhHHHHHHCCCEEEEEecCcccEEecCCe
Confidence            332110                         0 01345789999999999999999999999999999999999999999


Q ss_pred             EEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccc
Q psy11328        139 CVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS  218 (410)
Q Consensus       139 ~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~  218 (410)
                      ||||||++||++||+|||||+||++|++||++|+||||||.+++|++++..+.++.++                      
T Consensus       628 ~VERKSi~Dli~Sl~~gRL~~Q~~~m~~~Y~~PvLLIE~d~~~~f~l~~~~~~~~~~~----------------------  685 (814)
T TIGR00596       628 CVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKSFSLEPRNDLSQEIS----------------------  685 (814)
T ss_pred             EEEeCcHHHHHHHHhcchHHHHHHHHHHhcCCcEEEEEecCCcccccccccccccccC----------------------
Confidence            9999999999999999999999999999999999999999999999877555555444                      


Q ss_pred             cccccCh--HHHHHHHHHHHhhCCCeEEEecCChhhHHHHHHHHhcCCCCCCcccccccCCCCCCCc-cccccHHHHHHH
Q psy11328        219 RDIAAKS--SDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDY-TDRYNAAIEDFI  295 (410)
Q Consensus       219 ~~~~~~~--~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~ll~~Lk~~~eepd~~~a~~i~~~~~~~~-~~~~~~~~~~~l  295 (410)
                            +  ++|+++|++|+++||+++||||+|+++||.+|..||++++|||+.+++.+|.+..... ...++..++++|
T Consensus       686 ------~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i~~~Lk~~e~epd~~~~v~i~~~~~~~~k~~~~~~~~q~~L  759 (814)
T TIGR00596       686 ------SVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSDENTTAEGLKFNDGPQDFL  759 (814)
T ss_pred             ------ccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHHHHHHHhcCCCCCcccceecCcccccccccccccHHHHHHH
Confidence                  5  7999999999999999999999999999999999999988899999999985221110 235788999999


Q ss_pred             HcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHH
Q psy11328        296 SKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALC  375 (410)
Q Consensus       296 ~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~  375 (410)
                      .+|||                                                       ||++||++||.+|+|+++|+
T Consensus       760 ~~lPg-------------------------------------------------------I~~~~a~~ll~~f~si~~l~  784 (814)
T TIGR00596       760 LKLPG-------------------------------------------------------VTKKNYRNLRKKVKSIRELA  784 (814)
T ss_pred             HHCCC-------------------------------------------------------CCHHHHHHHHHHcCCHHHHH
Confidence            99999                                                       99999999999999999999


Q ss_pred             cCCHHHHHHhhCCchhHHHHHHHhccCC
Q psy11328        376 KLSEQELCSLVENTTLGNALYKALHTRP  403 (410)
Q Consensus       376 ~~s~eeL~~~~g~~~~a~~ly~fl~~~~  403 (410)
                      ++|++||++++|+++.|++||+|||++.
T Consensus       785 ~as~eeL~~~iG~~~~A~~i~~fl~~~~  812 (814)
T TIGR00596       785 KLSQNELNELIGDEEAAKRLYDFLRTEK  812 (814)
T ss_pred             hCCHHHHHHHhCCHHHHHHHHHHhcccc
Confidence            9999999999996689999999999874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
>KOG0442|consensus Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3 Back     alignment and domain information
>KOG2379|consensus Back     alignment and domain information
>KOG2841|consensus Back     alignment and domain information
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00597 rad10 DNA repair protein rad10 Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14667 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] 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
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; 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
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PRK14671 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG0354|consensus Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs) Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only] Back     alignment and domain information
>TIGR00194 uvrC excinuclease ABC, C subunit Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional Back     alignment and domain information
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found 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 ?
Query410
1j22_A143 Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF 2e-13
2bgw_A219 Xpf From Aeropyrum Pernix, Complex With Dna Length 4e-11
2bhn_A214 Xpf From Aeropyrum Pernix Length = 214 5e-11
>pdb|1J22|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM PYROCOCCUS Furiosus, Nuclease Domain, Selenomet Derivative Length = 143 Back     alignment and structure 
Iteration: 1

 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 81/160 (50%), Gaps = 39/160 (24%)
Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           +V+VD RE RSE+   L   G+ +E  T+ VGDYI+S D+ +ERKS +DLI S+  G L+
Sbjct: 6   KVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLF 65
Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
            QV+++   Y++P++++E          G+ Y  R++            P  ++G     
Sbjct: 66  DQVKRLKEAYSRPIMIVE----------GSLYGIRNV-----------HPNAIRGA---- 100
Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFF 258
             IAA + D            P   +I+SS P  TAQ  F
Sbjct: 101 --IAAVTVD---------FGVP---IIFSSTPEETAQYIF 126
>pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna Length = 219 Back     alignment and structure
>pdb|2BHN|A Chain A, Xpf From Aeropyrum Pernix Length = 214 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 ?
Query410
1j23_A143 HEF nuclease, ATP-dependent RNA helicase, putative 6e-34
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 2e-28
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative sp 1e-10
2zix_A307 Crossover junction endonuclease MUS81; helix-hairp 9e-10
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 1e-07
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 4e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
>1j23_A HEF nuclease, ATP-dependent RNA helicase, putative; structure-specific endonuclease, hydrolase; 1.78A {Pyrococcus furiosus} SCOP: c.52.1.20 PDB: 1j22_A 1j24_A 1j25_A Length = 143 Back     alignment and structure
 Score =  122 bits (308), Expect = 6e-34
 Identities = 49/175 (28%), Positives = 81/175 (46%), Gaps = 40/175 (22%)

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           +V+VD RE RSE+   L   G+ +E  T+ VGDYI+S D+ +ERKS +DLI S+  G L+
Sbjct: 6   KVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLF 65

Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
            QV+++   Y++P++++E        +  N                              
Sbjct: 66  DQVKRLKEAYSRPIMIVEGSLYGIRNVHPN------------------------------ 95

Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFEL-KQGRDEPSAEVA 272
                    I   +  +T+ F  + +I+SS P  TAQ  F + K+ ++E    V 
Sbjct: 96  --------AIRGAIAAVTVDFG-VPIIFSSTPEETAQYIFLIAKREQEEREKPVR 141
>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 Length = 219 Back     alignment and structure
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Length = 311 Back     alignment and structure
>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Length = 307 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* Length = 63 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* Length = 84 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
>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 ?
Query410
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 100.0
1j23_A143 HEF nuclease, ATP-dependent RNA helicase, putative 100.0
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative sp 100.0
2zix_A307 Crossover junction endonuclease MUS81; helix-hairp 100.0
4gfj_A 685 Topoisomerase V; helix-hairpin-helix, DNA repair e 99.86
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 99.49
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 99.31
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 99.23
2a1i_A146 DNA excision repair protein ERCC-1; XPF, central d 98.4
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 98.22
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 98.03
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 97.78
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 97.7
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 97.65
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 97.36
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 97.15
1wp9_A494 ATP-dependent RNA helicase, putative; ATPase, DNA 97.12
2ziu_B341 Crossover junction endonuclease EME1; helix-hairpi 96.96
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 96.95
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 96.85
4a2p_A556 RIG-I, retinoic acid inducible protein I; hydrolas 96.12
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 95.94
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 95.78
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 95.63
4a2q_A797 RIG-I, retinoic acid inducible protein I; hydrolas 95.56
4a2w_A936 RIG-I, retinoic acid inducible protein I; hydrolas 94.8
3tbk_A555 RIG-I helicase domain; DECH helicase, ATP binding, 94.27
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 93.82
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein- 93.51
1z5z_A271 Helicase of the SNF2/RAD54 family; hydrolase, reco 91.88
2duy_A75 Competence protein comea-related protein; helix-ha 91.83
2ykg_A696 Probable ATP-dependent RNA helicase DDX58; hydrola 90.54
3mwy_W800 Chromo domain-containing protein 1; SWI2/SNF2 ATPa 90.48
1z63_A500 Helicase of the SNF2/RAD54 hamily; protein-DNA com 88.33
1z3i_X644 Similar to RAD54-like; recombination ATPase helica 87.29
4gl2_A699 Interferon-induced helicase C domain-containing P; 86.55
2fwr_A472 DNA repair protein RAD25; DNA unwinding, XPB, DNA 85.56
3im1_A 328 Protein SNU246, PRE-mRNA-splicing helicase BRR2; A 84.31
3osn_A 420 DNA polymerase IOTA; hoogsteen base PAIR, protein- 82.1
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 81.18
1t5i_A172 C_terminal domain of A probable ATP-dependent RNA 80.91
2q0z_X 339 Protein Pro2281; SEC63, SEC, NESG, HR1979, structu 80.56
>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
Probab=100.00  E-value=3.9e-43  Score=327.35  Aligned_cols=212  Identities=26%  Similarity=0.369  Sum_probs=180.9

Q ss_pred             CCCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEE
Q psy11328         95 ESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLL  174 (410)
Q Consensus        95 ~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLL  174 (410)
                      ...+.||||+||++|.+|..|+.+|+++++++|++|||+|++++||||||++||++||++||||+|+.+|+++|++|+||
T Consensus         6 ~~~~~iivD~RE~~s~~~~~l~~~gv~~~~~~L~vgDy~~~~~~~VERKs~~Dl~~Si~~~Rl~~Q~~~l~~~~~~~~ll   85 (219)
T 2bgw_A            6 GGRPRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFII   85 (219)
T ss_dssp             CSSCEEEEETTTTTSSHHHHHHHTTCEEEEECCSSSSEEEETTEEEEEEEHHHHHHHHHHSHHHHHHHHHHHHCSEEEEE
T ss_pred             CCCeEEEEECCCcccHhHHHHHhCCCEEEEEEcCcCCEEeeCCeEEEeCCHHHHHHHhhcCcHHHHHHHHHHhcCCcEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhHH
Q psy11328        175 IEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTA  254 (410)
Q Consensus       175 IE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA  254 (410)
                      ||++.++.      .+   .++                            +.+++++|+.++++| +++|+||+|+++||
T Consensus        86 iE~d~~~~------~~---~~~----------------------------~~~i~~~l~~~~~~~-~~~vi~t~s~~eta  127 (219)
T 2bgw_A           86 VEGPPVPR------RY---RGR----------------------------ERSLYAAMAALQLDY-GIRLMNTMDPKGTA  127 (219)
T ss_dssp             EESCSSCG------GG---TTT----------------------------HHHHHHHHHHHHHHS-CCEEEEESSHHHHH
T ss_pred             EEecCccc------cc---cCC----------------------------HHHHHHHHHHHHHHC-CceEEEcCCHHHHH
Confidence            99986541      01   122                            678999999999999 99999999999999


Q ss_pred             HHHHHHhcCCCCCCcccccccCCCCCCCccccccHHHHHHHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhh
Q psy11328        255 QLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASS  334 (410)
Q Consensus       255 ~ll~~Lk~~~eepd~~~a~~i~~~~~~~~~~~~~~~~~~~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  334 (410)
                      ++|..|++.. ++....+..++....   ...++.....+|.++||                                  
T Consensus       128 ~~l~~l~~~~-~~~~~~ai~~~~~~~---~~~~~~~~~~~L~~i~g----------------------------------  169 (219)
T 2bgw_A          128 LVIESLARLS-TREGGQRIVIHKKPR---LSDVREWQLYILQSFPG----------------------------------  169 (219)
T ss_dssp             HHHHHHHHHH-SCBCCTTCCCCCCCC---CCHHHHHHHHHHHTSTT----------------------------------
T ss_pred             HHHHHHHHhc-ccccccccccccccc---cccHHHHHHHHHhcCCC----------------------------------
Confidence            9999999854 333233443432221   11234455568889999                                  


Q ss_pred             hhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328        335 FFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP  403 (410)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~  403 (410)
                                           ||+++|+.|+++|+|+.+|++++.++|.++-| .+..|+.|++||+.++
T Consensus       170 ---------------------Vg~~~a~~Ll~~fgs~~~l~~a~~e~L~~v~GiG~~~a~~i~~~~~~~~  218 (219)
T 2bgw_A          170 ---------------------IGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPY  218 (219)
T ss_dssp             ---------------------CCHHHHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHHHSCC
T ss_pred             ---------------------CCHHHHHHHHHHcCCHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHhccc
Confidence                                 99999999999999999999999999999944 3589999999999876
>1j23_A HEF nuclease, ATP-dependent RNA helicase, putative; structure-specific endonuclease, hydrolase; 1.78A {Pyrococcus furiosus} SCOP: c.52.1.20 PDB: 1j22_A 1j24_A 1j25_A Back     alignment and structure
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Back     alignment and structure
>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} 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
>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
>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
>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
>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A* 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
>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
>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
>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
>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
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Back     alignment and structure
>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B 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
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* 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
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} 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
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Back     alignment and structure
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Back     alignment and structure
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B 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
>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7 Back     alignment and structure
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Back     alignment and structure
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Back     alignment and structure
>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A Back     alignment and structure
>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19 Back     alignment and structure
>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens} Back     alignment and structure
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Back     alignment and structure
>3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular model mRNA splicing; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A Back     alignment and structure
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex, Y-family DNA polym translesion synthesis, nucleoside triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens} PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A* 2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A* 3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 4ebc_A* 4ebd_A* ... 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
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Back     alignment and structure
>2q0z_X Protein Pro2281; SEC63, SEC, NESG, HR1979, structural genomics, translocase, northeast structural genomics consortium, PSI-2; 2.00A {Homo sapiens} SCOP: a.289.1.1 b.1.18.22 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 410
d1j23a_131 c.52.1.20 (A:) Putative ATP-dependent RNA helicase 7e-32
d2bgwa2133 c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum p 1e-31
d2a1ja162 a.60.2.5 (A:837-898) DNA repair endonuclease XPF { 3e-04
>d1j23a_ c.52.1.20 (A:) Putative ATP-dependent RNA helicase Hef, nuclease domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 131 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: Putative ATP-dependent RNA helicase Hef, nuclease domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score =  115 bits (290), Expect = 7e-32
 Identities = 48/169 (28%), Positives = 80/169 (47%), Gaps = 40/169 (23%)

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           +V+VD RE RSE+   L   G+ +E  T+ VGDYI+S D+ +ERKS +DLI S+  G L+
Sbjct: 2   KVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLF 61

Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
            QV+++   Y++P++++E        +  N                              
Sbjct: 62  DQVKRLKEAYSRPIMIVEGSLYGIRNVHPN------------------------------ 91

Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFEL-KQGRDE 266
                    I   +  +T+ F  + +I+SS P  TAQ  F + K+ ++E
Sbjct: 92  --------AIRGAIAAVTVDF-GVPIIFSSTPEETAQYIFLIAKREQEE 131
>d2bgwa2 c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum pernix [TaxId: 56636]} Length = 133 Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Length = 62 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 ?
Query410
d2bgwa2133 XPF endonuclease {Aeropyrum pernix [TaxId: 56636]} 100.0
d1j23a_131 Putative ATP-dependent RNA helicase Hef, nuclease 99.98
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 99.44
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 98.81
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 98.74
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 98.66
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 98.65
d2a1ia1129 DNA excision repair protein ERCC-1 {Human (Homo sa 98.39
d1wp9a2286 putative ATP-dependent RNA helicase PF2015 {Pyroco 98.01
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 98.01
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 97.98
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 97.74
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 95.25
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 94.45
d1z5za1244 Helicase of the SNF2/Rad54 hamily {Sulfolobus solf 93.65
d1z3ix1346 Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI 92.75
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 86.59
d1jx4a2240 DinB homolog (DBH) {Archaeon Sulfolobus solfataric 86.52
d1zeta2273 DNA polymerase iota {Human (Homo sapiens) [TaxId: 85.63
d1c4oa2174 Nucleotide excision repair enzyme UvrB {Thermus th 84.93
d1hv8a2155 Putative DEAD box RNA helicase {Archaeon Methanoco 84.71
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 84.49
d2q0zx1176 Protein pro2281 {Human (Homo sapiens) [TaxId: 9606 84.4
d1fuka_162 Initiation factor 4a {Baker's yeast (Saccharomyces 84.37
d1t5la2181 Nucleotide excision repair enzyme UvrB {Bacillus c 84.14
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 83.57
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 82.73
>d2bgwa2 c.52.1.20 (A:16-148) XPF endonuclease {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: XPF endonuclease
species: Aeropyrum pernix [TaxId: 56636]

Probab=100.00  E-value=3e-34  Score=249.46  Aligned_cols=129  Identities=32%  Similarity=0.479  Sum_probs=118.4

Q ss_pred             CCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEE
Q psy11328         96 SCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLI  175 (410)
Q Consensus        96 ~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLI  175 (410)
                      ..|+||||+||++|.+|..|+..|+++++++|++|||+|++++||||||++||++|++|||+++|+.+|+++|++|+|||
T Consensus         2 ~~p~IiiD~RE~~s~~~~~l~~~gi~~~~~~L~~GDy~i~~~~iIERKt~~Dl~~Si~dgR~~eQ~~rL~~~~~~~~~LI   81 (133)
T d2bgwa2           2 GRPRVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLFEQASRLAEHYETVFIIV   81 (133)
T ss_dssp             SSCEEEEETTTTTSSHHHHHHHTTCEEEEECCSSSSEEEETTEEEEEEEHHHHHHHHHHSHHHHHHHHHHHHCSEEEEEE
T ss_pred             CCCEEEEECCCCcchhhHHHHHCCCEEEEEEcCCcCEEEecCEEEEEechhHhhhhccCChHHHHHHHHHhcCCCeEEEE
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhHHH
Q psy11328        176 EFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQ  255 (410)
Q Consensus       176 E~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~  255 (410)
                      ||+.....         ..++                            ++++.++|+.+.+.+ |++|+||.|+.+||.
T Consensus        82 Eg~~~~~~---------~~~~----------------------------~~~l~~al~~l~~~~-g~~vi~t~~~~eTa~  123 (133)
T d2bgwa2          82 EGPPVPRR---------YRGR----------------------------ERSLYAAMAALQLDY-GIRLMNTMDPKGTAL  123 (133)
T ss_dssp             ESCSSCGG---------GTTT----------------------------HHHHHHHHHHHHHHS-CCEEEEESSHHHHHH
T ss_pred             EcCcchhh---------ccCC----------------------------HHHHHHHHHHHHHHc-CceEEEeCCHHHHHH
Confidence            99854311         1121                            689999999999999 999999999999999


Q ss_pred             HHHHHhc
Q psy11328        256 LFFELKQ  262 (410)
Q Consensus       256 ll~~Lk~  262 (410)
                      +|..|++
T Consensus       124 ~l~~lak  130 (133)
T d2bgwa2         124 VIESLAR  130 (133)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9999976
>d1j23a_ c.52.1.20 (A:) Putative ATP-dependent RNA helicase Hef, nuclease domain {Archaeon 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
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>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
>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} 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
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} 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
>d1jx4a2 e.8.1.7 (A:1-240) DinB homolog (DBH) {Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287]} Back     information, alignment and structure
>d1zeta2 e.8.1.7 (A:27-299) DNA polymerase iota {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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
>d2q0zx1 a.289.1.1 (X:33-208) Protein pro2281 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} 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