Psyllid ID: psy14294

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----
AQRKTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPAPAQTVQDEEEDSDSDDTEAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHccccEEEEEHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccEEEccccHHHHHHHHHHcccEEEEEccccccccccccEEEEccccccccEEEEEHHHHHHcc
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHcccccccccccccccccccccccccccccccccccccEEEEEccccEEEcccHHHccccccHHHHHHHHHHHHcccccccccccccccHccccHHHHHHHHHHHcccEEEEEHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccEEEcccHHHHHHHHHHHcccEEEEEcccHHHHHcccHHHHHHHHccccccEEEcHHHHHccc
aqrktlkskaasNADKVRSDLLKNLLEQQLLNDvlgknemalpppsvsrevdmfelppapaqtvqdeeedsdsddteAKFRyadlhsvdinseqfsalppdmRHEILTELLEQRKLSSwhkmhempqndqhSMLEFRCNIVINKLLVDLISDVSIWLHQLTkgthdlaggsvpnahLIGLYHRICKLLFFKikpvfvfdggvpqlkKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGvpfivapgeaEAQCASLElgnhtqgvitddsdiwLFGARTVYKNffdkkshvlrytapdiryyf
aqrktlkskaasnadkvRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPapaqtvqdeeedsdSDDTEAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYknffdkkshvlrytapdiryyf
AQRKTLKSKAASNADKVRSDllknlleqqllnDVLGKNEMALPPPSVSREVDMFELPPAPAQTVQdeeedsdsddTEAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
**********************************************************************************************************L*************************MLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI********************************QELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY*
********************LLKNLLE**************************FE******************************HSVDINSEQFSALPPDMRHEILT**************************EFRCNIVINKLLVDLISDVSIWLHQLTKGT**********AHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQ**************************TEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
**************DKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPAP****************EAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
*****LKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPP********FE*P******************TEAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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AQRKTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPAPAQTVQDEEEDSDSDDTEAKFRYADLHSVDINSEQFSALPPDMRHEILTELLEQRKLSSWHKMHEMPQNDQHSMLEFRCNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTISTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYF
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 ?
Query314 2.2.26 [Sep-21-2011]
P14629 1196 DNA repair protein comple N/A N/A 0.216 0.056 0.670 2e-26
P35689 1170 DNA repair protein comple yes N/A 0.257 0.069 0.578 1e-24
P28715 1186 DNA repair protein comple yes N/A 0.257 0.068 0.568 2e-24
Q9ATY5 1479 DNA repair protein UVH3 O yes N/A 0.296 0.062 0.480 5e-22
Q17RS7 908 Flap endonuclease GEN hom no N/A 0.493 0.170 0.365 2e-19
B4J6M4 388 Flap endonuclease 1 OS=Dr N/A N/A 0.436 0.353 0.363 8e-19
Q8BMI4 908 Flap endonuclease GEN hom no N/A 0.5 0.172 0.351 2e-18
P07276 1031 DNA repair protein RAD2 O yes N/A 0.292 0.089 0.483 4e-18
Q8W5R1 641 Flap endonuclease GEN-lik no N/A 0.487 0.238 0.364 1e-17
B4LM90 386 Flap endonuclease 1 OS=Dr N/A N/A 0.436 0.354 0.357 1e-17
>sp|P14629|ERCC5_XENLA DNA repair protein complementing XP-G cells homolog OS=Xenopus laevis GN=ercc5 PE=2 SV=1 Back     alignment and function desciption
 Score =  120 bits (300), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 64/82 (78%)

Query: 229 RLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 288
           R+A+T+T QM  E+QELLQLFG+P+IVAP EAEAQCA L+L + T G ITDDSDIWLFGA
Sbjct: 792 RIAATVTGQMCLESQELLQLFGIPYIVAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGA 851

Query: 289 RTVYKNFFDKKSHVLRYTAPDI 310
           R VYKNFF +  HV  Y   DI
Sbjct: 852 RHVYKNFFSQNKHVEYYQYADI 873
Single-stranded structure-specific DNA endonuclease involved in DNA excision repair. Makes the 3'incision in DNA nucleotide excision repair (NER). Acts as a cofactor for a DNA glycosylase that removes oxidized pyrimidines from DNA. May also be involved in transcription-coupled repair of this kind of damage, in transcription by RNA polymerase II, and perhaps in other processes too.
Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|P35689|ERCC5_MOUSE DNA repair protein complementing XP-G cells homolog OS=Mus musculus GN=Ercc5 PE=1 SV=4 Back     alignment and function description
>sp|P28715|ERCC5_HUMAN DNA repair protein complementing XP-G cells OS=Homo sapiens GN=ERCC5 PE=1 SV=3 Back     alignment and function description
>sp|Q9ATY5|UVH3_ARATH DNA repair protein UVH3 OS=Arabidopsis thaliana GN=UVH3 PE=2 SV=1 Back     alignment and function description
>sp|Q17RS7|GEN_HUMAN Flap endonuclease GEN homolog 1 OS=Homo sapiens GN=GEN1 PE=1 SV=2 Back     alignment and function description
>sp|B4J6M4|FEN1_DROGR Flap endonuclease 1 OS=Drosophila grimshawi GN=Fen1 PE=3 SV=1 Back     alignment and function description
>sp|Q8BMI4|GEN_MOUSE Flap endonuclease GEN homolog 1 OS=Mus musculus GN=Gen1 PE=2 SV=2 Back     alignment and function description
>sp|P07276|RAD2_YEAST DNA repair protein RAD2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD2 PE=1 SV=2 Back     alignment and function description
>sp|Q8W5R1|GENL2_ORYSJ Flap endonuclease GEN-like 2 OS=Oryza sativa subsp. japonica GN=SEND1 PE=2 SV=1 Back     alignment and function description
>sp|B4LM90|FEN1_DROVI Flap endonuclease 1 OS=Drosophila virilis GN=Fen1 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 ?
Query314
443703547 464 hypothetical protein CAPTEDRAFT_17841 [C 0.490 0.331 0.608 4e-52
156395868250 predicted protein [Nematostella vectensi 0.515 0.648 0.514 1e-44
196004776247 hypothetical protein TRIADDRAFT_23638 [T 0.480 0.611 0.534 2e-43
449676998 431 PREDICTED: DNA repair protein complement 0.503 0.366 0.523 2e-41
323456781238 hypothetical protein AURANDRAFT_4733, pa 0.512 0.676 0.488 6e-37
328857380288 hypothetical protein MELLADRAFT_36164 [M 0.515 0.562 0.426 7e-33
357620639 1103 hypothetical protein KGM_08405 [Danaus p 0.286 0.081 0.590 5e-29
328774021284 hypothetical protein BATDEDRAFT_2594, pa 0.496 0.549 0.421 3e-28
242019297 1052 DNA excision repair protein, putative [P 0.359 0.107 0.555 4e-28
195454489 1247 GK18419 [Drosophila willistoni] gi|19417 0.340 0.085 0.564 7e-27
>gi|443703547|gb|ELU01026.1| hypothetical protein CAPTEDRAFT_17841 [Capitella teleta] Back     alignment and taxonomy information
 Score =  211 bits (536), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 98/161 (60%), Positives = 121/161 (75%), Gaps = 7/161 (4%)

Query: 149 LISDVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQ 208
           L  DVS+W+HQL KG  D  G  VPNAHLIGLYHRICKLL+++IKPVFVFDGGVP LKKQ
Sbjct: 27  LAVDVSMWMHQLMKGMRDSHGNPVPNAHLIGLYHRICKLLYYRIKPVFVFDGGVPALKKQ 86

Query: 209 TI-------STLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAE 261
           T          LE +  +L   R +Q R+A+++TEQM+ EAQEL++LFG+P++V+P EAE
Sbjct: 87  TTDELIDLQKVLEVENTELHNTRNQQDRMATSLTEQMNIEAQELVRLFGLPYVVSPMEAE 146

Query: 262 AQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHV 302
           AQCA L+L + T G +TDDSDIWLFG R VYKN F+ K HV
Sbjct: 147 AQCAFLDLTSQTNGTVTDDSDIWLFGGRNVYKNLFNSKRHV 187

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota
>gi|156395868|ref|XP_001637332.1| predicted protein [Nematostella vectensis] gi|156224443|gb|EDO45269.1| predicted protein [Nematostella vectensis] Back     alignment and taxonomy information
>gi|196004776|ref|XP_002112255.1| hypothetical protein TRIADDRAFT_23638 [Trichoplax adhaerens] gi|190586154|gb|EDV26222.1| hypothetical protein TRIADDRAFT_23638 [Trichoplax adhaerens] Back     alignment and taxonomy information
>gi|449676998|ref|XP_002156033.2| PREDICTED: DNA repair protein complementing XP-G cells-like, partial [Hydra magnipapillata] Back     alignment and taxonomy information
>gi|323456781|gb|EGB12647.1| hypothetical protein AURANDRAFT_4733, partial [Aureococcus anophagefferens] Back     alignment and taxonomy information
>gi|328857380|gb|EGG06497.1| hypothetical protein MELLADRAFT_36164 [Melampsora larici-populina 98AG31] Back     alignment and taxonomy information
>gi|357620639|gb|EHJ72769.1| hypothetical protein KGM_08405 [Danaus plexippus] Back     alignment and taxonomy information
>gi|328774021|gb|EGF84058.1| hypothetical protein BATDEDRAFT_2594, partial [Batrachochytrium dendrobatidis JAM81] Back     alignment and taxonomy information
>gi|242019297|ref|XP_002430098.1| DNA excision repair protein, putative [Pediculus humanus corporis] gi|212515179|gb|EEB17360.1| DNA excision repair protein, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
>gi|195454489|ref|XP_002074261.1| GK18419 [Drosophila willistoni] gi|194170346|gb|EDW85247.1| GK18419 [Drosophila willistoni] 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 ?
Query314
UNIPROTKB|Q3B7N6 1201 ERCC5 "Uncharacterized protein 0.315 0.082 0.565 1.2e-42
UNIPROTKB|E1BC95 1615 ERCC5 "Uncharacterized protein 0.315 0.061 0.565 3.3e-42
FB|FBgn0002887 1257 mus201 "mutagen-sensitive 201" 0.340 0.085 0.537 2.2e-39
SGD|S000003490 1031 RAD2 "Single-stranded DNA endo 0.296 0.090 0.483 9.9e-36
POMBASE|SPBC3E7.08c 1112 rad13 "DNA repair nuclease Rad 0.318 0.089 0.450 1.8e-34
UNIPROTKB|I3LQY2 1562 ERCC5 "Uncharacterized protein 0.350 0.070 0.516 1.2e-31
ZFIN|ZDB-GENE-050327-28 1010 ercc5 "excision repair cross-c 0.308 0.096 0.571 1.9e-31
MGI|MGI:103582 1170 Ercc5 "excision repair cross-c 0.315 0.084 0.565 6.1e-31
UNIPROTKB|J9P9A3 1185 BIVM "Uncharacterized protein" 0.324 0.086 0.547 6.4e-31
UNIPROTKB|P28715 1186 ERCC5 "DNA repair protein comp 0.315 0.083 0.555 1.3e-30
UNIPROTKB|Q3B7N6 ERCC5 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
 Score = 274 (101.5 bits), Expect = 1.2e-42, Sum P(2) = 1.2e-42
 Identities = 56/99 (56%), Positives = 71/99 (71%)

Query:   211 STLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELG 270
             S L   ++ L  ++ +Q R+A+T+T QM  E+QELL+LFG+P+I AP EAEAQCA L+L 
Sbjct:   757 SNLLTQQNTLKAQKQQQERVAATVTGQMFLESQELLRLFGIPYIEAPMEAEAQCAILDLT 816

Query:   271 NHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPD 309
             + T G ITDDSDIWLFGAR VYKNFF+K   V  Y   D
Sbjct:   817 DQTSGTITDDSDIWLFGARHVYKNFFNKNKFVEYYQYVD 855
GO:0047485 "protein N-terminus binding" evidence=ISS
GO:0043066 "negative regulation of apoptotic process" evidence=ISS
GO:0042803 "protein homodimerization activity" evidence=ISS
GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS
GO:0010225 "response to UV-C" evidence=ISS
GO:0009411 "response to UV" evidence=ISS
GO:0006295 "nucleotide-excision repair, DNA incision, 3'-to lesion" evidence=ISS
GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=ISS
GO:0005675 "holo TFIIH complex" evidence=ISS
GO:0005634 "nucleus" evidence=ISS
GO:0004520 "endodeoxyribonuclease activity" evidence=ISS
GO:0003697 "single-stranded DNA binding" evidence=ISS
GO:0003690 "double-stranded DNA binding" evidence=ISS
GO:0000405 "bubble DNA binding" evidence=ISS
UNIPROTKB|E1BC95 ERCC5 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
FB|FBgn0002887 mus201 "mutagen-sensitive 201" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
SGD|S000003490 RAD2 "Single-stranded DNA endonuclease" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
POMBASE|SPBC3E7.08c rad13 "DNA repair nuclease Rad13" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|I3LQY2 ERCC5 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-050327-28 ercc5 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
MGI|MGI:103582 Ercc5 "excision repair cross-complementing rodent repair deficiency, complementation group 5" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|J9P9A3 BIVM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P28715 ERCC5 "DNA repair protein complementing XP-G cells" [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 ?
Query314
cd09868249 cd09868, PIN_XPG, PIN domain of Xeroderma pigmento 6e-79
cd09856207 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc 2e-44
cd09869233 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 4e-36
TIGR00600 1034 TIGR00600, rad2, DNA excision repair protein (rad2 3e-32
cd09870239 cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas 4e-29
cd09867261 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease 1e-27
PTZ00217 393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 3e-26
PRK03980 292 PRK03980, PRK03980, flap endonuclease-1; Provision 2e-24
TIGR03674 338 TIGR03674, fen_arch, flap structure-specific endon 2e-23
TIGR00600 1034 TIGR00600, rad2, DNA excision repair protein (rad2 1e-22
cd09857210 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a 4e-22
cd00128209 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E 5e-22
smart0048473 smart00484, XPGI, Xeroderma pigmentosum G I-region 2e-21
smart0048599 smart00485, XPGN, Xeroderma pigmentosum G N-region 1e-18
pfam00752100 pfam00752, XPG_N, XPG N-terminal domain 2e-18
pfam0086746 pfam00867, XPG_I, XPG I-region 5e-17
COG0258 310 COG0258, Exo, 5'-3' exonuclease (including N-termi 4e-15
TIGR00600 1034 TIGR00600, rad2, DNA excision repair protein (rad2 1e-11
cd09853163 cd09853, PIN_StructSpec-5'-nucleases, PIN domains 1e-11
cd09852120 cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup 3e-11
cd09858215 cd09858, PIN_MKT1, PIN domain of Mkt1: A global re 8e-08
pfam12813 223 pfam12813, XPG_I_2, XPG domain containing 1e-04
>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs Back     alignment and domain information 
 Score =  240 bits (614), Expect = 6e-79
 Identities = 88/184 (47%), Positives = 115/184 (62%), Gaps = 21/184 (11%)

Query: 152 DVSIWLHQLTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQLKKQTI- 210
           D SIW++Q  KG  D  G ++ NAHL+G + RICKLLF+ IKPVFVFDGG P+LK++T+ 
Sbjct: 30  DASIWIYQFLKGMRDREGNALKNAHLLGFFRRICKLLFYGIKPVFVFDGGAPELKRRTLA 89

Query: 211 ----------STLEKDRDQLLL----------ERGKQTRLASTITEQMSREAQELLQLFG 250
                        +K  ++LL           ++ +Q R A  IT++M  E QELL+LFG
Sbjct: 90  KRRQQREKAEINAKKTAEKLLASQLKKSAVKSQQQQQERDADEITQEMYDECQELLRLFG 149

Query: 251 VPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
           +P+IVAP EAEAQCA L       GVITDDSD++LFGA+ VYKNFF+   +V  Y A DI
Sbjct: 150 IPYIVAPMEAEAQCAILNQLGLVDGVITDDSDVFLFGAKRVYKNFFNGNKYVEYYLAEDI 209

Query: 311 RYYF 314
               
Sbjct: 210 EKEL 213

The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain). In XPG PIN domains, this arch region can be quite variable and extensive (400 - 800 residues) in length and is required for NER activity and for efficient processing of bubble substrates. Inserted within the PIN domain of these 5' nucleases is a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 249
>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases Back     alignment and domain information
>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs Back     alignment and domain information
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2) Back     alignment and domain information
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and fungal homologs Back     alignment and domain information
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs Back     alignment and domain information
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease Back     alignment and domain information
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2) Back     alignment and domain information
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs Back     alignment and domain information
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1 (FEN1)-like and Exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases Back     alignment and domain information
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region Back     alignment and domain information
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region Back     alignment and domain information
>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain Back     alignment and domain information
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region 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|233044 TIGR00600, rad2, DNA excision repair protein (rad2) 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|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily Back     alignment and domain information
>gnl|CDD|189028 cd09858, PIN_MKT1, PIN domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs Back     alignment and domain information
>gnl|CDD|221785 pfam12813, XPG_I_2, XPG domain containing Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 314
cd00128 316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 100.0
PTZ00217 393 flap endonuclease-1; Provisional 100.0
TIGR03674 338 fen_arch flap structure-specific endonuclease. End 100.0
KOG2518|consensus 556 100.0
KOG2519|consensus 449 100.0
PRK03980 292 flap endonuclease-1; Provisional 99.97
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.95
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 99.87
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 99.87
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 99.81
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 99.8
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.79
KOG2520|consensus 815 99.75
smart00475259 53EXOc 5'-3' exonuclease. 99.71
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 99.68
COG0258 310 Exo 5'-3' exonuclease (including N-terminal domain 99.67
PRK14976 281 5'-3' exonuclease; Provisional 99.64
TIGR00593 887 pola DNA polymerase I. This family is based on the 99.52
PRK05755 880 DNA polymerase I; Provisional 99.52
PF02739169 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv 99.32
PRK09482256 flap endonuclease-like protein; Provisional 99.27
PHA00439 286 exonuclease 98.94
PF12813 246 XPG_I_2: XPG domain containing 98.91
PHA02567 304 rnh RnaseH; Provisional 98.61
PF03159237 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: 98.05
PHA03065 438 Hypothetical protein; Provisional 95.79
PF04599 425 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P 95.69
PF05991166 NYN_YacP: YacP-like NYN domain; InterPro: IPR01029 95.03
COG5366 531 Protein involved in propagation of M2 dsRNA satell 91.46
PF11977155 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domai 80.27
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information 
Probab=100.00  E-value=3.4e-39  Score=308.23  Aligned_cols=188  Identities=40%  Similarity=0.588  Sum_probs=163.7

Q ss_pred             CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhhhhC--CCCCchHHHHHHHHHHHHHHhCCCeeEEEee
Q psy14294        125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTHDLA--GGSVPNAHLIGLYHRICKLLFFKIKPVFVFD  199 (314)
Q Consensus       125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~--G~~~~~~~l~~f~~rL~~Ll~~gI~PIFVFD  199 (314)
                      |||+|||+++.+.+   +|+.++ |++|||||++||||++++++...  |+..+ +++.+|++++..|+++||+||||||
T Consensus         1 MGI~gL~~~l~~~~~~~~i~~l~-gk~laID~~~~l~r~~~a~~~~~~~~g~~~-~~l~~~~~rl~~L~~~~i~pvfVFD   78 (316)
T cd00128           1 MGIKGLWPLLKPVARPVHLEELR-GKKVAIDASIWLYQFLKACRQELGSGGETT-SHLQGFFYRTCRLLELGIKPVFVFD   78 (316)
T ss_pred             CchhhHHHHHHhhCCCCCHHHhC-CcEEEecHHHHHHHHHHHhhhhccCCCCCc-HHHHHHHHHHHHHHHCCCEEEEEEc
Confidence            89999999999776   577887 99999999999999998885432  33333 3999999999999999999999999


Q ss_pred             CCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHH
Q psy14294        200 GGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASL  267 (314)
Q Consensus       200 G~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L  267 (314)
                      |.+++.|..+..+|+.++.++..            ++.++.+++..+++.++..++++|+.+||||++||||||||||+|
T Consensus        79 G~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l  158 (316)
T cd00128          79 GKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYL  158 (316)
T ss_pred             CCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHH
Confidence            99999999999998877665321            223344566788999999999999999999999999999999999


Q ss_pred             HhcCCeeEEEcCCccEEeecCCeeeeeccCCC-CcEEEEehhhhhhcC
Q psy14294        268 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKK-SHVLRYTAPDIRYYF  314 (314)
Q Consensus       268 ~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~-~~v~~y~~~~i~~~~  314 (314)
                      ++.|+||+|+|+|||+|+||+++||++++..+ .++++|+.+++..+|
T Consensus       159 ~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~l  206 (316)
T cd00128         159 AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKEL  206 (316)
T ss_pred             HhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHc
Confidence            99999999999999999999999999999876 589999999997754

XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>KOG2518|consensus Back     alignment and domain information
>KOG2519|consensus Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>smart00485 XPGN Xeroderma pigmentosum G N-region Back     alignment and domain information
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer Back     alignment and domain information
>smart00484 XPGI Xeroderma pigmentosum G I-region 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
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>KOG2520|consensus Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease 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
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14976 5'-3' exonuclease; Provisional 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
>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
>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information
>PHA00439 exonuclease Back     alignment and domain information
>PF12813 XPG_I_2: XPG domain containing Back     alignment and domain information
>PHA02567 rnh RnaseH; Provisional 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
>PHA03065 Hypothetical protein; Provisional Back     alignment and domain information
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses Back     alignment and domain information
>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
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only] 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query314
1mc8_A 343 Crystal Structure Of Flap Endonuclease-1 R42e Mutan 4e-15
3q8k_A 341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 3e-14
1ul1_X 379 Crystal Structure Of The Human Fen1-Pcna Complex Le 3e-14
1b43_A 340 Fen-1 From P. Furiosus Length = 340 4e-14
3ory_A 363 Crystal Structure Of Flap Endonuclease 1 From Hyper 2e-13
3q8m_A 341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 2e-13
1rxv_A 336 Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna 2e-12
1a76_A 326 Flap Endonuclease-1 From Methanococcus Jannaschii L 1e-11
2izo_A 346 Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L 1e-10
3qea_Z 352 Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) 2e-08
3qe9_Y 352 Crystal Structure Of Human Exonuclease 1 Exo1 (D173 2e-07
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343 Back     alignment and structure 
Iteration: 1

 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 83/171 (48%), Gaps = 14/171 (8%)
Query: 139 NIVINKLLVDLISDVSIWLHQLTK--GTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVF 196
           N+   K+ +D ++ +  +L  + +  GT  +       +HL GL++R   L+   IKP +
Sbjct: 18  NLYGKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAY 77
Query: 197 VFDGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQE 244
           VFDG  P+ K++ +    + R++  L            E  K  + A+ + E +  +A++
Sbjct: 78  VFDGKPPEFKRKELEKRREAREEAELKWKEALAKGNLEEARKYAQRATKVNEMLIEDAKK 137
Query: 245 LLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNF 295
           LLQL G+P I AP E EAQ A +          + D D  LFGA  + +N 
Sbjct: 138 LLQLMGIPIIQAPSEGEAQAAYMASKGDVYASASQDYDSLLFGAPRLIRNL 188
>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In Complex With Product 5'-Flap Dna, Sm3+, And K+ Length = 341 Back     alignment and structure
>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex Length = 379 Back     alignment and structure
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340 Back     alignment and structure
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363 Back     alignment and structure
>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a) In Complex With Substrate 5'-Flap Dna And K+ Length = 341 Back     alignment and structure
>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna Length = 336 Back     alignment and structure
>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326 Back     alignment and structure
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346 Back     alignment and structure
>pdb|3QEA|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In Complex With Dna (Complex Ii) Length = 352 Back     alignment and structure
>pdb|3QE9|Y Chain Y, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In Complex With Dna (Complex I) Length = 352 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 ?
Query314
1a76_A 326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 4e-48
2izo_A 346 FEN1, flap structure-specific endonuclease; hydrol 1e-46
1rxw_A 336 Flap structure-specific endonuclease; helical clam 1e-46
3q8k_A 341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 1e-46
3ory_A 363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 2e-46
1ul1_X 379 Flap endonuclease-1; protein complex, DNA-binding 5e-46
1b43_A 340 Protein (FEN-1); nuclease, DNA repair, DNA replica 1e-44
3qe9_Y 352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 3e-36
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-06
>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
 Score =  163 bits (413), Expect = 4e-48
 Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 18/177 (10%)

Query: 152 DVSIWLHQLTKGTHDLAGGSV------PNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
           D    L+Q         G  +        +   G++++   LL   I P++VFDG  P+L
Sbjct: 27  DGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKL 86

Query: 206 KKQTIS------------TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
           K++T                E  + +   E  K  +  S +T +M    + LL L G+P+
Sbjct: 87  KEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPY 146

Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
           + AP E EAQ + +        V++ D D  L+GA  V +N    K         ++
Sbjct: 147 VEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEV 203
>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
>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
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363 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
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Length = 340 Back     alignment and structure
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352 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 ?
Query314
3qe9_Y 352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 100.0
3ory_A 363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 100.0
1b43_A 340 Protein (FEN-1); nuclease, DNA repair, DNA replica 100.0
1a76_A 326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 100.0
3q8k_A 341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 100.0
1rxw_A 336 Flap structure-specific endonuclease; helical clam 100.0
1ul1_X 379 Flap endonuclease-1; protein complex, DNA-binding 100.0
2izo_A 346 FEN1, flap structure-specific endonuclease; hydrol 99.98
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 99.8
1exn_A 290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 99.76
3h7i_A 305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 98.91
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 96.59
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 96.32
3fqd_A 899 Protein DHP1, 5'-3' exoribonuclease 2; protein-pro 95.83
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Back     alignment and structure
Probab=100.00  E-value=1.2e-37  Score=300.93  Aligned_cols=182  Identities=25%  Similarity=0.289  Sum_probs=152.4

Q ss_pred             CCcccccccccccc---cccccCCCCEEEeeHHHHHHHHHHHhh--hhCCCCCchHHHHHHHHHH-HHHHhCCCeeEEEe
Q psy14294        125 MPQNDQHSMLEFRC---NIVINKLLVDLISDVSIWLHQLTKGTH--DLAGGSVPNAHLIGLYHRI-CKLLFFKIKPVFVF  198 (314)
Q Consensus       125 m~i~~l~~~l~~~~---~Ls~~~~g~rIaIDas~WL~q~~~a~~--~~~G~~~~~~~l~~f~~rL-~~Ll~~gI~PIFVF  198 (314)
                      |||+|||+++.+.+   +|..+. |++|||||++||||+++++.  ...|.++.  ++.++|.+. ..|+++||+|||||
T Consensus         1 MGI~GL~~~L~~~~~~~~l~~l~-Gk~vaIDas~wL~~~~~~~~~~l~~G~~t~--~l~~~~~r~l~~L~~~gI~PvfVF   77 (352)
T 3qe9_Y            1 MGIQGLLQFIKEASEPIHVRKYK-GQVVAVDTYCWLHKGAIACAEKLAKGEPTD--RYVGFCMKFVNMLLSHGIKPILVF   77 (352)
T ss_dssp             -CCTTHHHHTTTSEEEEEGGGGT-TSEEEEETHHHHHHHHHHTHHHHHTTCCCC--HHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CCcchHHHHHHhhCCcCCHHHhC-CcEEEEecHHHHHHhhhccchhhcCCCCcH--HHHHHHHHHHHHHHHcCCEEEEEE
Confidence            89999999999886   666777 99999999999999877663  35677765  777776654 56789999999999


Q ss_pred             eCCCccchhhhhhhhhhhhHHHHH------------HhcccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHH
Q psy14294        199 DGGVPQLKKQTISTLEKDRDQLLL------------ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCAS  266 (314)
Q Consensus       199 DG~~~~~K~~t~~kR~~~r~~~~~------------~~~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~  266 (314)
                      ||.+++.|+.+..+|+++|.+..+            ++.+..+++..+++.++..++++|+.+||||++||||||+|||+
T Consensus        78 DG~~~p~Kk~~~~~Rr~~r~~~~~~~~~~~~~g~~~~a~~~f~~~~~vt~~~~~~i~~~L~~~gIp~i~ap~EADaqiA~  157 (352)
T 3qe9_Y           78 DGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAY  157 (352)
T ss_dssp             CCSCCTTTHHHHHHHHHHHHHHHHHHHHHTTSSCCHHHHHHHGGGCCCCHHHHHHHHHHHHHTTCEEEECSSCHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCcEEECCcchHHHHHH
Confidence            999999999998888877664322            12233456778999999999999999999999999999999999


Q ss_pred             HHhcCCeeEEEcCCccEEeecCCeeeeeccCCCCcEEEEehhhh
Q psy14294        267 LELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI  310 (314)
Q Consensus       267 L~~~g~vdaViS~DSD~llfG~~~Vi~~l~~~~~~v~~y~~~~i  310 (314)
                      |+++|++++|+|+|+|+|+||+++|+++++..++.+ .|+.+++
T Consensus       158 La~~g~~~~I~S~D~Dll~~~~~~v~~~~~~~~~~~-~~~~~~~  200 (352)
T 3qe9_Y          158 LNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGL-EIDQARL  200 (352)
T ss_dssp             HHHTTSCSEEECSCGGGGGGTCSEEEESCCTTSEEE-EEEGGGG
T ss_pred             HHHCCCeEEEEeCCcCcccccCCeEEEeccCCCCcE-EEeHHHH
Confidence            999999999999999999999999999998876543 4676664
>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
>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
>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
>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
>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
>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
>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
>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
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster} Back     alignment and structure
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo domain, mRNA turnover, RRN processing, RNA binding, DNA binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A Back     alignment and structure
>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex, exonuclease, hydrolase, mRNA proces nuclease, nucleus, rRNA processing, transcription; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure

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 314
d1a77a2207 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc 5e-33
d1rxwa2217 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc 2e-32
d1ul1x2216 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc 4e-30
d1b43a2219 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc 2e-29
>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 207 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: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  119 bits (298), Expect = 5e-33
 Identities = 44/177 (24%), Positives = 73/177 (41%), Gaps = 18/177 (10%)

Query: 152 DVSIWLHQ------LTKGTHDLAGGSVPNAHLIGLYHRICKLLFFKIKPVFVFDGGVPQL 205
           D    L+Q      L  G+          +   G++++   LL   I P++VFDG  P+L
Sbjct: 26  DGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKL 85

Query: 206 KKQTIS------------TLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPF 253
           K++T                E  + +   E  K  +  S +T +M    + LL L G+P+
Sbjct: 86  KEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPY 145

Query: 254 IVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDI 310
           + AP E EAQ + +        V++ D D  L+GA  V +N    K         ++
Sbjct: 146 VEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKEMPELIELNEV 202
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 217 Back     information, alignment and structure
>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 216 Back     information, alignment and structure
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 219 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 ?
Query314
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 100.0
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 100.0
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 100.0
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 100.0
d1cmwa2164 5' to 3' exonuclease domain of DNA polymerase Taq 99.12
d1xo1a2167 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 98.63
d1tfra2169 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 98.48
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 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: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=9.3e-43  Score=313.24  Aligned_cols=170  Identities=27%  Similarity=0.364  Sum_probs=145.0

Q ss_pred             ccccccccc-ccccccCCCCEEEeeHHHHHHHHHHHhhhhCCCCCc------hHHHHHHHHHHHHHHhCCCeeEEEeeCC
Q psy14294        129 DQHSMLEFR-CNIVINKLLVDLISDVSIWLHQLTKGTHDLAGGSVP------NAHLIGLYHRICKLLFFKIKPVFVFDGG  201 (314)
Q Consensus       129 ~l~~~l~~~-~~Ls~~~~g~rIaIDas~WL~q~~~a~~~~~G~~~~------~~~l~~f~~rL~~Ll~~gI~PIFVFDG~  201 (314)
                      +|+.++..+ .+|+.++ |++|||||++||||++.+|+...|.++.      ++++.+|++++..|+++||+|||||||.
T Consensus         2 ~~~~l~~~~~~~l~~l~-Gk~vAIDas~wL~k~l~~~~~~~~~~l~~~~~~~~~~l~~~~~ri~~l~~~~I~pifVFDG~   80 (217)
T d1rxwa2           2 DIGDLFEREEVELEYFS-GKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGE   80 (217)
T ss_dssp             TGGGGCCCEECCGGGGT-TCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHHTCEEEEEECCS
T ss_pred             ChhHhccCcccCHHHhC-CCEEEEECHHHHHHHHHHhccccCCchhhccCCccHHHHHHHHHHHHHHHcCCeEEEEECCC
Confidence            345555544 4899999 9999999999999999888765444331      2599999999999999999999999999


Q ss_pred             CccchhhhhhhhhhhhHHHHHHh-----------cccccccCcccHHHHHHHHHHHHHhCCceEeccchHHHHHHHHHhc
Q psy14294        202 VPQLKKQTISTLEKDRDQLLLER-----------GKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELG  270 (314)
Q Consensus       202 ~~~~K~~t~~kR~~~r~~~~~~~-----------~k~~r~~~~i~~~~i~~~~~lLk~lGV~~I~AP~EADAq~A~L~~~  270 (314)
                      +|+.|..|..+|++++.++++.+           .+....+..++++++..++++|+.+|||||+||||||||||||+++
T Consensus        81 ~p~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~Ap~EAeaqcA~L~~~  160 (217)
T d1rxwa2          81 PPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAK  160 (217)
T ss_dssp             CCGGGHHHHHHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHHCCCCHHHHHHHHHHHHHTTCCEEECSSCHHHHHHHHHHT
T ss_pred             CCcchhhHHHHHHHHHHhhhhhhhhhhhhhhHHHHHHHHhhccCCHHHHHHHHHHHHHcCceEEecCchHHHHHHHHHhC
Confidence            99999999999988887665322           1123346678999999999999999999999999999999999999


Q ss_pred             CCeeEEEcCCccEEeecCCeeeeeccCCC
Q psy14294        271 NHTQGVITDDSDIWLFGARTVYKNFFDKK  299 (314)
Q Consensus       271 g~vdaViS~DSD~llfG~~~Vi~~l~~~~  299 (314)
                      |+||+|+|+|||+|+|||++||++|+..+
T Consensus       161 g~vd~v~seDsD~l~fG~~~vir~l~~~~  189 (217)
T d1rxwa2         161 GDVEYTGSQDYDSLLFGSPRLARNLAITG  189 (217)
T ss_dssp             TSSSEEECSSSHHHHTTCSEEEESCCC--
T ss_pred             CCeEEEEecccceeeeCCCEEEEeccccc
Confidence            99999999999999999999999999866
>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
>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
>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