Psyllid ID: psy12967

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--
MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARLKGLQT
cccccccccccccccccccccccccEEEEEccEEEEEccccccccccccccccccccHHHHHHHHcccccccccccccccEEEEEHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHccccHHHHccHHHHHHHHHHcccccccccccccccccccccc
ccHcHHHHHHccccccccHHHccccEEEEEEEHHHHHHHHcccccHHHHHHHHHHcccccHHHHHccccccccHHHHcccEEEEEHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccccHcccccHHHHHHccccccccccccccccccccccc
mgvkdlwgiltpicerkpiwelqDKTIAIDLSawicdsstiaehssQKNMYLRAIMGVKDLwgiltpicerkpiwelqDKTIAIDLSawicdsstiaehssqknmylrnlFFRTSYLLLlgvkpifvlegkapvlkhdTIEKRQQAqgrsagrnvqagsrarnlFFRTSYLLLLgvkpifvlegkapvlkhdTIEKRQQAqgrsagrnvqaGSRARLKGLQT
mgvkdlwgiltpicerkpiweLQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKrqqaqgrsagrnvqagsrarnLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKrqqaqgrsagrnvqagsrarlkglqt
MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARLKGLQT
***KDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKH***********************ARNLFFRTSYLLLLGVKPIFVLEGKAPVLK********************************
MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA***SQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKH*************************NLFFRTSYLLLLGVKPIFVLEGKAPVLKH*******************************
MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEK**************AGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEK***************GSRARLKGLQT
*GVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAP***********************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRAIMGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSRARLKGLQT
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 ?
Query222 2.2.26 [Sep-21-2011]
Q9VRJ0 726 Flap endonuclease GEN OS= yes N/A 0.387 0.118 0.542 4e-24
Q29FC1 754 Flap endonuclease GEN OS= yes N/A 0.387 0.114 0.521 5e-22
Q17RS7 908 Flap endonuclease GEN hom yes N/A 0.445 0.109 0.48 1e-19
Q8BMI4 908 Flap endonuclease GEN hom yes N/A 0.445 0.109 0.46 4e-19
P07276 1031 DNA repair protein RAD2 O yes N/A 0.481 0.103 0.353 7e-12
P28706 1112 DNA repair protein rad13 yes N/A 0.400 0.080 0.402 2e-10
Q8W5R1 641 Flap endonuclease GEN-lik yes N/A 0.472 0.163 0.345 7e-10
P14629 1196 DNA repair protein comple N/A N/A 0.427 0.079 0.352 3e-09
Q9M2Z3 600 Flap endonuclease GEN-lik yes N/A 0.490 0.181 0.315 2e-08
P35689 1170 DNA repair protein comple no N/A 0.405 0.076 0.365 3e-08
>sp|Q9VRJ0|GEN_DROME Flap endonuclease GEN OS=Drosophila melanogaster GN=Gen PE=1 SV=1 Back     alignment and function desciption
 Score =  111 bits (277), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 51/94 (54%), Positives = 66/94 (70%)

Query: 56  MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTS 115
           MGVK+LWG+LTP CERKPI EL+ K +AIDL+ W+C+S  + ++      +L+NLFFRT 
Sbjct: 1   MGVKELWGVLTPHCERKPINELRGKKVAIDLAGWVCESLNVVDYFVHPRHHLKNLFFRTC 60

Query: 116 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGR 149
           YL+   V P+FVLEG AP LK   I KR + Q R
Sbjct: 61  YLIWEQVTPVFVLEGVAPKLKSQVIAKRNELQFR 94
Endonuclease which cleaves flap structures at the junction between single-stranded DNA and double-stranded DNA. Specific for 5'-overhanging flap structures in which the 5'-upstream of the flap is completely double-stranded. Prefers the blocked-flap structures similar to those occurring at replication forks, in which the 5' single-strand overhang of the flap is double-stranded. Also possesses weak 5'- to 3'-exonuclease activity on nicked but not gapped double-stranded DNA. Does not cleave bubble-like or Holliday junction substrates.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>sp|Q29FC1|GEN_DROPS Flap endonuclease GEN OS=Drosophila pseudoobscura pseudoobscura GN=Gen PE=3 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|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|P28706|RAD13_SCHPO DNA repair protein rad13 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad13 PE=2 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|P14629|ERCC5_XENLA DNA repair protein complementing XP-G cells homolog OS=Xenopus laevis GN=ercc5 PE=2 SV=1 Back     alignment and function description
>sp|Q9M2Z3|GENL2_ARATH Flap endonuclease GEN-like 2 OS=Arabidopsis thaliana GN=GEN2 PE=2 SV=2 Back     alignment and function description
>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

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 ?
Query222
340709477 725 PREDICTED: flap endonuclease GEN-like [B 0.603 0.184 0.524 1e-31
350420439 724 PREDICTED: flap endonuclease GEN-like [B 0.603 0.185 0.524 1e-31
307184932 738 Flap endonuclease GEN [Camponotus florid 0.504 0.151 0.571 1e-31
328792793 713 PREDICTED: flap endonuclease GEN-like [A 0.481 0.150 0.583 3e-30
307212664 741 Flap endonuclease GEN [Harpegnathos salt 0.481 0.144 0.555 1e-29
383854420 717 PREDICTED: flap endonuclease GEN-like [M 0.441 0.136 0.551 6e-29
156555588 736 PREDICTED: flap endonuclease GEN-like [N 0.481 0.145 0.555 5e-28
270011949 591 hypothetical protein TcasGA2_TC006044 [T 0.599 0.225 0.482 1e-27
189239788 565 PREDICTED: similar to XPG-like endonucle 0.599 0.235 0.482 1e-27
193643497 477 PREDICTED: flap endonuclease GEN-like [A 0.396 0.184 0.636 2e-27
>gi|340709477|ref|XP_003393334.1| PREDICTED: flap endonuclease GEN-like [Bombus terrestris] Back     alignment and taxonomy information
 Score =  142 bits (358), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/141 (52%), Positives = 93/141 (65%), Gaps = 7/141 (4%)

Query: 56  MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTS 115
           MGVKDLW IL+P+ ERKP++ELQ KT+AID+S WI DS T+ +HS+Q  MYLRNL+FRT+
Sbjct: 1   MGVKDLWNILSPLSERKPMFELQGKTVAIDMSCWIVDSQTVTDHSAQPKMYLRNLYFRTA 60

Query: 116 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQAGSR-ARNLFFRTSYLLLL 174
           +LL+ G+ P+FVLEGKAP LKH TI KR     RS  R  +  S+  R  F R    +L 
Sbjct: 61  FLLMQGISPVFVLEGKAPTLKHKTIAKRNDV--RSGFREKKTASKGGRTQFNR----ILN 114

Query: 175 GVKPIFVLEGKAPVLKHDTIE 195
             K +  L G A V  H   E
Sbjct: 115 ECKEMLQLMGLACVQGHGEAE 135

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|350420439|ref|XP_003492509.1| PREDICTED: flap endonuclease GEN-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|307184932|gb|EFN71197.1| Flap endonuclease GEN [Camponotus floridanus] Back     alignment and taxonomy information
>gi|328792793|ref|XP_001120033.2| PREDICTED: flap endonuclease GEN-like [Apis mellifera] Back     alignment and taxonomy information
>gi|307212664|gb|EFN88367.1| Flap endonuclease GEN [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|383854420|ref|XP_003702719.1| PREDICTED: flap endonuclease GEN-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|156555588|ref|XP_001605190.1| PREDICTED: flap endonuclease GEN-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|270011949|gb|EFA08397.1| hypothetical protein TcasGA2_TC006044 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|189239788|ref|XP_969346.2| PREDICTED: similar to XPG-like endonuclease CG10670-PA [Tribolium castaneum] Back     alignment and taxonomy information
>gi|193643497|ref|XP_001947849.1| PREDICTED: flap endonuclease GEN-like [Acyrthosiphon pisum] 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 ?
Query222
FB|FBgn0263831 726 Gen "XPG-like endonuclease" [D 0.423 0.129 0.542 1.5e-22
UNIPROTKB|Q29FC1 754 Gen "Flap endonuclease GEN" [D 0.423 0.124 0.521 1.4e-20
UNIPROTKB|E9PLG0126 GEN1 "Flap endonuclease GEN ho 0.445 0.785 0.48 2.7e-20
UNIPROTKB|E9PM3093 GEN1 "Flap endonuclease GEN ho 0.414 0.989 0.494 2.5e-19
UNIPROTKB|Q17RS7 908 GEN1 "Flap endonuclease GEN ho 0.445 0.109 0.48 4.8e-19
MGI|MGI:2443149 908 Gen1 "Gen homolog 1, endonucle 0.445 0.109 0.46 1.3e-18
UNIPROTKB|E1B8D0 914 GEN1 "Uncharacterized protein" 0.441 0.107 0.464 5.6e-18
UNIPROTKB|E2QU72 908 GEN1 "Uncharacterized protein" 0.441 0.107 0.454 3.1e-17
RGD|1559792 908 Gen1 "Gen endonuclease homolog 0.445 0.109 0.44 5.1e-17
UNIPROTKB|F1SCS5 914 GEN1 "Uncharacterized protein" 0.441 0.107 0.444 1.8e-16
FB|FBgn0263831 Gen "XPG-like endonuclease" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 271 (100.5 bits), Expect = 1.5e-22, P = 1.5e-22
 Identities = 51/94 (54%), Positives = 66/94 (70%)

Query:    56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTS 115
             MGVK+LWG+LTP CERKPI EL+ K +AIDL+ W+C+S  + ++      +L+NLFFRT 
Sbjct:     1 MGVKELWGVLTPHCERKPINELRGKKVAIDLAGWVCESLNVVDYFVHPRHHLKNLFFRTC 60

Query:   116 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGR 149
             YL+   V P+FVLEG AP LK   I KR + Q R
Sbjct:    61 YLIWEQVTPVFVLEGVAPKLKSQVIAKRNELQFR 94
GO:0006284 "base-excision repair" evidence=ISS
GO:0048256 "flap endonuclease activity" evidence=ISS
GO:0003684 "damaged DNA binding" evidence=ISS
GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISS;IDA
GO:0004519 "endonuclease activity" evidence=ISS
GO:0035312 "5'-3' exodeoxyribonuclease activity" evidence=IDA
GO:0008310 "single-stranded DNA specific 3'-5' exodeoxyribonuclease activity" evidence=IDA
GO:0000738 "DNA catabolic process, exonucleolytic" evidence=IDA
GO:0004520 "endodeoxyribonuclease activity" evidence=IDA
GO:0000737 "DNA catabolic process, endonucleolytic" evidence=IDA
GO:0008311 "double-stranded DNA specific 3'-5' exodeoxyribonuclease activity" evidence=IDA
GO:0006302 "double-strand break repair" evidence=IMP
UNIPROTKB|Q29FC1 Gen "Flap endonuclease GEN" [Drosophila pseudoobscura pseudoobscura (taxid:46245)] Back     alignment and assigned GO terms
UNIPROTKB|E9PLG0 GEN1 "Flap endonuclease GEN homolog 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E9PM30 GEN1 "Flap endonuclease GEN homolog 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q17RS7 GEN1 "Flap endonuclease GEN homolog 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:2443149 Gen1 "Gen homolog 1, endonuclease (Drosophila)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E1B8D0 GEN1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2QU72 GEN1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1559792 Gen1 "Gen endonuclease homolog 1 (Drosophila)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1SCS5 GEN1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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 ?
Query222
cd09869233 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 5e-38
smart0048599 smart00485, XPGN, Xeroderma pigmentosum G N-region 1e-25
cd09868 249 cd09868, PIN_XPG, PIN domain of Xeroderma pigmento 4e-19
TIGR00600 1034 TIGR00600, rad2, DNA excision repair protein (rad2 3e-16
cd09856207 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc 4e-16
pfam00752100 pfam00752, XPG_N, XPG N-terminal domain 2e-13
PTZ00217 393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 7e-11
cd09867261 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease 2e-10
TIGR03674 338 TIGR03674, fen_arch, flap structure-specific endon 6e-10
smart0048599 smart00485, XPGN, Xeroderma pigmentosum G N-region 2e-09
cd09857210 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a 7e-09
cd09867 261 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease 1e-08
PRK03980 292 PRK03980, PRK03980, flap endonuclease-1; Provision 1e-08
PRK03980 292 PRK03980, PRK03980, flap endonuclease-1; Provision 1e-08
TIGR03674 338 TIGR03674, fen_arch, flap structure-specific endon 6e-08
PTZ00217 393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 1e-07
cd09870239 cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas 5e-07
cd00128209 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E 9e-05
>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 
 Score =  131 bits (332), Expect = 5e-38
 Identities = 52/116 (44%), Positives = 67/116 (57%), Gaps = 5/116 (4%)

Query: 56  MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAEHSSQKNMYLRNLFFRTS 115
           MGVK LW IL P+ +RKP+  LQ K +A+DLS W+ +S T+ ++      +LRNLFFRT 
Sbjct: 1   MGVKGLWDILEPVKKRKPLDHLQGKRVAVDLSCWVVESQTVVKYFVVPKPHLRNLFFRTR 60

Query: 116 YLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSAGRNVQ-----AGSRARNLFF 166
           YL+ LGV P+FV++G AP LK   I KR Q Q   A             R R   F
Sbjct: 61  YLIALGVLPVFVVDGAAPPLKLPVIIKRNQLQSGIAKPGDNPTPKNGSKRNRRSRF 116

Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 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) of variable length (approximately 30 - 50 residues in GEN1 PIN domains) and 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 = 233
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region Back     alignment and domain information
>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
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2) Back     alignment and domain information
>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|216098 pfam00752, XPG_N, XPG N-terminal domain Back     alignment and domain information
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional 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|234306 TIGR03674, fen_arch, flap structure-specific endonuclease Back     alignment and domain information
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region 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|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|235185 PRK03980, PRK03980, 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|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional 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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 222
KOG2518|consensus 556 100.0
PTZ00217 393 flap endonuclease-1; Provisional 100.0
TIGR03674 338 fen_arch flap structure-specific endonuclease. End 100.0
cd00128 316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 100.0
KOG2519|consensus 449 100.0
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 99.95
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 99.95
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.93
PRK03980 292 flap endonuclease-1; Provisional 99.91
COG0258 310 Exo 5'-3' exonuclease (including N-terminal domain 99.4
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 99.34
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 99.32
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.23
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 99.08
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 99.06
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 99.01
smart00475 259 53EXOc 5'-3' exonuclease. 98.99
PRK14976 281 5'-3' exonuclease; Provisional 98.93
KOG2519|consensus 449 98.78
cd00128316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 98.72
KOG2520|consensus 815 98.7
PRK05755 880 DNA polymerase I; Provisional 98.65
PTZ00217 393 flap endonuclease-1; Provisional 98.65
TIGR00593 887 pola DNA polymerase I. This family is based on the 98.56
TIGR03674 338 fen_arch flap structure-specific endonuclease. End 98.39
KOG2518|consensus 556 97.99
PRK09482 256 flap endonuclease-like protein; Provisional 97.44
PF02739169 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv 97.37
PRK03980 292 flap endonuclease-1; Provisional 96.62
PHA00439 286 exonuclease 96.37
PF03159237 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: 95.87
PHA02567 304 rnh RnaseH; Provisional 95.56
PF05991166 NYN_YacP: YacP-like NYN domain; InterPro: IPR01029 92.22
PHA03065 438 Hypothetical protein; Provisional 91.52
PF04599 425 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P 88.98
COG2454211 Uncharacterized conserved protein [Function unknow 80.63
>KOG2518|consensus Back     alignment and domain information 
Probab=100.00  E-value=6.1e-37  Score=283.11  Aligned_cols=157  Identities=27%  Similarity=0.366  Sum_probs=140.7

Q ss_pred             hccccccccccccceeeccccccCcEEEeecchhhhhhhhhhh---hcCCchH-HHHHHHHHHHHHHhcCCeeEEEeeCC
Q psy12967         56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIAE---HSSQKNM-YLRNLFFRTSYLLLLGVKPIFVLEGK  131 (222)
Q Consensus        56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~~---~~~~~~~-~l~~~f~R~~~Ll~~gI~PIfVFDG~  131 (222)
                      |||+||+++++++.+++|+++|+|+++|||+|+|||++...+.   ..|++|. |+.+++.|+..|+.+||+||+||||.
T Consensus         1 MGI~GLlp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~   80 (556)
T KOG2518|consen    1 MGIQGLLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGD   80 (556)
T ss_pred             CCcchhHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            9999999999999999999999999999999999999965432   3577765 88999999999999999999999999


Q ss_pred             CCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH------------HHHHHhCCceEEEecCCCCccCcccH
Q psy12967        132 APVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVLKHDTI  194 (222)
Q Consensus       132 ~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l~a~~~  194 (222)
                      ++|.|+.|+.+||.+|+++...+.+   .|+  +|+.+|+|+            ++|+.+|| +++||||||+       
T Consensus        81 ~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nV-e~IVAPyEAD-------  152 (556)
T KOG2518|consen   81 PLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNV-EYIVAPYEAD-------  152 (556)
T ss_pred             CcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCC-ceEecCcccc-------
Confidence            9999999999999999988876654   444  689999886            48899999 9999999986       


Q ss_pred             HHHHHHhhhhcCC---eeecCcceeeccccC
Q psy12967        195 EKRQQAQGRSAGR---NVQAGSRARLKGLQT  222 (222)
Q Consensus       195 ae~~~a~l~~~g~---~~T~DsD~~lFG~~~  222 (222)
                        +|.++|++.|.   +||||||+++|||++
T Consensus       153 --AQlayL~~~~~i~~IITEDSDLl~fGc~~  181 (556)
T KOG2518|consen  153 --AQLAYLEREGIVDAIITEDSDLLVFGCKK  181 (556)
T ss_pred             --chhHHHHhcCcceEEEeccccccccCchh
Confidence              58999999987   799999999999985

>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information
>KOG2519|consensus 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
>smart00485 XPGN Xeroderma pigmentosum G N-region Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>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
>TIGR00600 rad2 DNA excision repair protein (rad2) 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
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment Back     alignment and domain information
>smart00484 XPGI Xeroderma pigmentosum G I-region Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>PRK14976 5'-3' exonuclease; Provisional Back     alignment and domain information
>KOG2519|consensus Back     alignment and domain information
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information
>KOG2520|consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>KOG2518|consensus Back     alignment and domain information
>PRK09482 flap endonuclease-like protein; 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
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>PHA00439 exonuclease 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
>PHA02567 rnh RnaseH; Provisional 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
>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
>COG2454 Uncharacterized conserved protein [Function unknown] 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 ?
Query222
3ory_A 363 Crystal Structure Of Flap Endonuclease 1 From Hyper 1e-05
3ory_A 363 Crystal Structure Of Flap Endonuclease 1 From Hyper 2e-04
1mc8_A 343 Crystal Structure Of Flap Endonuclease-1 R42e Mutan 3e-05
2izo_A 346 Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L 4e-05
2izo_A 346 Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L 5e-04
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363 Back     alignment and structure 
Iteration: 1

 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 40/66 (60%)
Query: 92  DSSTIAEHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQAQGRSA 151
           D + + +++ +   +L  LF+RT  ++  G+KP++V +GK P LK   IE+R+  +  +A
Sbjct: 57  DGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAA 116
Query: 152 GRNVQA 157
            +  +A
Sbjct: 117 KKYEEA 122
>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363 Back     alignment and structure
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343 Back     alignment and structure
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346 Back     alignment and structure
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346 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 ?
Query222
3ory_A 363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 2e-22
1rxw_A 336 Flap structure-specific endonuclease; helical clam 1e-21
3q8k_A 341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 1e-21
3qe9_Y 352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 4e-21
1ul1_X 379 Flap endonuclease-1; protein complex, DNA-binding 4e-21
1b43_A 340 Protein (FEN-1); nuclease, DNA repair, DNA replica 5e-21
2izo_A 346 FEN1, flap structure-specific endonuclease; hydrol 4e-20
1a76_A 326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 1e-19
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363 Back     alignment and structure
 Score = 92.6 bits (230), Expect = 2e-22
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 12/101 (11%)

Query: 56  MGVKDLWGILTPICER--KPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKN 104
           MGV  L  I+    +   + +  L  K I ID    +          D + + +++ +  
Sbjct: 11  MGVD-LKDIIPGEAKTVIEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRIT 69

Query: 105 MYLRNLFFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
            +L  LF+RT  ++  G+KP++V +GK P LK   IE+R+ 
Sbjct: 70  SHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKA 110
>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
>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
>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
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Length = 346 Back     alignment and structure
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Length = 326 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query222
3qe9_Y 352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 100.0
3ory_A 363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 99.97
3q8k_A 341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 99.97
1b43_A 340 Protein (FEN-1); nuclease, DNA repair, DNA replica 99.97
1a76_A 326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 99.96
1rxw_A 336 Flap structure-specific endonuclease; helical clam 99.96
1ul1_X 379 Flap endonuclease-1; protein complex, DNA-binding 99.96
2izo_A 346 FEN1, flap structure-specific endonuclease; hydrol 99.94
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 99.55
1exn_A 290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 99.44
3qe9_Y 352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 98.99
3ory_A 363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 98.4
1b43_A 340 Protein (FEN-1); nuclease, DNA repair, DNA replica 98.24
1a76_A 326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 98.16
1rxw_A 336 Flap structure-specific endonuclease; helical clam 98.11
3q8k_A 341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 98.1
1ul1_X 379 Flap endonuclease-1; protein complex, DNA-binding 97.91
3h7i_A 305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 96.65
2izo_A 346 FEN1, flap structure-specific endonuclease; hydrol 95.96
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 86.78
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 86.46
>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=7.6e-36  Score=269.81  Aligned_cols=156  Identities=21%  Similarity=0.268  Sum_probs=133.0

Q ss_pred             hccccccccccccceeeccccccCcEEEeecchhhhhhhhhh---hhcCCchHHHHHHHHHHHHH-HhcCCeeEEEeeCC
Q psy12967         56 MGVKDLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA---EHSSQKNMYLRNLFFRTSYL-LLLGVKPIFVLEGK  131 (222)
Q Consensus        56 MGI~gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~---~~~~~~~~~l~~~f~R~~~L-l~~gI~PIfVFDG~  131 (222)
                      |||+|||++|++..+++++++|+|++||||+|+||||+...+   ...|++|+|+.++|+|.+++ +++||+|||||||.
T Consensus         1 MGI~GL~~~L~~~~~~~~l~~l~Gk~vaIDas~wL~~~~~~~~~~l~~G~~t~~l~~~~~r~l~~L~~~gI~PvfVFDG~   80 (352)
T 3qe9_Y            1 MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGC   80 (352)
T ss_dssp             -CCTTHHHHTTTSEEEEEGGGGTTSEEEEETHHHHHHHHHHTHHHHHTTCCCCHHHHHHHHHHHHHHHTTCEEEEEECCS
T ss_pred             CCcchHHHHHHhhCCcCCHHHhCCcEEEEecHHHHHHhhhccchhhcCCCCcHHHHHHHHHHHHHHHHcCCEEEEEECCC
Confidence            999999999999999999999999999999999999975432   24688999999999999875 69999999999999


Q ss_pred             CCCCchhhHHHHHHHhhhhccCccc---ccc--chhhhhhHH------------HHHHHhCCceEEEecCCCCccCcccH
Q psy12967        132 APVLKHDTIEKRQQAQGRSAGRNVQ---AGS--RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVLKHDTI  194 (222)
Q Consensus       132 ~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs--~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l~a~~~  194 (222)
                      +|+.|+.|+.+|+++|+++..++.+   +++  +++++|+|+            .+|+++|| |++++||||        
T Consensus        81 ~~p~Kk~~~~~Rr~~r~~~~~~~~~~~~~g~~~~a~~~f~~~~~vt~~~~~~i~~~L~~~gI-p~i~ap~EA--------  151 (352)
T 3qe9_Y           81 TLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGV-DCLVAPYEA--------  151 (352)
T ss_dssp             CCTTTHHHHHHHHHHHHHHHHHHHHHTTSSCCHHHHHHHGGGCCCCHHHHHHHHHHHHHTTC-EEEECSSCH--------
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCC-cEEECCcch--------
Confidence            9999999999999999877665532   232  466666543            38899999 999999876        


Q ss_pred             HHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967        195 EKRQQAQGRSAGR---NVQAGSRARLKGLQ  221 (222)
Q Consensus       195 ae~~~a~l~~~g~---~~T~DsD~~lFG~~  221 (222)
                       +++||.+.+.|.   ++|+|||+|+||+.
T Consensus       152 -DaqiA~La~~g~~~~I~S~D~Dll~~~~~  180 (352)
T 3qe9_Y          152 -DAQLAYLNKAGIVQAIITEDSALLAFGCK  180 (352)
T ss_dssp             -HHHHHHHHHTTSCSEEECSCGGGGGGTCS
T ss_pred             -HHHHHHHHHCCCeEEEEeCCcCcccccCC
Confidence             678999999887   68999999999985
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} 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
>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
>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
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Back     alignment and structure
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Back     alignment and structure
>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
>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
>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
>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
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>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
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster} 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 222
d1rxwa2217 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc 5e-14
d1ul1x2216 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc 6e-14
d1a77a2207 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc 1e-12
d1a77a2207 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc 2e-04
d1b43a2219 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc 2e-11
>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

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]

 Score = 66.3 bits (161), Expect = 5e-14
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 11/95 (11%)

Query: 60  DLWGILTPICERKPIWELQDKTIAIDLSAWIC---------DSSTIAEHSSQKNMYLRNL 110
           D+  +     E   +     K IA+D    +          D + + +   +   +L  +
Sbjct: 2   DIGDLFER--EEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGI 59

Query: 111 FFRTSYLLLLGVKPIFVLEGKAPVLKHDTIEKRQQ 145
            +R S ++ +G++P+FV +G+ P  K   IE+R++
Sbjct: 60  LYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKK 94
>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
>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
>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
>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 ?
Query222
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 100.0
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 100.0
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 100.0
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 100.0
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 98.72
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 98.38
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 97.82
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 97.79
d1cmwa2164 5' to 3' exonuclease domain of DNA polymerase Taq 97.78
d1xo1a2167 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 96.1
d1tfra2169 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 95.98
>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=2.2e-36  Score=254.33  Aligned_cols=150  Identities=21%  Similarity=0.342  Sum_probs=123.9

Q ss_pred             cccccccccceeeccccccCcEEEeecchhhhhhhhhh---------hhcCCchHHHHHHHHHHHHHHhcCCeeEEEeeC
Q psy12967         60 DLWGILTPICERKPIWELQDKTIAIDLSAWICDSSTIA---------EHSSQKNMYLRNLFFRTSYLLLLGVKPIFVLEG  130 (222)
Q Consensus        60 gL~~~l~~~~~~~~i~~l~Gk~iAID~s~wl~~~~~~~---------~~~~~~~~~l~~~f~R~~~Ll~~gI~PIfVFDG  130 (222)
                      .|++++.  .+++++++|+|||||||+|+||||+.+.+         +..|.+++|+.++|+|+..|+++||+|||||||
T Consensus         2 ~~~~l~~--~~~~~l~~l~Gk~vAIDas~wL~k~l~~~~~~~~~~l~~~~~~~~~~l~~~~~ri~~l~~~~I~pifVFDG   79 (217)
T d1rxwa2           2 DIGDLFE--REEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDG   79 (217)
T ss_dssp             TGGGGCC--CEECCGGGGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHHTCEEEEEECC
T ss_pred             ChhHhcc--CcccCHHHhCCCEEEEECHHHHHHHHHHhccccCCchhhccCCccHHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            4777776  48999999999999999999999985432         234677899999999999999999999999999


Q ss_pred             CCCCCchhhHHHHHHHhhhhccCccc---ccc-chhhhhhHH------------HHHHHhCCceEEEecCCCCccCcccH
Q psy12967        131 KAPVLKHDTIEKRQQAQGRSAGRNVQ---AGS-RARNLFFRT------------SYLLLLGVKPIFVLEGKAPVLKHDTI  194 (222)
Q Consensus       131 ~~p~~K~~t~~~Rr~~r~~~~~~~~e---~gs-~ar~lf~R~------------~lL~~~GI~p~~vapGeap~l~a~~~  194 (222)
                      .+|+.|..|..+|+++|.++...+.+   .++ ....+..+.            .+|+.+|| ||++|||||        
T Consensus        80 ~~p~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~gi-~~i~Ap~EA--------  150 (217)
T d1rxwa2          80 EPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGI-PFVDAPSEG--------  150 (217)
T ss_dssp             SCCGGGHHHHHHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHHCCCCHHHHHHHHHHHHHTTC-CEEECSSCH--------
T ss_pred             CCCcchhhHHHHHHHHHHhhhhhhhhhhhhhhHHHHHHHHhhccCCHHHHHHHHHHHHHcCc-eEEecCchH--------
Confidence            99999999999999999877654432   121 222232222            38999999 999999986        


Q ss_pred             HHHHHHhhhhcCC---eeecCcceeecccc
Q psy12967        195 EKRQQAQGRSAGR---NVQAGSRARLKGLQ  221 (222)
Q Consensus       195 ae~~~a~l~~~g~---~~T~DsD~~lFG~~  221 (222)
                       +++||++...|.   |+|+|||+|+|||.
T Consensus       151 -eaqcA~L~~~g~vd~v~seDsD~l~fG~~  179 (217)
T d1rxwa2         151 -EAQAAYMAAKGDVEYTGSQDYDSLLFGSP  179 (217)
T ss_dssp             -HHHHHHHHHTTSSSEEECSSSHHHHTTCS
T ss_pred             -HHHHHHHHhCCCeEEEEecccceeeeCCC
Confidence             789999999987   78999999999996
>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
>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
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 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
>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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