Citrus Sinensis ID: 011802

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------
MSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKSKPKSSAAEIDQKLQALMLDIESENSTSSNASFSSRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
cccccccccccHHHHHHHHHHHHHHccccEEEcccHHHHHHHHHHHcccEEEEEccccccccccccEEEEcccccccccEEEEEHHHHHHHccccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccEEcccccccccccEEEEccccccccccccHHHHHHHccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccc
cccHHHcHHHHHHHHHHHHHHHHHHHcccEEEccHHHHHHHHHHHHcccccEEEEccccEEEEcccHHEHHHEcccccEEEEEEHHHHHHHHcccHHHHHHHHHHHccccccccccccHHHHHHHHHHccccHHHHHHHHHcccHHHHcccccccccHHHccccHccccccHcccccccEcccccccHHHHHHHccccccccccccccccccccHcccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccEEccccccccccccccHHHHHHHHHHHccHHHHHHHHHHccccccccHHHHHHHHccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccEEEHccccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHcc
msslrrnmgseFSCMIKEAKALGlslgvpclegVEEAEAQCALLNLESlcdgcfssdsdifLFGARTVYRDIWLGERGYVVCYEMDDierklgfgrNSLITLALLLgsdysqgvrglgpesACQIVKSVGDNVVLQRIASEGLSFVKRAKnskkegwsfkcnnkeeslnqeinvngtdhslqretpfsqvidaysnpkcysadsEAVHRVLAQHLFQHARLHQVCAQffqwppektdeyilpkiAERDLRRFANLRANTLalgvdlplqkvpvkcpitgiiksrklqgkecfevsweesyglkssvvpadliesacpeKIVEFEERralrqpkkskpkssAAEIDQKLQALMLDIesenstssnasfssrvvmsedwtaATEIDLTRRQDLLLDAesksnanmscyptgstaakaeiidlvspspvqcrnvsriremsdqpintielsdseteksPELERKARALRMFIASIRDDIS
msslrrnmgsEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIaseglsfvkraknskkegwsfkcnnkeeslNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTlalgvdlplqkvpvKCPITgiiksrklqgkECFEVSWEESYGLKSSVVPADLIESACPEKIVEFeerralrqpkkskpkssaaEIDQKLQALMLDIESenstssnasfssrVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNvsriremsdqpintielsdsetekspeleRKARALRMFIASIRDDIS
MSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQpkkskpkssAAEIDQKLQALMLDIesenstssnasfssrvvmsEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
***********FSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK****************************************SQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVE******************************************************WTAATEIDLT****************************AEIIDLV********************************************************
*************CMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAER*****************************************************GLKS*VVPADLIESAC*********************************************************************************************************************************************************ASIRD***
**********EFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR***************EIDQKLQALMLDIES***********SRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELS*********LERKARALRMFIASIRDDIS
**S**RNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESY*********DLIESACPEKIVEFEERR***************************************************************************************AE*IDLVSPS*VQCRNVSRIREMSDQPINTIELSDSETEKSPELER*ARALRMFIASIR****
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKSKPKSSAAEIDQKLQALMLDIESENSTSSNASFSSRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
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 ?
Query477 2.2.26 [Sep-21-2011]
Q9M2Z3600 Flap endonuclease GEN-lik no no 0.968 0.77 0.517 1e-130
Q8W5R1641 Flap endonuclease GEN-lik yes no 0.784 0.583 0.536 1e-118
Q9ATY51479 DNA repair protein UVH3 O no no 0.519 0.167 0.319 2e-28
P072761031 DNA repair protein RAD2 O yes no 0.446 0.206 0.326 9e-26
Q17RS7 908 Flap endonuclease GEN hom yes no 0.651 0.342 0.264 3e-25
Q8BMI4 908 Flap endonuclease GEN hom yes no 0.643 0.338 0.243 2e-22
P287151186 DNA repair protein comple no no 0.454 0.182 0.307 2e-22
P146291196 DNA repair protein comple N/A no 0.433 0.173 0.317 2e-21
P356891170 DNA repair protein comple no no 0.436 0.177 0.310 2e-20
P287061112 DNA repair protein rad13 yes no 0.503 0.215 0.311 2e-20
>sp|Q9M2Z3|GENL2_ARATH Flap endonuclease GEN-like 2 OS=Arabidopsis thaliana GN=GEN2 PE=2 SV=2 Back     alignment and function desciption
 Score =  466 bits (1200), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 261/504 (51%), Positives = 346/504 (68%), Gaps = 42/504 (8%)

Query: 2   SSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIF 61
           +SL+RNMGSEFSC+IKEAK +  +LG+ CL+G+EEAEAQCALLN ESLCD CFS DSDIF
Sbjct: 108 TSLKRNMGSEFSCIIKEAKVIASTLGILCLDGIEEAEAQCALLNSESLCDACFSFDSDIF 167

Query: 62  LFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPES 121
           LFGA+TVYR+I LGE GYVVCYEMDDI++KLG GRNSLI LALLLGSDYSQGVRGL  E 
Sbjct: 168 LFGAKTVYREICLGEGGYVVCYEMDDIKKKLGLGRNSLIALALLLGSDYSQGVRGLRQEK 227

Query: 122 ACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSL 181
           AC++V+S+GDNV+L+++ASEGLSF ++ + SKK+     C+ K       + +NG +   
Sbjct: 228 ACELVRSIGDNVILEKVASEGLSFAEKPRKSKKQVRPSVCSKK--GTLPLVVINGNNRDP 285

Query: 182 QRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYIL 241
           +R     QVIDA+ NPKC+ ADS  V R LA+  FQ  +L ++C QFF+WPPEKTDEYIL
Sbjct: 286 ERLEEIKQVIDAFMNPKCHQADSNTVSRALAEFSFQRTKLQEICHQFFEWPPEKTDEYIL 345

Query: 242 PKIAERDLRRFANLRANTLALGVDLPLQK--VPVKCPITGIIKSRKLQGKECFEVSWEES 299
           PK+AER+LRRFANL++ +  + V+LPL K  +P KCP++ IIK+RK+QG+ECFEVSW + 
Sbjct: 346 PKVAERNLRRFANLQSRSTEVEVNLPLHKPQMPEKCPVSEIIKTRKVQGRECFEVSWNDL 405

Query: 300 YGLKSSVVPADLIESACPEKIVEFEERRALRQPKK---------SKPKSSAAEIDQKLQA 350
            GL+SS+VPADL+E ACPEKI+EF+E+ A ++ K          S P  S++ ++  L+ 
Sbjct: 406 EGLESSIVPADLVERACPEKIIEFKEKMAAKKKKPKPKQKQKETSSPTKSSSLVELSLEL 465

Query: 351 LMLDIESENSTSSNASFSSRVVMSEDWTAATEIDLTRRQDL-LLDAESKSNAN------- 402
             LD+   NST    S  SR  + E      + +  +   L L+D+  + N N       
Sbjct: 466 QHLDL---NST----SLVSRSTLEEAEQENEQQNSKKHDYLRLIDSPDRENCNNAWSNRD 518

Query: 403 -----MSCYPTGSTAAKAEIIDLVSPSP-VQCRNVSRI---REMSDQPINT-IELSDSET 452
                MS +P      + E+IDL+SP P  + R+VSR    ++  D  + T IELSDSET
Sbjct: 519 RLGVGMSSFP---LYPETEVIDLISPCPEARSRSVSRSYQEQKSHDHQLETVIELSDSET 575

Query: 453 EKSPELERKARALRMFIASIRDDI 476
           +   E  +KAR LR+F+ +IR DI
Sbjct: 576 DDE-EHCKKARELRIFLQNIRKDI 598

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -
>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|Q9ATY5|UVH3_ARATH DNA repair protein UVH3 OS=Arabidopsis thaliana GN=UVH3 PE=2 SV=1 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|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|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|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|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|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

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 ?
Query477
359490377565 PREDICTED: flap endonuclease GEN-like 2- 0.920 0.776 0.627 1e-161
255539481 586 conserved hypothetical protein [Ricinus 0.972 0.791 0.620 1e-160
224136982541 predicted protein [Populus trichocarpa] 0.886 0.781 0.597 1e-149
449446177563 PREDICTED: flap endonuclease GEN-like 2- 0.939 0.795 0.575 1e-148
357498397571 Flap endonuclease GEN-like protein [Medi 0.941 0.786 0.566 1e-142
356559829 588 PREDICTED: flap endonuclease GEN-like 2- 0.962 0.780 0.554 1e-141
186510818536 Flap endonuclease GEN-like 2 [Arabidopsi 0.966 0.860 0.514 1e-129
186510820 600 Flap endonuclease GEN-like 2 [Arabidopsi 0.968 0.77 0.517 1e-129
297816098 600 hypothetical protein ARALYDRAFT_485245 [ 0.962 0.765 0.506 1e-122
115474331 641 Os08g0101600 [Oryza sativa Japonica Grou 0.784 0.583 0.536 1e-116
>gi|359490377|ref|XP_002263340.2| PREDICTED: flap endonuclease GEN-like 2-like [Vitis vinifera] gi|297741051|emb|CBI31782.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  575 bits (1482), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 292/465 (62%), Positives = 360/465 (77%), Gaps = 26/465 (5%)

Query: 3   SLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFL 62
           SLRRNMGSEFSCMIKEAK LGL+LG+PCL+G+EEAEAQCALLN ESLCDGCF+SDSD+FL
Sbjct: 109 SLRRNMGSEFSCMIKEAKVLGLALGIPCLDGIEEAEAQCALLNSESLCDGCFTSDSDVFL 168

Query: 63  FGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESA 122
           FGARTVYRDI LGE GYVVCYEM DIE  LGFGRNSLITLALLLGSDYSQGV G GPESA
Sbjct: 169 FGARTVYRDICLGEGGYVVCYEMADIESTLGFGRNSLITLALLLGSDYSQGVHGFGPESA 228

Query: 123 CQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQ 182
           CQIVKSVG+ VVL++IA EG+SF K++K S+K+G   KCN+KE   + E+N+NG++HS Q
Sbjct: 229 CQIVKSVGEEVVLKKIALEGISFAKKSKGSRKQGQVLKCNDKENCSDHEMNINGSEHSSQ 288

Query: 183 RETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP 242
           RE  F +VIDAY  PKC+SADS+AVHR LA   FQ     ++CAQ F+WPPEKTDEYILP
Sbjct: 289 RE--FLRVIDAYLKPKCHSADSDAVHRALALLPFQRTEAQKICAQLFEWPPEKTDEYILP 346

Query: 243 KIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGL 302
           KIAERDLRRFANLR+ +  LG+  PL ++PVKCPI+GIIK RK+QG+ECFEVSWEE  GL
Sbjct: 347 KIAERDLRRFANLRSTSSNLGIHFPLHEIPVKCPISGIIKHRKVQGRECFEVSWEEFDGL 406

Query: 303 KSSVVPADLIESACPEKIVEFEERRALRQ--------PKKSKPKSSAAEIDQKLQALMLD 354
           KSS++PA+L++SACPEKIVEFE R+   +        PKKS  ++  AEID++LQ L+LD
Sbjct: 407 KSSIIPAELVKSACPEKIVEFEGRKPQEKKQNHRKPRPKKSNNRTPLAEIDKQLQNLLLD 466

Query: 355 IESENSTSSNASFSSRVVMSEDWTAATEIDLT---RRQDLLLDAESKS-----NANMSCY 406
           IES  ++  N SFSS +  S+     T+ID T   + Q +LLD ES+S     N  + C+
Sbjct: 467 IESGGNSFQNVSFSSSMTPSK-----TQIDATKAAKTQYMLLDTESESDNDNHNEAIICH 521

Query: 407 PTGSTAAKAEIIDLVSPSP-VQCRNVSRIREMSD-QPINTIELSD 449
             G   A+  +IDL+SPSP ++ R VS+ ++ ++ Q I+ I+LSD
Sbjct: 522 QNGRCGAEI-VIDLLSPSPAIRARKVSKCQQGNNGQQIDVIDLSD 565

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255539481|ref|XP_002510805.1| conserved hypothetical protein [Ricinus communis] gi|223549920|gb|EEF51407.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|224136982|ref|XP_002322464.1| predicted protein [Populus trichocarpa] gi|222869460|gb|EEF06591.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449446177|ref|XP_004140848.1| PREDICTED: flap endonuclease GEN-like 2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|357498397|ref|XP_003619487.1| Flap endonuclease GEN-like protein [Medicago truncatula] gi|355494502|gb|AES75705.1| Flap endonuclease GEN-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|356559829|ref|XP_003548199.1| PREDICTED: flap endonuclease GEN-like 2-like [Glycine max] Back     alignment and taxonomy information
>gi|186510818|ref|NP_190459.2| Flap endonuclease GEN-like 2 [Arabidopsis thaliana] gi|332644950|gb|AEE78471.1| Flap endonuclease GEN-like 2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|186510820|ref|NP_001118795.1| Flap endonuclease GEN-like 2 [Arabidopsis thaliana] gi|166221584|sp|Q9M2Z3.2|GENL2_ARATH RecName: Full=Flap endonuclease GEN-like 2 gi|332644951|gb|AEE78472.1| Flap endonuclease GEN-like 2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297816098|ref|XP_002875932.1| hypothetical protein ARALYDRAFT_485245 [Arabidopsis lyrata subsp. lyrata] gi|297321770|gb|EFH52191.1| hypothetical protein ARALYDRAFT_485245 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|115474331|ref|NP_001060762.1| Os08g0101600 [Oryza sativa Japonica Group] gi|75162699|sp|Q8W5R1.1|GENL2_ORYSJ RecName: Full=Flap endonuclease GEN-like 2; AltName: Full=OsSEND-1; AltName: Full=Single-strand DNA endonuclease 1 gi|16923283|dbj|BAB72003.1| single-strand DNA endonuclease-1 [Oryza sativa Japonica Group] gi|113622731|dbj|BAF22676.1| Os08g0101600 [Oryza sativa Japonica Group] gi|222639760|gb|EEE67892.1| hypothetical protein OsJ_25722 [Oryza sativa Japonica Group] 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 ?
Query477
TAIR|locus:2099463600 AT3G48900 [Arabidopsis thalian 0.983 0.781 0.490 9.8e-119
UNIPROTKB|F1SCS5 914 GEN1 "Uncharacterized protein" 0.268 0.140 0.423 3.6e-23
UNIPROTKB|E1B8D0 914 GEN1 "Uncharacterized protein" 0.268 0.140 0.423 5.2e-23
TAIR|locus:20913431479 UVH3 "ULTRAVIOLET HYPERSENSITI 0.519 0.167 0.333 8.4e-23
UNIPROTKB|E1BWF2538 Gga.42587 "Uncharacterized pro 0.268 0.237 0.430 2.9e-22
SGD|S0000034901031 RAD2 "Single-stranded DNA endo 0.459 0.212 0.327 1.2e-21
UNIPROTKB|Q17RS7 908 GEN1 "Flap endonuclease GEN ho 0.268 0.140 0.407 2.5e-21
UNIPROTKB|E2QU72 908 GEN1 "Uncharacterized protein" 0.268 0.140 0.407 4.3e-21
UNIPROTKB|E1C986190 Gga.42587 "Uncharacterized pro 0.251 0.631 0.420 6e-21
UNIPROTKB|E1C3E4246 Gga.42587 "Uncharacterized pro 0.245 0.475 0.418 7.8e-20
TAIR|locus:2099463 AT3G48900 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1169 (416.6 bits), Expect = 9.8e-119, P = 9.8e-119
 Identities = 244/497 (49%), Positives = 333/497 (67%)

Query:     2 SSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIF 61
             +SL+RNMGSEFSC+IKEAK +  +LG+ CL+G+EEAEAQCALLN ESLCD CFS DSDIF
Sbjct:   108 TSLKRNMGSEFSCIIKEAKVIASTLGILCLDGIEEAEAQCALLNSESLCDACFSFDSDIF 167

Query:    62 LFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPES 121
             LFGA+TVYR+I LGE GYVVCYEMDDI++KLG GRNSLI LALLLGSDYSQGVRGL  E 
Sbjct:   168 LFGAKTVYREICLGEGGYVVCYEMDDIKKKLGLGRNSLIALALLLGSDYSQGVRGLRQEK 227

Query:   122 ACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSL 181
             AC++V+S+GDNV+L+++ASEGLSF ++ + SKK+     C+ K+ +L   + +NG +   
Sbjct:   228 ACELVRSIGDNVILEKVASEGLSFAEKPRKSKKQVRPSVCS-KKGTLPLVV-INGNNRDP 285

Query:   182 QRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYIL 241
             +R     QVIDA+ NPKC+ ADS  V R LA+  FQ  +L ++C QFF+WPPEKTDEYIL
Sbjct:   286 ERLEEIKQVIDAFMNPKCHQADSNTVSRALAEFSFQRTKLQEICHQFFEWPPEKTDEYIL 345

Query:   242 PKIAERDLRRFANLRANTLALGVDLPLQK--VPVKCPITGIIKSRKLQGKECFEVSWEES 299
             PK+AER+LRRFANL++ +  + V+LPL K  +P KCP++ IIK+RK+QG+ECFEVSW + 
Sbjct:   346 PKVAERNLRRFANLQSRSTEVEVNLPLHKPQMPEKCPVSEIIKTRKVQGRECFEVSWNDL 405

Query:   300 YGLKSSVVPADLIESACPEKIVEFEERRALRQXXXXXXXXXAAEIDQKLQALMLDIXXXX 359
              GL+SS+VPADL+E ACPEKI+EF+E+ A ++                  + ++++    
Sbjct:   406 EGLESSIVPADLVERACPEKIIEFKEKMAAKKKKPKPKQKQKETSSPTKSSSLVELSLEL 465

Query:   360 XXXXXXXXXXXXXXX-EDWTAATEIDLTRRQDLL--LDAESKSNAN------------MS 404
                             E+     E   +++ D L  +D+  + N N            MS
Sbjct:   466 QHLDLNSTSLVSRSTLEEAEQENEQQNSKKHDYLRLIDSPDRENCNNAWSNRDRLGVGMS 525

Query:   405 CYPTGSTAAKAEIIDLVSPSP-VQCRNVSRI---REMSDQPINTIELSDSETEKSPELE- 459
              +P      + E+IDL+SP P  + R+VSR    ++  D  + T+ +  S++E   E   
Sbjct:   526 SFPL---YPETEVIDLISPCPEARSRSVSRSYQEQKSHDHQLETV-IELSDSETDDEEHC 581

Query:   460 RKARALRMFIASIRDDI 476
             +KAR LR+F+ +IR DI
Sbjct:   582 KKARELRIFLQNIRKDI 598
GO:0003677 "DNA binding" evidence=IEA
GO:0003824 "catalytic activity" evidence=IEA
GO:0004518 "nuclease activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0006281 "DNA repair" evidence=IEA;ISS
UNIPROTKB|F1SCS5 GEN1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E1B8D0 GEN1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
TAIR|locus:2091343 UVH3 "ULTRAVIOLET HYPERSENSITIVE 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|E1BWF2 Gga.42587 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
SGD|S000003490 RAD2 "Single-stranded DNA endonuclease" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
UNIPROTKB|Q17RS7 GEN1 "Flap endonuclease GEN homolog 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2QU72 GEN1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E1C986 Gga.42587 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E1C3E4 Gga.42587 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query477
cd09869233 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 2e-41
TIGR006001034 TIGR00600, rad2, DNA excision repair protein (rad2 1e-27
cd09868249 cd09868, PIN_XPG, PIN domain of Xeroderma pigmento 3e-20
PRK03980292 PRK03980, PRK03980, flap endonuclease-1; Provision 4e-18
TIGR03674338 TIGR03674, fen_arch, flap structure-specific endon 4e-16
cd09856207 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc 4e-15
smart0048473 smart00484, XPGI, Xeroderma pigmentosum G I-region 4e-13
PTZ00217393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 5e-13
pfam0086746 pfam00867, XPG_I, XPG I-region 3e-10
cd0990052 cd09900, H3TH_XPG-like, H3TH domains of Flap endon 5e-10
cd0990497 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmen 7e-09
cd0989768 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap 8e-09
cd09870239 cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas 6e-08
COG0258310 COG0258, Exo, 5'-3' exonuclease (including N-termi 1e-07
cd09905108 cd09905, H3TH_GEN1, H3TH domain of Gap Endonucleas 1e-07
cd09867261 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease 9e-07
cd0990365 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu 3e-06
cd09906105 cd09906, H3TH_YEN1, H3TH domain of Yeast Endonucle 5e-04
cd09857210 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a 0.002
cd0990173 cd09901, H3TH_FEN1-like, H3TH domains of Flap endo 0.003
>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 =  147 bits (373), Expect = 2e-41
 Identities = 49/92 (53%), Positives = 61/92 (66%), Gaps = 1/92 (1%)

Query: 2   SSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIF 61
           +  +RN  S FS ++KE   L   LG+PCL+   EAEA CA LN E L DGC + DSD F
Sbjct: 106 NGSKRNRRSRFSHVLKECVELLELLGIPCLQAAGEAEALCAELNSEGLVDGCITQDSDAF 165

Query: 62  LFGARTVYRDIWLGE-RGYVVCYEMDDIERKL 92
           L+GARTVYR+  + E  GYV CY+M DI+ KL
Sbjct: 166 LYGARTVYRNFQMSEKGGYVDCYDMSDIKSKL 197

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|233044 TIGR00600, rad2, DNA excision repair protein (rad2) 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|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|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|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region Back     alignment and domain information
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region Back     alignment and domain information
>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG Back     alignment and domain information
>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease Back     alignment and domain information
>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases Back     alignment and domain information
>gnl|CDD|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|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|188625 cd09905, H3TH_GEN1, H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease 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|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs Back     alignment and domain information
>gnl|CDD|188626 cd09906, H3TH_YEN1, H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease 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|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 477
TIGR006001034 rad2 DNA excision repair protein (rad2). All prote 100.0
KOG2520815 consensus 5'-3' exonuclease [Replication, recombin 100.0
PTZ00217393 flap endonuclease-1; Provisional 100.0
PRK03980292 flap endonuclease-1; Provisional 100.0
cd00128316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN 100.0
TIGR03674338 fen_arch flap structure-specific endonuclease. End 100.0
KOG2519449 consensus 5'-3' exonuclease [Replication, recombin 100.0
smart00475259 53EXOc 5'-3' exonuclease. 99.94
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 99.93
PRK14976281 5'-3' exonuclease; Provisional 99.92
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 99.91
PRK09482256 flap endonuclease-like protein; Provisional 99.91
KOG2518556 consensus 5'-3' exonuclease [Replication, recombin 99.9
TIGR00593 887 pola DNA polymerase I. This family is based on the 99.88
PRK05755 880 DNA polymerase I; Provisional 99.88
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain 99.86
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 99.75
PHA00439286 exonuclease 99.56
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 99.42
PHA02567304 rnh RnaseH; Provisional 99.15
PF01367101 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold 99.07
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 98.96
PF02739169 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv 98.6
PF12813246 XPG_I_2: XPG domain containing 98.39
PF0038555 Chromo: Chromo (CHRromatin Organisation MOdifier) 97.01
smart0029855 CHROMO Chromatin organization modifier domain. 95.92
cd0002455 CHROMO Chromatin organization modifier (chromo) do 95.43
COG5366531 Protein involved in propagation of M2 dsRNA satell 94.11
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 92.19
KOG1911270 consensus Heterochromatin-associated protein HP1 a 91.83
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 89.96
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 89.66
KOG2748 369 consensus Uncharacterized conserved protein, conta 89.49
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 88.43
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 88.18
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 86.52
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 86.21
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 84.91
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 84.79
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 84.49
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 83.91
PF04599425 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P 83.8
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 82.35
PHA03065438 Hypothetical protein; Provisional 81.42
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 81.0
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information 
Probab=100.00  E-value=1.1e-42  Score=392.49  Aligned_cols=225  Identities=32%  Similarity=0.520  Sum_probs=184.5

Q ss_pred             ccCCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEe
Q 011802            5 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE   84 (477)
Q Consensus         5 ~Rn~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~   84 (477)
                      +|..-.++..|+..|++||++||||||+||||||||||+|++.|+||+|+|+|+|+|+||+++||||++. .+.+|++|.
T Consensus       763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~-~~~~ve~~~  841 (1034)
T TIGR00600       763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFN-QNKFVEYYQ  841 (1034)
T ss_pred             ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccC-CCCceEEee
Confidence            5777889999999999999999999999999999999999999999999999999999999999999875 457899999


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC--HHHHHHHHhcChhHHHHhhhhcccCcccccC
Q 011802           85 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD--NVVLQRIASEGLSFVKRAKNSKKEGWSFKCN  162 (477)
Q Consensus        85 ~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs--~~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~  162 (477)
                      .++|.+.+||++++||+||+|+||||++||+|||+++|++||++||+  ++-|..|..    |+....... ....    
T Consensus       842 ~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~----w~~~~~~~~-~~~~----  912 (1034)
T TIGR00600       842 YVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKE----WWHEAQKDK-KKRE----  912 (1034)
T ss_pred             HHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHH----HHHHhhhcc-cccc----
Confidence            99999999999999999999999999999999999999999999996  555555554    333221100 0000    


Q ss_pred             CccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeeh
Q 011802          163 NKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP  242 (477)
Q Consensus       163 ~~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP  242 (477)
                      +......   ....+...+|.+||+..|+++|++|.|+.+...+.|+.     .+..+|+.||.++|+|+..++++.|.|
T Consensus       913 ~~~~~~~---~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~~~f~W~~-----PD~e~L~~Fl~~~~gws~eRv~~~l~p  984 (1034)
T TIGR00600       913 NPNDTKV---KKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGK-----PDLDKIREFCQRYFGWNREKTDEVLLP  984 (1034)
T ss_pred             ccchhhh---hhcccccccCCCCCcHHHHHHhcCCCCCCCcCCCCCCC-----CCHHHHHHHHHHccCCCHHHHHHHHHH
Confidence            0000000   00112345899999999999999999997655554432     267899999999999999999999999


Q ss_pred             hhhHH
Q 011802          243 KIAER  247 (477)
Q Consensus       243 ll~e~  247 (477)
                      ++..+
T Consensus       985 likk~  989 (1034)
T TIGR00600       985 VLKKL  989 (1034)
T ss_pred             HHHHH
Confidence            99733

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional 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
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair] 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
>PRK14976 5'-3' exonuclease; Provisional 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
>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00484 XPGI Xeroderma pigmentosum G I-region Back     alignment and domain information
>PHA00439 exonuclease Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>PHA02567 rnh RnaseH; Provisional Back     alignment and domain information
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs 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
>PF12813 XPG_I_2: XPG domain containing Back     alignment and domain information
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation Back     alignment and domain information
>smart00298 CHROMO Chromatin organization modifier domain Back     alignment and domain information
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus 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
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics] Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics] Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ] Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; 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
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PHA03065 Hypothetical protein; Provisional Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] 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 ?
Query477
2izo_A346 Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L 5e-15
1mc8_A343 Crystal Structure Of Flap Endonuclease-1 R42e Mutan 2e-11
1rxv_A336 Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna 3e-11
3ory_A363 Crystal Structure Of Flap Endonuclease 1 From Hyper 3e-11
1b43_A340 Fen-1 From P. Furiosus Length = 340 1e-09
3q8k_A341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 2e-09
1ul1_X379 Crystal Structure Of The Human Fen1-Pcna Complex Le 2e-09
3q8m_A341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 2e-08
1a76_A326 Flap Endonuclease-1 From Methanococcus Jannaschii L 2e-07
3qea_Z352 Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) 7e-06
3qe9_Y352 Crystal Structure Of Human Exonuclease 1 Exo1 (D173 6e-05
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346 Back     alignment and structure 
Iteration: 1

 Score = 79.0 bits (193), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 46/130 (35%), Positives = 74/130 (56%), Gaps = 12/130 (9%)
Query: 13  SCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDI 72
           + M++E+K L  ++G+P ++   E EA+ A LN   L     S D D  LFGA+ + R++
Sbjct: 126 NIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNL 185
Query: 73  WL-GERG------YVVC----YEMDDIERKLGFGRNSLITLALLLGSDYS-QGVRGLGPE 120
            + G+R       YV       E + + +KLG  R  LI + +L+G+DY+  G+RG+GPE
Sbjct: 186 TITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPE 245
Query: 121 SACQIVKSVG 130
            A +I+K  G
Sbjct: 246 RALKIIKKYG 255
>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343 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|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363 Back     alignment and structure
>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340 Back     alignment and structure
>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|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|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326 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 ?
Query477
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 6e-35
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 6e-34
1rxw_A336 Flap structure-specific endonuclease; helical clam 2e-32
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 2e-31
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 1e-29
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 2e-29
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 3e-28
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 3e-28
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-06
2d9u_A74 Chromobox protein homolog 2 (isoform 2); chromobox 2e-04
>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
 Score =  132 bits (333), Expect = 6e-35
 Identities = 45/203 (22%), Positives = 77/203 (37%), Gaps = 21/203 (10%)

Query: 1   MSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDI 60
           +    + +         E K L   +G+P L+   EAEA CA L          + D D 
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDC 181

Query: 61  FLFGARTVYRDIWLGE--RGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLG 118
             FG+  + R +   E  +  +  + +  I ++LG  +   + L +LLGSDY + +RG+G
Sbjct: 182 LTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIG 241

Query: 119 PESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFK------------CNNKEE 166
           P+ A  +++       ++ I    +  +   K    E W  K                 E
Sbjct: 242 PKRAVDLIQKHKS---IEEI----VRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVE 294

Query: 167 SLNQEINVNGTDHSLQRETPFSQ 189
               E N       +  E  FS+
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSE 317
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Length = 379 Back     alignment and structure
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Length = 336 Back     alignment and structure
>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
>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
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363 Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Length = 340 Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Length = 346 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2d9u_A Chromobox protein homolog 2 (isoform 2); chromobox homolog 2, chromo domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query477
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 100.0
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 100.0
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 100.0
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 100.0
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 100.0
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 100.0
1rxw_A336 Flap structure-specific endonuclease; helical clam 100.0
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 99.97
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 99.93
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 99.9
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 99.59
3lwe_A62 M-phase phosphoprotein 8; MPP8, structural genomic 97.54
3mts_A64 Histone-lysine N-methyltransferase SUV39H1; histon 97.37
1ap0_A73 Modifier protein 1; chromatin-binding, protein int 97.33
3f2u_A55 Chromobox protein homolog 1; human chromobox homol 97.19
2d9u_A74 Chromobox protein homolog 2 (isoform 2); chromobox 97.14
3fdt_A59 Chromobox protein homolog 5; chromobox homolog5, C 97.1
2kvm_A74 Chromobox protein homolog 7; histone modification, 97.08
3i91_A54 Chromobox protein homolog 8; chromobox homolog 8, 97.05
1pfb_A55 Polycomb protein; chromatin, histone methylation, 97.03
3h91_A54 Chromobox protein homolog 2; human chromobox homol 96.92
2dnt_A78 Chromodomain protein, Y chromosome-like, isoform B 96.88
1q3l_A69 Heterochromatin protein 1; chromodomain, HP1, chro 96.82
1g6z_A70 CLR4 protein; transferase; NMR {Schizosaccharomyce 96.77
1pdq_A72 Polycomb protein; methyllysine, chromodomain, poly 96.72
2k1b_A73 Chromobox protein homolog 7; alpha/beta protein, c 96.44
3g7l_A61 Chromo domain-containing protein 1; chromodomain, 96.28
2dnv_A64 Chromobox protein homolog 8; chromo domain, histon 95.99
2rso_A92 Chromatin-associated protein SWI6; chromodomain, s 95.96
2rsn_A75 Chromo domain-containing protein 1; chromodomain, 95.83
4hae_A81 CDY-like 2, chromodomain Y-like protein 2; protein 94.83
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 93.98
2epb_A68 Chromodomain-helicase-DNA-binding protein 6; struc 93.3
1x3p_A54 Cpsrp43; chromo-2 domain, chloroplasts, LHCP, prot 92.24
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 92.09
3fqd_A 899 Protein DHP1, 5'-3' exoribonuclease 2; protein-pro 90.76
3kup_A65 Chromobox protein homolog 3; chromo shadow domain, 90.65
2ee1_A64 Chromodomain helicase-DNA-binding protein 4; EC 3. 90.59
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 90.07
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 90.07
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 89.93
2b2y_A187 CHD-1, chromodomain-helicase-DNA-binding protein 1 89.56
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 89.48
2h1e_A177 Chromo domain protein 1; CHD1, tandem chromodomain 89.1
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 88.96
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 88.81
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 88.37
2fmm_A74 Chromobox protein homolog 1; ENT domain, chromo sh 88.31
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 87.51
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 87.49
3i3c_A75 Chromobox protein homolog 5; CBX5, chromo shadow d 86.59
3q6s_A78 Chromobox protein homolog 1; incenp, heterochromat 84.96
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 84.31
3p7j_A87 Heterochromatin protein 1; chromo shadow domain, g 81.68
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Back     alignment and structure
Probab=100.00  E-value=1.2e-38  Score=327.66  Aligned_cols=197  Identities=21%  Similarity=0.323  Sum_probs=167.5

Q ss_pred             CCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCC-------c-
Q 011802            7 NMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER-------G-   78 (477)
Q Consensus         7 n~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~-------~-   78 (477)
                      +....+.+|++.++++|++|||||++||||||||||+|++.|++|+|+|+|+|+|+||+++|+++++..+.       . 
T Consensus       137 ~~~~vt~~~~~~i~~lL~~~GIp~i~apgEADaqiA~La~~g~~~~I~S~D~D~l~fg~~~v~~~l~~~~~~~~p~~~~~  216 (363)
T 3ory_A          137 MSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEY  216 (363)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTCCEEECSSCHHHHHHHHHHTTSCSEEECSSSHHHHTTCSEEEESTTTCEEEECSSTTCE
T ss_pred             ccccCCHHHHHHHHHHHHHCCCCEEEeCccHHHHHHHHHHCCCeEEEECCCcCccccCCCeEEEEeeccccccCCccccc
Confidence            34456778899999999999999999999999999999999999999999999999999999999875321       1 


Q ss_pred             ---eEEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCC-CCCCCcHHHHHHHHHHhCCHH-HHHHHHhcChhHHHHhhhhc
Q 011802           79 ---YVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQ-GVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSK  153 (477)
Q Consensus        79 ---~v~~y~~~~I~~~lgL~r~q~IdlaiL~GsDY~p-GVpGIG~ktA~kLIk~~gs~~-iL~~i~~~~~~~~~k~~~~~  153 (477)
                         .+++|+.+.|.+++|++|+||+|+|+|+||||+| ||||||+|||++||++||+++ ++++++.             
T Consensus       217 v~~~~~~~~~~~v~~~~gl~~~q~id~~~L~GsDy~p~GVpGIG~KtA~kLl~~~gsle~il~~~~~-------------  283 (363)
T 3ory_A          217 VEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPILK-------------  283 (363)
T ss_dssp             EEECCEEEEHHHHHHHHTCCHHHHHHHHHHHCBTTBTTCSTTCCHHHHHHHHHHHTSSTTSCGGGCC-------------
T ss_pred             cccceEEEcHHHHHHHhCcCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhccc-------------
Confidence               2478999999999999999999999999999999 999999999999999999963 5544321             


Q ss_pred             ccCcccccCCccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCc
Q 011802          154 KEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPP  233 (477)
Q Consensus       154 k~~~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~  233 (477)
                                               ..+  +||..+|.++|++|.|..+ .++.|+     ..+.++|++|+.+.++|+.
T Consensus       284 -------------------------~~~--~~~~~~~~~~f~~p~v~~~-~~~~w~-----~pd~~~l~~fl~~~~~f~~  330 (363)
T 3ory_A          284 -------------------------SPI--EVDVIAIKKYFLQPQVTDN-YRIEWH-----TPDPDAVKRILVDEHDFSI  330 (363)
T ss_dssp             -------------------------CSS--CCCHHHHHHHHHSCCCCSC-CCCCCC-----CCCHHHHHHHHTTTTCCCH
T ss_pred             -------------------------ccC--CCCHHHHHHHhcCCCCCCC-CCCCCC-----CCCHHHHHHHHHhccCCCH
Confidence                                     012  4788999999999999852 233222     2267899999999999999


Q ss_pred             ccccceeehhhhHHHH
Q 011802          234 EKTDEYILPKIAERDL  249 (477)
Q Consensus       234 ~~~~e~llPll~e~~l  249 (477)
                      +++++.+.|+.+.+.-
T Consensus       331 ~rv~~~~~~l~~~~~~  346 (363)
T 3ory_A          331 DRVSTALERYVKAFKE  346 (363)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999876654
>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
>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
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Back     alignment and structure
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Back     alignment and structure
>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
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* 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
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Back     alignment and structure
>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A Back     alignment and structure
>3lwe_A M-phase phosphoprotein 8; MPP8, structural genomics, structural genomics consortium, S repeat, nucleus, cell cycle; 2.05A {Homo sapiens} SCOP: b.34.13.0 PDB: 3r93_A* 3svm_A* 3qo2_A* Back     alignment and structure
>3mts_A Histone-lysine N-methyltransferase SUV39H1; histone methyltransferase, histone-lysine N-methyltransferas SUV39H1, histone H3, TRI-methylation; 2.20A {Homo sapiens} Back     alignment and structure
>1ap0_A Modifier protein 1; chromatin-binding, protein interaction motif, alpha+beta; NMR {Mus musculus} SCOP: b.34.13.2 PDB: 1guw_A* Back     alignment and structure
>3f2u_A Chromobox protein homolog 1; human chromobox homolog 1, CBX1, structural genomics, struct genomics consortium, SGC, centromere, nucleus; 1.80A {Homo sapiens} PDB: 3tzd_A* 2l11_A* 3dm1_A* Back     alignment and structure
>2d9u_A Chromobox protein homolog 2 (isoform 2); chromobox homolog 2, chromo domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3fdt_A Chromobox protein homolog 5; chromobox homolog5, CBX5, structural GENO structural genomics consortium, SGC, centromere, nucleus, phosphoprotein; HET: M3L; 2.00A {Homo sapiens} Back     alignment and structure
>2kvm_A Chromobox protein homolog 7; histone modification, lysine methylation, chromobox, polycom chromatin-binding; HET: MLY; NMR {Mus musculus} Back     alignment and structure
>3i91_A Chromobox protein homolog 8; chromobox homolog 8, CBX8, structural genomics structural genomics consortium, SGC, chromatin regulator, N phosphoprotein, repressor; HET: M3L; 1.55A {Homo sapiens} SCOP: b.34.13.2 PDB: 3gv6_A* 3i90_A* Back     alignment and structure
>1pfb_A Polycomb protein; chromatin, histone methylation, polycomb, chromodomain, peptide binding protein; HET: M3L; 1.40A {Drosophila melanogaster} SCOP: b.34.13.2 Back     alignment and structure
>3h91_A Chromobox protein homolog 2; human chromobox homolog 2, CBX2, structural genomics, structural genomics consortium, SGC, chromatin regulator, D binding, nucleus; HET: M3L; 1.50A {Homo sapiens} SCOP: b.34.13.2 PDB: 2k28_A 3i8z_A Back     alignment and structure
>2dnt_A Chromodomain protein, Y chromosome-like, isoform B; histone H3 tail, choromatin organization modifier, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.34.13.2 Back     alignment and structure
>1q3l_A Heterochromatin protein 1; chromodomain, HP1, chromatin, methyllysine, monomethyllysine, structural protein; HET: MLZ; 1.64A {Drosophila melanogaster} SCOP: b.34.13.2 PDB: 1kne_A* 1kna_A* Back     alignment and structure
>1g6z_A CLR4 protein; transferase; NMR {Schizosaccharomyces pombe} SCOP: b.34.13.2 Back     alignment and structure
>1pdq_A Polycomb protein; methyllysine, chromodomain, polycomb, lysine methylation, trimethyllysine, cation-PI, chromo, structural protein; HET: M3L; 1.76A {Drosophila melanogaster} SCOP: b.34.13.2 Back     alignment and structure
>2k1b_A Chromobox protein homolog 7; alpha/beta protein, chromatin regulator, nucleus, repressor, transcription, transcription regulation; NMR {Homo sapiens} PDB: 2l12_A* 2l1b_A* Back     alignment and structure
>3g7l_A Chromo domain-containing protein 1; chromodomain, protein-peptide complex, silencing, cell cycle, chromosome partition, DNA-binding, nucleus; HET: M3L; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>2dnv_A Chromobox protein homolog 8; chromo domain, histone H3 tail, choromatin organization modifier, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: b.34.13.2 Back     alignment and structure
>2rso_A Chromatin-associated protein SWI6; chromodomain, silencing, chromosomal protein, Met transcription; NMR {Schizosaccharomyces pombe} Back     alignment and structure
>2rsn_A Chromo domain-containing protein 1; chromodomain, protein-peptide complex, RNA-mediated gene SIL chromosomal protein, methylation; HET: M3L; NMR {Schizosaccharomyces pombe} Back     alignment and structure
>4hae_A CDY-like 2, chromodomain Y-like protein 2; protein binding, structural genomics consortiu; 2.00A {Homo sapiens} 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
>2epb_A Chromodomain-helicase-DNA-binding protein 6; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x3p_A Cpsrp43; chromo-2 domain, chloroplasts, LHCP, protein translocation, unknown function; NMR {Arabidopsis thaliana} SCOP: b.34.13.2 Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>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
>3kup_A Chromobox protein homolog 3; chromo shadow domain, structural genomics consortium, SGC, acetylation, chromatin regulator, nucleus, phosphoprotein; 1.77A {Homo sapiens} SCOP: b.34.13.2 PDB: 1dz1_A Back     alignment and structure
>2ee1_A Chromodomain helicase-DNA-binding protein 4; EC 3.6.1.-, ATP- dependent helicase CHD4, CHD-4, MI-2 autoantigen 218 kDa protein, MI2-beta; NMR {Homo sapiens} Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>2b2y_A CHD-1, chromodomain-helicase-DNA-binding protein 1; three stranded antiparallel beta sheet, alpha helix linker, peptide binding protein; 2.35A {Homo sapiens} SCOP: b.34.13.2 b.34.13.2 PDB: 2b2u_A* 2b2v_A* 2b2w_A 2b2t_A* Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>2h1e_A Chromo domain protein 1; CHD1, tandem chromodomains, three-stranded ANT B-sheet, hydrolase; 2.20A {Saccharomyces cerevisiae} PDB: 2dy7_A 2dy8_A Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>2fmm_A Chromobox protein homolog 1; ENT domain, chromo shadow domain, EMSY protein, heterochroma protein 1, transcription; 1.80A {Homo sapiens} SCOP: b.34.13.2 PDB: 1s4z_A Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>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
>3i3c_A Chromobox protein homolog 5; CBX5, chromo shadow domain, structural genomics, structural consortium, SGC, centromere, nucleus, phosphoprotein; 2.48A {Homo sapiens} SCOP: b.34.13.2 Back     alignment and structure
>3q6s_A Chromobox protein homolog 1; incenp, heterochromatin, centromere, cell cycle; 1.93A {Homo sapiens} SCOP: b.34.13.2 Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>3p7j_A Heterochromatin protein 1; chromo shadow domain, gene silenc epigenetics, transcription; 2.30A {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 477
d1rxwa2217 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc 5e-17
d1a77a2207 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc 1e-16
d1ul1x2216 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc 2e-16
d1b43a2219 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc 3e-13
d1rxwa1105 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu 7e-05
d1ul1x1140 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu 2e-04
d1b43a1120 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu 0.001
>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 = 77.5 bits (190), Expect = 5e-17
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 1/103 (0%)

Query: 1   MSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDI 60
                +  G     ++  AK L   +G+P ++   E EAQ A +  +   +   S D D 
Sbjct: 114 AKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDS 173

Query: 61  FLFGARTVYRDI-WLGERGYVVCYEMDDIERKLGFGRNSLITL 102
            LFG+  + R++   G+R         D++ ++    ++L  L
Sbjct: 174 LLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRL 216
>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
>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
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105 Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140 Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query477
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.76
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.76
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.74
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.7
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.7
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.69
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.67
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.67
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 99.2
d1cmwa1116 5' to 3' exonuclease domain of DNA polymerase Taq 99.03
d1cmwa2164 5' to 3' exonuclease domain of DNA polymerase Taq 98.45
d1xo1a2167 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 97.51
d1tfra2169 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 97.12
d1q3la_52 Heterochromatin protein 1, HP1 {Fruit fly (Drosoph 97.05
d2dnva152 Chromobox protein homolog 8 {Mouse (Mus musculus) 96.8
d1pfba_55 Polycomb protein, Pc {Fruit fly (Drosophila melano 96.73
d1guwa_73 Heterochromatin protein 1, HP1 {Mouse (Mus musculu 96.71
d2dnta166 Chromodomain protein, Y-like isoform {Human (Homo 96.52
d1g6za_70 Histone methyltransferase clr4, chromo domain {Fis 96.44
d2dy8a169 ATP-dependent helicase CHD1 (Chromo domain protein 95.59
d1x3pa154 CpSRP43 {Thale cress (Arabidopsis thaliana) [TaxId 94.09
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 93.69
d2b2ya180 ATP-dependent helicase CHD1 (Chromo domain protein 93.67
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 93.49
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 93.44
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 93.37
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 93.22
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 92.86
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 92.7
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 87.66
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 84.72
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 84.04
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 81.52
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.76  E-value=1.1e-19  Score=158.09  Aligned_cols=105  Identities=20%  Similarity=0.327  Sum_probs=82.9

Q ss_pred             CCHHHHHHHHHHhCCCCC-CCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhhhhcccCcccccCCccccccccc
Q 011802           94 FGRNSLITLALLLGSDYS-QGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEI  172 (477)
Q Consensus        94 L~r~q~IdlaiL~GsDY~-pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~  172 (477)
                      |+++||||+|+||||||+ +|||||||++|++||++||+.+      .   .                            
T Consensus         1 lt~eqfIdl~iL~G~DY~~~gI~GIGpktAlklikk~~~~~------~---~----------------------------   43 (120)
T d1b43a1           1 LTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPL------A---K----------------------------   43 (120)
T ss_dssp             CCHHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTCSSGG------G---G----------------------------
T ss_pred             CCHHHHHHHHHHhCCCCCcccCCCcCHHHHHHHHHHhCCHH------H---H----------------------------
Confidence            689999999999999999 5999999999999999998752      0   0                            


Q ss_pred             cccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeehhhhHH
Q 011802          173 NVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAER  247 (477)
Q Consensus       173 ~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~e~  247 (477)
                            ...+.+||...+.++|++|.|... .+..|     ...+..+|++||.+..+|+..++...|-++.+..
T Consensus        44 ------~~~~~~~~~~~~~~~f~~p~v~d~-~~~~~-----~~pd~~~l~~fL~~e~~f~~~rv~~~l~kl~k~~  106 (120)
T d1b43a1          44 ------FQKQSDVDLYAIKEFFLNPPVTDN-YNLVW-----RDPDEEGILKFLCDEHDFSEERVKNGLERLKKAI  106 (120)
T ss_dssp             ------TGGGCSSCHHHHHHHHHSCCCCCC-CCCCC-----CCCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHH
T ss_pred             ------HHhccccchHHHHHHhcCCCCCCC-CCcCC-----CCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence                  012347899999999999998532 22111     1337789999999999999998888877765543
>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
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Back     information, alignment and structure
>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
>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
>d1q3la_ b.34.13.2 (A:) Heterochromatin protein 1, HP1 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2dnva1 b.34.13.2 (A:7-58) Chromobox protein homolog 8 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pfba_ b.34.13.2 (A:) Polycomb protein, Pc {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1guwa_ b.34.13.2 (A:) Heterochromatin protein 1, HP1 {Mouse (Mus musculus), HP1 beta (MOD1, M31) [TaxId: 10090]} Back     information, alignment and structure
>d2dnta1 b.34.13.2 (A:8-73) Chromodomain protein, Y-like isoform {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1g6za_ b.34.13.2 (A:) Histone methyltransferase clr4, chromo domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure
>d2dy8a1 b.34.13.2 (A:279-347) ATP-dependent helicase CHD1 (Chromo domain protein 1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x3pa1 b.34.13.2 (A:1-54) CpSRP43 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2b2ya1 b.34.13.2 (A:108-187) ATP-dependent helicase CHD1 (Chromo domain protein 1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure