Citrus Sinensis ID: 007971

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-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580---
MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKSKPKSSAAEIDQKLQALMLDIESENSTSSNASFSSRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
ccHHHHHHHHHHHccccccccccccEEEEEHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHcccEEEEEEEcccccccHHHHHHHHHcccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEccccHHHHHHHHHHcccEEEEEccccccccccccEEEEcccccccccEEEEEHHHHHHHHcccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccEEccccccccccccccccHHHHcccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccc
ccHHHHHHHHHHHHccccHHHccccEEEEEHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccEEEcccHHHHHHHHHHHcccEEEEEEccccHHHccccHEHEEccccccccEEEEcHHHHHHHccccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHHccccccccccccccccccccHHHHHHcccccccccccccccccccccHHHHHHHHcccccccHHHHHccHHHHHHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccccHccccccccccccccccccEEEEccEcccEEEEEEEEcccccccccccHHHHHHHHcHHHHHHHHHHHHHHcccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccHHEHHccccccEEEcccccccccHHHHHHHHHHHHHHHHHHHHcc
MGVKNLWDILESCkktlplhhlqnkrvciDLSCWIVQLQNvnksyrpqtdKLFLRGLFHRLRALIALNCGlifvsdgsipaiklSTYRRrlnsgsevtqddknlDKMSSLRRNMGSEFSCMIKEAKALGlslgvpclegVEEAEAQCALLNLESlcdgcfssdsdifLFGARTVYRDIWLGERGYVVCYEMDDierklgfgrNSLITLALLLgsdysqgvrglgpesACQIVKSVGDNVVLQRIASEGLSFVKRAKnskkegwsfkcnnkeeslnqeinvngtdhslqretpfsqvidaysnpkcysadsEAVHRVLAQHLFQHARLHQVCAQffqwppektdeyilpkiAERDLRRFANLRANTLalgvdlplqkvpvkcpitgiiksrklqgkecfevsweesyglkssvvpadliesacpeKIVEFEERralrqpkkskpkssAAEIDQKLQALMLDIesenstssnasfssrvvmsedwtaATEIDLTRRQDLLLDAesksnanmscyptgstaakaeiidlvspspvqcrnvsriremsdqpintielsdseteksPELERKARALRMFIASIRDDIS
MGVKNLWDILESCKktlplhhlqnKRVCIDLSCWIVQLQnvnksyrpqtDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKlstyrrrlnsgsevtqddknldkMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIaseglsfvkraknskkegwsfkcnnkeeslNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTlalgvdlplqkvpvKCPITgiiksrklqgkECFEVSWEESYGLKSSVVPADLIESACPEKIVEFeerralrqpkkskpkssaaEIDQKLQALMLDIESenstssnasfssrVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNvsriremsdqpintielsdsetekspeleRKARALRMFIASIRDDIS
MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQpkkskpkssAAEIDQKLQALMLDIesenstssnasfssrvvmsEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
****NLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYR*****************************FSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK****************************************SQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVE******************************************************WTAATEIDLT****************************AEIIDLV********************************************************
MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVN******TDKLFLRGLFHRLRALIALNCGLIFVSDGSIPA**********************LDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAE*******************************************************************************************************************************************************************************************************************************ASIRD***
MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR***************EIDQKLQALMLDIES***********SRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELS*********LERKARALRMFIASIRDDIS
*GVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRAL*****************K**ALML***************************************************C****STAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSP******RALRMFIASIR****
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKSKPKSSAAEIDQKLQALMLDIESENSTSSNASFSSRVVMSEDWTAATEIDLTRRQDLLLDAESKSNANMSCYPTGSTAAKAEIIDLVSPSPVQCRNVSRIREMSDQPINTIELSDSETEKSPELERKARALRMFIASIRDDIS
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 ?
Query583 2.2.26 [Sep-21-2011]
Q9M2Z3600 Flap endonuclease GEN-lik yes no 0.975 0.948 0.538 1e-175
Q8W5R1641 Flap endonuclease GEN-lik yes no 0.826 0.751 0.554 1e-161
Q17RS7 908 Flap endonuclease GEN hom yes no 0.716 0.460 0.271 2e-40
Q8BMI4 908 Flap endonuclease GEN hom yes no 0.710 0.455 0.261 4e-38
Q9LPD2599 Flap endonuclease GEN-lik no no 0.406 0.395 0.372 3e-30
Q64MA3629 Flap endonuclease GEN-lik no no 0.420 0.389 0.325 2e-28
Q9ATY51479 DNA repair protein UVH3 O no no 0.433 0.171 0.317 2e-28
P072761031 DNA repair protein RAD2 O yes no 0.365 0.206 0.326 2e-25
Q9VRJ0 726 Flap endonuclease GEN OS= yes no 0.365 0.293 0.339 4e-25
P61942339 Flap endonuclease 1 OS=Na yes no 0.408 0.702 0.316 1e-24
>sp|Q9M2Z3|GENL2_ARATH Flap endonuclease GEN-like 2 OS=Arabidopsis thaliana GN=GEN2 PE=2 SV=2 Back     alignment and function desciption
 Score =  613 bits (1582), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 329/611 (53%), Positives = 427/611 (69%), Gaps = 42/611 (6%)

Query: 1   MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHR 60
           MGVK LWD+LE CKKT PL HLQNKRVC+DLSCW+V+L  VNKSY    +K++LRG FHR
Sbjct: 1   MGVKYLWDVLEPCKKTFPLDHLQNKRVCVDLSCWMVELHKVNKSYCATKEKVYLRGFFHR 60

Query: 61  LRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSC 120
           LRALIALNC +I VSDG+IP IK+ TY+RRL +  E+  D     K +SL+RNMGSEFSC
Sbjct: 61  LRALIALNCSIILVSDGAIPGIKVPTYKRRLKARFEIADDGVEPSKETSLKRNMGSEFSC 120

Query: 121 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 180
           +IKEAK +  +LG+ CL+G+EEAEAQCALLN ESLCD CFS DSDIFLFGA+TVYR+I L
Sbjct: 121 IIKEAKVIASTLGILCLDGIEEAEAQCALLNSESLCDACFSFDSDIFLFGAKTVYREICL 180

Query: 181 GERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVV 240
           GE GYVVCYEMDDI++KLG GRNSLI LALLLGSDYSQGVRGL  E AC++V+S+GDNV+
Sbjct: 181 GEGGYVVCYEMDDIKKKLGLGRNSLIALALLLGSDYSQGVRGLRQEKACELVRSIGDNVI 240

Query: 241 LQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAY 300
           L+++ASEGLSF ++ + SKK+     C+ K       + +NG +   +R     QVIDA+
Sbjct: 241 LEKVASEGLSFAEKPRKSKKQVRPSVCSKK--GTLPLVVINGNNRDPERLEEIKQVIDAF 298

Query: 301 SNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFAN 360
            NPKC+ ADS  V R LA+  FQ  +L ++C QFF+WPPEKTDEYILPK+AER+LRRFAN
Sbjct: 299 MNPKCHQADSNTVSRALAEFSFQRTKLQEICHQFFEWPPEKTDEYILPKVAERNLRRFAN 358

Query: 361 LRANTLALGVDLPLQK--VPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLI 418
           L++ +  + V+LPL K  +P KCP++ IIK+RK+QG+ECFEVSW +  GL+SS+VPADL+
Sbjct: 359 LQSRSTEVEVNLPLHKPQMPEKCPVSEIIKTRKVQGRECFEVSWNDLEGLESSIVPADLV 418

Query: 419 ESACPEKIVEFEERRALRQPKK---------SKPKSSAAEIDQKLQALMLDIESENSTSS 469
           E ACPEKI+EF+E+ A ++ K          S P  S++ ++  L+   LD+   NST  
Sbjct: 419 ERACPEKIIEFKEKMAAKKKKPKPKQKQKETSSPTKSSSLVELSLELQHLDL---NST-- 473

Query: 470 NASFSSRVVMSEDWTAATEIDLTRRQDL-LLDAESKSNAN------------MSCYPTGS 516
             S  SR  + E      + +  +   L L+D+  + N N            MS +P   
Sbjct: 474 --SLVSRSTLEEAEQENEQQNSKKHDYLRLIDSPDRENCNNAWSNRDRLGVGMSSFP--- 528

Query: 517 TAAKAEIIDLVSPSP-VQCRNVSRI---REMSDQPINT-IELSDSETEKSPELERKARAL 571
              + E+IDL+SP P  + R+VSR    ++  D  + T IELSDSET+   E  +KAR L
Sbjct: 529 LYPETEVIDLISPCPEARSRSVSRSYQEQKSHDHQLETVIELSDSETDDE-EHCKKAREL 587

Query: 572 RMFIASIRDDI 582
           R+F+ +IR DI
Sbjct: 588 RIFLQNIRKDI 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|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|Q9LPD2|GENL1_ARATH Flap endonuclease GEN-like 1 OS=Arabidopsis thaliana GN=GEN1 PE=2 SV=3 Back     alignment and function description
>sp|Q64MA3|GENL1_ORYSJ Flap endonuclease GEN-like 1 OS=Oryza sativa subsp. japonica GN=RAD 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|Q9VRJ0|GEN_DROME Flap endonuclease GEN OS=Drosophila melanogaster GN=Gen PE=1 SV=1 Back     alignment and function description
>sp|P61942|FEN_NANEQ Flap endonuclease 1 OS=Nanoarchaeum equitans (strain Kin4-M) GN=fen PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query583
359490377565 PREDICTED: flap endonuclease GEN-like 2- 0.943 0.973 0.659 0.0
224136982541 predicted protein [Populus trichocarpa] 0.910 0.981 0.632 0.0
449446177563 PREDICTED: flap endonuclease GEN-like 2- 0.950 0.984 0.604 0.0
357498397571 Flap endonuclease GEN-like protein [Medi 0.953 0.973 0.605 0.0
356559829588 PREDICTED: flap endonuclease GEN-like 2- 0.970 0.962 0.590 0.0
255539481586 conserved hypothetical protein [Ricinus 0.857 0.853 0.620 1e-173
186510820600 Flap endonuclease GEN-like 2 [Arabidopsi 0.975 0.948 0.538 1e-173
297816098600 hypothetical protein ARALYDRAFT_485245 [ 0.970 0.943 0.534 1e-167
115474331641 Os08g0101600 [Oryza sativa Japonica Grou 0.826 0.751 0.554 1e-160
357139431 706 PREDICTED: flap endonuclease GEN-like 2- 0.778 0.643 0.577 1e-158
>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 =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 376/570 (65%), Positives = 456/570 (80%), Gaps = 20/570 (3%)

Query: 1   MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHR 60
           MGVKNLWDILESCKKTLPL+HLQNKRVCIDLSCW+VQLQNVNKS+    DKL+L+GLFHR
Sbjct: 1   MGVKNLWDILESCKKTLPLYHLQNKRVCIDLSCWMVQLQNVNKSHASIKDKLYLKGLFHR 60

Query: 61  LRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSC 120
           LRALIALNC L+FV+DGSIPAIKL+TYRRRLNSG+EVT+D+ N   + SLRRNMGSEFSC
Sbjct: 61  LRALIALNCSLLFVTDGSIPAIKLATYRRRLNSGTEVTRDETNSHNVPSLRRNMGSEFSC 120

Query: 121 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 180
           MIKEAK LGL+LG+PCL+G+EEAEAQCALLN ESLCDGCF+SDSD+FLFGARTVYRDI L
Sbjct: 121 MIKEAKVLGLALGIPCLDGIEEAEAQCALLNSESLCDGCFTSDSDVFLFGARTVYRDICL 180

Query: 181 GERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVV 240
           GE GYVVCYEM DIE  LGFGRNSLITLALLLGSDYSQGV G GPESACQIVKSVG+ VV
Sbjct: 181 GEGGYVVCYEMADIESTLGFGRNSLITLALLLGSDYSQGVHGFGPESACQIVKSVGEEVV 240

Query: 241 LQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAY 300
           L++IA EG+SF K++K S+K+G   KCN+KE   + E+N+NG++HS QRE  F +VIDAY
Sbjct: 241 LKKIALEGISFAKKSKGSRKQGQVLKCNDKENCSDHEMNINGSEHSSQRE--FLRVIDAY 298

Query: 301 SNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFAN 360
             PKC+SADS+AVHR LA   FQ     ++CAQ F+WPPEKTDEYILPKIAERDLRRFAN
Sbjct: 299 LKPKCHSADSDAVHRALALLPFQRTEAQKICAQLFEWPPEKTDEYILPKIAERDLRRFAN 358

Query: 361 LRANTLALGVDLPLQKVPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIES 420
           LR+ +  LG+  PL ++PVKCPI+GIIK RK+QG+ECFEVSWEE  GLKSS++PA+L++S
Sbjct: 359 LRSTSSNLGIHFPLHEIPVKCPISGIIKHRKVQGRECFEVSWEEFDGLKSSIIPAELVKS 418

Query: 421 ACPEKIVEFEERRALRQ--------PKKSKPKSSAAEIDQKLQALMLDIESENSTSSNAS 472
           ACPEKIVEFE R+   +        PKKS  ++  AEID++LQ L+LDIES  ++  N S
Sbjct: 419 ACPEKIVEFEGRKPQEKKQNHRKPRPKKSNNRTPLAEIDKQLQNLLLDIESGGNSFQNVS 478

Query: 473 FSSRVVMSEDWTAATEIDLTRRQDLLLDAESKS-----NANMSCYPTGSTAAKAEIIDLV 527
           FSS +  S+    AT+    + Q +LLD ES+S     N  + C+  G   A+  +IDL+
Sbjct: 479 FSSSMTPSKTQIDATKA--AKTQYMLLDTESESDNDNHNEAIICHQNGRCGAEI-VIDLL 535

Query: 528 SPSP-VQCRNVSRIREMSD-QPINTIELSD 555
           SPSP ++ R VS+ ++ ++ Q I+ I+LSD
Sbjct: 536 SPSPAIRARKVSKCQQGNNGQQIDVIDLSD 565

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|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|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
>gi|357139431|ref|XP_003571285.1| PREDICTED: flap endonuclease GEN-like 2-like [Brachypodium distachyon] 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 ?
Query583
TAIR|locus:2099463600 AT3G48900 [Arabidopsis thalian 0.987 0.96 0.516 6.1e-158
UNIPROTKB|E1B8D0 914 GEN1 "Uncharacterized protein" 0.403 0.257 0.375 1.5e-38
UNIPROTKB|F1SCS5 914 GEN1 "Uncharacterized protein" 0.403 0.257 0.363 1.6e-37
UNIPROTKB|Q17RS7 908 GEN1 "Flap endonuclease GEN ho 0.403 0.258 0.363 2e-37
UNIPROTKB|E2QU72 908 GEN1 "Uncharacterized protein" 0.403 0.258 0.371 4.5e-37
MGI|MGI:2443149 908 Gen1 "Gen homolog 1, endonucle 0.403 0.258 0.363 2.5e-34
RGD|1559792 908 Gen1 "Gen endonuclease homolog 0.403 0.258 0.363 2.9e-34
TAIR|locus:20913431479 UVH3 "ULTRAVIOLET HYPERSENSITI 0.433 0.171 0.330 8.7e-33
SGD|S0000034901031 RAD2 "Single-stranded DNA endo 0.437 0.247 0.309 2.8e-31
UNIPROTKB|E1C3E4246 Gga.42587 "Uncharacterized pro 0.385 0.914 0.347 2.5e-29
TAIR|locus:2099463 AT3G48900 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1539 (546.8 bits), Expect = 6.1e-158, P = 6.1e-158
 Identities = 312/604 (51%), Positives = 414/604 (68%)

Query:     1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHR 60
             MGVK LWD+LE CKKT PL HLQNKRVC+DLSCW+V+L  VNKSY    +K++LRG FHR
Sbjct:     1 MGVKYLWDVLEPCKKTFPLDHLQNKRVCVDLSCWMVELHKVNKSYCATKEKVYLRGFFHR 60

Query:    61 LRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSC 120
             LRALIALNC +I VSDG+IP IK+ TY+RRL +  E+  D     K +SL+RNMGSEFSC
Sbjct:    61 LRALIALNCSIILVSDGAIPGIKVPTYKRRLKARFEIADDGVEPSKETSLKRNMGSEFSC 120

Query:   121 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 180
             +IKEAK +  +LG+ CL+G+EEAEAQCALLN ESLCD CFS DSDIFLFGA+TVYR+I L
Sbjct:   121 IIKEAKVIASTLGILCLDGIEEAEAQCALLNSESLCDACFSFDSDIFLFGAKTVYREICL 180

Query:   181 GERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVV 240
             GE GYVVCYEMDDI++KLG GRNSLI LALLLGSDYSQGVRGL  E AC++V+S+GDNV+
Sbjct:   181 GEGGYVVCYEMDDIKKKLGLGRNSLIALALLLGSDYSQGVRGLRQEKACELVRSIGDNVI 240

Query:   241 LQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAY 300
             L+++ASEGLSF ++ + SKK+     C+ K+ +L   + +NG +   +R     QVIDA+
Sbjct:   241 LEKVASEGLSFAEKPRKSKKQVRPSVCS-KKGTLPLVV-INGNNRDPERLEEIKQVIDAF 298

Query:   301 SNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFAN 360
              NPKC+ ADS  V R LA+  FQ  +L ++C QFF+WPPEKTDEYILPK+AER+LRRFAN
Sbjct:   299 MNPKCHQADSNTVSRALAEFSFQRTKLQEICHQFFEWPPEKTDEYILPKVAERNLRRFAN 358

Query:   361 LRANTLALGVDLPLQK--VPVKCPITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLI 418
             L++ +  + V+LPL K  +P KCP++ IIK+RK+QG+ECFEVSW +  GL+SS+VPADL+
Sbjct:   359 LQSRSTEVEVNLPLHKPQMPEKCPVSEIIKTRKVQGRECFEVSWNDLEGLESSIVPADLV 418

Query:   419 ESACPEKIVEFEERRALRQXXXXXXXXXAAEIDQKLQALMLDIXXXXXXXXXXXXXXXXX 478
             E ACPEKI+EF+E+ A ++                  + ++++                 
Sbjct:   419 ERACPEKIIEFKEKMAAKKKKPKPKQKQKETSSPTKSSSLVELSLELQHLDLNSTSLVSR 478

Query:   479 XX-EDWTAATEIDLTRRQDLL--LDAESKSNAN------------MSCYPTGSTAAKAEI 523
                E+     E   +++ D L  +D+  + N N            MS +P      + E+
Sbjct:   479 STLEEAEQENEQQNSKKHDYLRLIDSPDRENCNNAWSNRDRLGVGMSSFPL---YPETEV 535

Query:   524 IDLVSPSP-VQCRNVSRI---REMSDQPINTIELSDSETEKSPELE-RKARALRMFIASI 578
             IDL+SP P  + R+VSR    ++  D  + T+ +  S++E   E   +KAR LR+F+ +I
Sbjct:   536 IDLISPCPEARSRSVSRSYQEQKSHDHQLETV-IELSDSETDDEEHCKKARELRIFLQNI 594

Query:   579 RDDI 582
             R DI
Sbjct:   595 RKDI 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|E1B8D0 GEN1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1SCS5 GEN1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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
MGI|MGI:2443149 Gen1 "Gen homolog 1, endonuclease (Drosophila)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1559792 Gen1 "Gen endonuclease homolog 1 (Drosophila)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
TAIR|locus:2091343 UVH3 "ULTRAVIOLET HYPERSENSITIVE 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
SGD|S000003490 RAD2 "Single-stranded DNA endonuclease" [Saccharomyces cerevisiae (taxid:4932)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9M2Z3GENL2_ARATH3, ., 1, ., -, ., -0.53840.97590.9483yesno
Q8W5R1GENL2_ORYSJ3, ., 1, ., -, ., -0.55440.82670.7519yesno

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

Your Input:
GSVIVG00009204001
SubName- Full=Chromosome undetermined scaffold_225, whole genome shotgun sequence; (564 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query583
cd09869233 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 5e-93
cd09868249 cd09868, PIN_XPG, PIN domain of Xeroderma pigmento 7e-39
TIGR006001034 TIGR00600, rad2, DNA excision repair protein (rad2 1e-27
cd09856207 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc 2e-27
TIGR03674338 TIGR03674, fen_arch, flap structure-specific endon 9e-22
cd09870239 cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas 4e-20
PRK03980292 PRK03980, PRK03980, flap endonuclease-1; Provision 1e-19
PTZ00217393 PTZ00217, PTZ00217, flap endonuclease-1; Provision 8e-18
smart0048599 smart00485, XPGN, Xeroderma pigmentosum G N-region 1e-15
smart0048473 smart00484, XPGI, Xeroderma pigmentosum G I-region 4e-13
cd09867261 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease 3e-12
cd09857210 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a 9e-12
pfam0086746 pfam00867, XPG_I, XPG I-region 2e-10
TIGR00600 1034 TIGR00600, rad2, DNA excision repair protein (rad2 3e-10
cd0990052 cd09900, H3TH_XPG-like, H3TH domains of Flap endon 9e-10
cd0990497 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmen 1e-08
cd0989768 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap 2e-08
pfam00752100 pfam00752, XPG_N, XPG N-terminal domain 1e-07
COG0258310 COG0258, Exo, 5'-3' exonuclease (including N-termi 1e-07
cd09905108 cd09905, H3TH_GEN1, H3TH domain of Gap Endonucleas 2e-07
cd0990365 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu 4e-06
cd00128209 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E 1e-05
cd09906105 cd09906, H3TH_YEN1, H3TH domain of Yeast Endonucle 8e-04
cd0990173 cd09901, H3TH_FEN1-like, H3TH domains of Flap endo 0.004
>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 =  284 bits (729), Expect = 5e-93
 Identities = 99/199 (49%), Positives = 121/199 (60%), Gaps = 3/199 (1%)

Query: 1   MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHR 60
           MGVK LWDILE  KK  PL HLQ KRV +DLSCW+V+ Q V K +     K  LR LF R
Sbjct: 1   MGVKGLWDILEPVKKRKPLDHLQGKRVAVDLSCWVVESQTVVKYF--VVPKPHLRNLFFR 58

Query: 61  LRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSC 120
            R LIAL    +FV DG+ P +KL    +R    S + +   N    +  +RN  S FS 
Sbjct: 59  TRYLIALGVLPVFVVDGAAPPLKLPVIIKRNQLQSGIAKPGDNPTPKNGSKRNRRSRFSH 118

Query: 121 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL 180
           ++KE   L   LG+PCL+   EAEA CA LN E L DGC + DSD FL+GARTVYR+  +
Sbjct: 119 VLKECVELLELLGIPCLQAAGEAEALCAELNSEGLVDGCITQDSDAFLYGARTVYRNFQM 178

Query: 181 GE-RGYVVCYEMDDIERKL 198
            E  GYV CY+M DI+ KL
Sbjct: 179 SEKGGYVDCYDMSDIKSKL 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|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|234306 TIGR03674, fen_arch, flap structure-specific endonuclease 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|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional Back     alignment and domain information
>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region Back     alignment and domain information
>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region 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|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|216163 pfam00867, XPG_I, XPG I-region Back     alignment and domain information
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2) 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|216098 pfam00752, XPG_N, XPG N-terminal domain 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|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|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1 (FEN1)-like and Exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases Back     alignment and domain information
>gnl|CDD|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|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 583
PTZ00217393 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
PRK03980292 flap endonuclease-1; Provisional 100.0
KOG2518556 consensus 5'-3' exonuclease [Replication, recombin 100.0
TIGR006001034 rad2 DNA excision repair protein (rad2). All prote 100.0
KOG2520815 consensus 5'-3' exonuclease [Replication, recombin 100.0
smart00475259 53EXOc 5'-3' exonuclease. 100.0
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas 100.0
PRK14976281 5'-3' exonuclease; Provisional 99.97
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain 99.97
PRK09482256 flap endonuclease-like protein; Provisional 99.96
TIGR00593 887 pola DNA polymerase I. This family is based on the 99.96
PRK05755 880 DNA polymerase I; Provisional 99.95
PF0086794 XPG_I: XPG I-region; InterPro: IPR006086 This entr 99.9
smart0048599 XPGN Xeroderma pigmentosum G N-region. domain in n 99.87
PF00752101 XPG_N: XPG N-terminal domain; InterPro: IPR006085 99.87
PHA00439286 exonuclease 99.82
TIGR00600 1034 rad2 DNA excision repair protein (rad2). All prote 99.77
smart0048473 XPGI Xeroderma pigmentosum G I-region. domain in n 99.74
PHA02567304 rnh RnaseH; Provisional 99.57
PF02739169 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv 99.55
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 99.24
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 98.8
PF12813246 XPG_I_2: XPG domain containing 98.66
PF01367101 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold 98.62
PF03159237 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: 97.89
PF04599425 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P 97.64
PHA03065438 Hypothetical protein; Provisional 97.48
COG5366531 Protein involved in propagation of M2 dsRNA satell 97.07
PF0038555 Chromo: Chromo (CHRromatin Organisation MOdifier) 96.47
COG5049 953 XRN1 5'-3' exonuclease [DNA replication, recombina 96.17
smart0029855 CHROMO Chromatin organization modifier domain. 95.61
cd0002455 CHROMO Chromatin organization modifier (chromo) do 94.98
KOG2045 1493 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involve 93.7
KOG2044 931 consensus 5'-3' exonuclease HKE1/RAT1 [Replication 92.32
PF05991166 NYN_YacP: YacP-like NYN domain; InterPro: IPR01029 92.25
KOG1911270 consensus Heterochromatin-associated protein HP1 a 89.18
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 89.09
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 88.31
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 88.04
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 87.03
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 86.04
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 85.82
KOG2748 369 consensus Uncharacterized conserved protein, conta 85.52
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 85.51
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 85.33
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 85.19
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 83.73
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information 
Probab=100.00  E-value=7.1e-61  Score=512.43  Aligned_cols=310  Identities=20%  Similarity=0.326  Sum_probs=267.2

Q ss_pred             CCccchHHHHhh----hcccccccccCCCEEEeeHHHHHHHhhcccCC--C------CCCCchhHHHHHHHHHHHHHHcC
Q 007971            1 MGVKNLWDILES----CKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKS--Y------RPQTDKLFLRGLFHRLRALIALN   68 (583)
Q Consensus         1 MGIkgL~~~L~~----~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~--~------~g~~~~~~Lr~lf~rl~~Ll~~g   68 (583)
                      |||+||+++|++    +.++++|+.|+|++|||||++||||++++++.  .      ..|.+++||++||+|+.+|+++|
T Consensus         1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~g   80 (393)
T PTZ00217          1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAG   80 (393)
T ss_pred             CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCC
Confidence            999999999986    46889999999999999999999999987653  1      12456799999999999999999


Q ss_pred             CEEEEEEcCCCCcchhhhhHhhhhcCcccc------cccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCccc
Q 007971           69 CGLIFVSDGSIPAIKLSTYRRRLNSGSEVT------QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEE  142 (583)
Q Consensus        69 I~PIFVFDG~~P~~K~~t~~~R~~~r~~a~------~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~E  142 (583)
                      |+|||||||.+|++|..++.+|++.|.++.      .+.++.+.+.++.+....++..++..++++|+.|||||++||||
T Consensus        81 ikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~E  160 (393)
T PTZ00217         81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE  160 (393)
T ss_pred             CCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcC
Confidence            999999999999999999999998886543      23566677777776666788999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccC--CCceEEEEeHHHHHHHhCCChHHHHHHHHHhCCCCCCCC
Q 007971          143 AEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLG--ERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGV  220 (583)
Q Consensus       143 ADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~--~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G~DY~pGv  220 (583)
                      ||||||+|++.|+||+|+|+|+|+|+||++.++++++..  ....+++|+++.+.+.+|++++||+++|+|+||||+|||
T Consensus       161 Adaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi  240 (393)
T PTZ00217        161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI  240 (393)
T ss_pred             HHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC
Confidence            999999999999999999999999999999999998752  234578999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCCcHHHHHH
Q 007971          221 RGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDA  299 (583)
Q Consensus       221 pGiG~ktA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~  299 (583)
                      ||||+|||++||++||+++ ++++++..                                    +..+|++||+.++.+.
T Consensus       241 ~GIG~ktA~~Li~~~gsle~il~~~~~~------------------------------------k~~~p~~~~~~~~~~~  284 (393)
T PTZ00217        241 KGIGPKTAYKLIKKYKSIEEILEHLDKT------------------------------------KYPVPENFDYKEAREL  284 (393)
T ss_pred             CCccHHHHHHHHHHcCCHHHHHHHHHhc------------------------------------CCCCCCCCChHHHHHH
Confidence            9999999999999999984 66655421                                    1235779999999999


Q ss_pred             hcCCccCCCC-hHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhHH
Q 007971          300 YSNPKCYSAD-SEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIA  351 (583)
Q Consensus       300 Yl~P~v~~~~-~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l~  351 (583)
                      |++|.|..+. .++.|     .+.+...|++||.+.++|+.+++++.|-++.+
T Consensus       285 f~~p~V~~~~~~~l~w-----~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~  332 (393)
T PTZ00217        285 FLNPEVTPAEEIDLKW-----NEPDEEGLKKFLVKEKNFNEERVEKYIERLKK  332 (393)
T ss_pred             hcCCCcCCCCCCCCCC-----CCCCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Confidence            9999998643 22222     24578899999999999999999998765543

>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
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair] Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>KOG2520 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
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09482 flap endonuclease-like protein; Provisional Back     alignment and domain information
>TIGR00593 pola DNA polymerase I Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>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
>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
>PHA00439 exonuclease Back     alignment and domain information
>TIGR00600 rad2 DNA excision repair protein (rad2) Back     alignment and domain information
>smart00484 XPGI Xeroderma pigmentosum G I-region Back     alignment and domain information
>PHA02567 rnh RnaseH; 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
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>PF12813 XPG_I_2: XPG domain containing 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
>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
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses Back     alignment and domain information
>PHA03065 Hypothetical protein; Provisional 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
>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
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation] 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
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification] 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
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics] Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK13901 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
>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
>PRK14606 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query583
2izo_A346 Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L 5e-20
1mc8_A343 Crystal Structure Of Flap Endonuclease-1 R42e Mutan 4e-15
1rxv_A336 Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna 5e-15
3ory_A363 Crystal Structure Of Flap Endonuclease 1 From Hyper 2e-14
1b43_A340 Fen-1 From P. Furiosus Length = 340 1e-12
3q8k_A341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 2e-10
1ul1_X379 Crystal Structure Of The Human Fen1-Pcna Complex Le 3e-10
1a76_A326 Flap Endonuclease-1 From Methanococcus Jannaschii L 3e-10
3q8m_A341 Crystal Structure Of Human Flap Endonuclease Fen1 ( 2e-09
3qea_Z352 Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) 8e-08
3qe9_Y352 Crystal Structure Of Human Exonuclease 1 Exo1 (D173 6e-07
>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346 Back     alignment and structure 
Iteration: 1

 Score = 95.9 bits (237), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 122/256 (47%), Gaps = 29/256 (11%)
Query: 8   DILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLF---------LRGLF 58
           D+++  K+ L    L+ KRV ID    + Q     +  +P    L          L GLF
Sbjct: 2   DLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIR--QPDGTPLMDSQGRVTSHLSGLF 59
Query: 59  HRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQD---DKNLDKMSSLRRNMG 115
           +R   ++      I+V DG  P  K     RR  +  E  +     K+  K+  LR+   
Sbjct: 60  YRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEELRKYSQ 119
Query: 116 SEF---SCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGAR 172
           +     + M++E+K L  ++G+P ++   E EA+ A LN   L     S D D  LFGA+
Sbjct: 120 AILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAK 179
Query: 173 TVYRDIWL-GERG------YVVC----YEMDDIERKLGFGRNSLITLALLLGSDYS-QGV 220
            + R++ + G+R       YV       E + + +KLG  R  LI + +L+G+DY+  G+
Sbjct: 180 RLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDGI 239
Query: 221 RGLGPESACQIVKSVG 236
           RG+GPE A +I+K  G
Sbjct: 240 RGIGPERALKIIKKYG 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|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326 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|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 ?
Query583
3q8k_A341 Flap endonuclease 1; helix-3 turn-helix, hydrophob 3e-59
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 1e-57
1rxw_A336 Flap structure-specific endonuclease; helical clam 4e-57
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 1e-55
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 5e-55
3ory_A363 Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco 1e-52
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replica 8e-51
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 7e-50
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-08
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 =  199 bits (508), Expect = 3e-59
 Identities = 66/324 (20%), Positives = 121/324 (37%), Gaps = 37/324 (11%)

Query: 2   GVKNLWDILES----CKKTLPLHHLQNKRVCIDLSCWIVQ-LQNVNKSYRPQTDKL---- 52
           G++ L  ++        +   +     ++V ID S  I Q L  V +      ++     
Sbjct: 1   GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60

Query: 53  -FLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDK------NLD 105
             L G+F+R   ++      ++V DG  P +K     +R    +E  +  +         
Sbjct: 61  SHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ 120

Query: 106 KMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSD 165
           ++    + +         E K L   +G+P L+   EAEA CA L          + D D
Sbjct: 121 EVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMD 180

Query: 166 IFLFGARTVYRDIWLGE--RGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGL 223
              FG+  + R +   E  +  +  + +  I ++LG  +   + L +LLGSDY + +RG+
Sbjct: 181 CLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGI 240

Query: 224 GPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFK------------CNNKE 271
           GP+ A  +++       ++ I    +  +   K    E W  K                 
Sbjct: 241 GPKRAVDLIQKHKS---IEEI----VRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESV 293

Query: 272 ESLNQEINVNGTDHSLQRETPFSQ 295
           E    E N       +  E  FS+
Sbjct: 294 ELKWSEPNEEELIKFMCGEKQFSE 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
>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
>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
>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 ?
Query583
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
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 100.0
1rxw_A336 Flap structure-specific endonuclease; helical clam 100.0
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding 100.0
2izo_A346 FEN1, flap structure-specific endonuclease; hydrol 100.0
3qe9_Y352 Exonuclease 1; exonuclease, hydrolase-DNA complex; 100.0
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 100.0
1bgx_T 832 TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi 99.97
3h7i_A305 Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu 99.8
2y35_A 1140 LD22664P; hydrolase-DNA complex, RNA degradation, 98.44
3pie_A 1155 5'->3' exoribonuclease (XRN1); beta berrel, tudor 98.12
3fqd_A 899 Protein DHP1, 5'-3' exoribonuclease 2; protein-pro 98.03
3lwe_A62 M-phase phosphoprotein 8; MPP8, structural genomic 97.34
1ap0_A73 Modifier protein 1; chromatin-binding, protein int 97.1
3mts_A64 Histone-lysine N-methyltransferase SUV39H1; histon 97.09
3f2u_A55 Chromobox protein homolog 1; human chromobox homol 96.93
1pfb_A55 Polycomb protein; chromatin, histone methylation, 96.87
2kvm_A74 Chromobox protein homolog 7; histone modification, 96.83
3fdt_A59 Chromobox protein homolog 5; chromobox homolog5, C 96.79
3i91_A54 Chromobox protein homolog 8; chromobox homolog 8, 96.74
2d9u_A74 Chromobox protein homolog 2 (isoform 2); chromobox 96.73
3h91_A54 Chromobox protein homolog 2; human chromobox homol 96.6
1q3l_A69 Heterochromatin protein 1; chromodomain, HP1, chro 96.48
1g6z_A70 CLR4 protein; transferase; NMR {Schizosaccharomyce 96.47
2dnt_A78 Chromodomain protein, Y chromosome-like, isoform B 96.38
1pdq_A72 Polycomb protein; methyllysine, chromodomain, poly 96.38
2k1b_A73 Chromobox protein homolog 7; alpha/beta protein, c 96.12
3g7l_A61 Chromo domain-containing protein 1; chromodomain, 95.87
2dnv_A64 Chromobox protein homolog 8; chromo domain, histon 95.49
2rso_A92 Chromatin-associated protein SWI6; chromodomain, s 95.1
2rsn_A75 Chromo domain-containing protein 1; chromodomain, 95.09
4hae_A81 CDY-like 2, chromodomain Y-like protein 2; protein 93.49
1x3p_A54 Cpsrp43; chromo-2 domain, chloroplasts, LHCP, prot 92.28
2epb_A68 Chromodomain-helicase-DNA-binding protein 6; struc 90.0
3kup_A65 Chromobox protein homolog 3; chromo shadow domain, 88.8
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 88.69
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 86.22
2fmm_A74 Chromobox protein homolog 1; ENT domain, chromo sh 86.01
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 85.0
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 84.62
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 84.44
3i3c_A75 Chromobox protein homolog 5; CBX5, chromo shadow d 84.18
2b2y_A187 CHD-1, chromodomain-helicase-DNA-binding protein 1 84.12
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 83.65
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 83.34
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 83.18
2h1e_A177 Chromo domain protein 1; CHD1, tandem chromodomain 83.14
3q6s_A78 Chromobox protein homolog 1; incenp, heterochromat 82.3
2ee1_A64 Chromodomain helicase-DNA-binding protein 4; EC 3. 82.22
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 81.19
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Back     alignment and structure
Probab=100.00  E-value=3.1e-58  Score=487.25  Aligned_cols=308  Identities=22%  Similarity=0.325  Sum_probs=262.2

Q ss_pred             CCccchHHHHh-hhcccc-cccccCCCEEEeeHHHHHHHhhcccCC----C---CCCCchhHHHHHHHHHHHHHHcCCEE
Q 007971            1 MGVKNLWDILE-SCKKTL-PLHHLQNKRVCIDLSCWIVQLQNVNKS----Y---RPQTDKLFLRGLFHRLRALIALNCGL   71 (583)
Q Consensus         1 MGIkgL~~~L~-~~~~~v-~L~~L~gk~IaIDas~wL~~~~~a~~~----~---~g~~~~~~Lr~lf~rl~~Ll~~gI~P   71 (583)
                      ||| |||++|+ ++.+.+ +|++|+|++|+|||++||||++++.+.    .   ..|.+++++++||+++.+|+.++|+|
T Consensus        11 MGv-~L~~ll~~~~~~~~~~l~~l~gk~l~IDg~~~l~r~~~~~~~~~g~~l~~~~G~~T~al~gf~~r~~~ll~~~i~P   89 (363)
T 3ory_A           11 MGV-DLKDIIPGEAKTVIEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKP   89 (363)
T ss_dssp             CSC-CCGGGCCGGGEEECSSGGGGTTCEEEEEHHHHHHHHHHHCBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEE
T ss_pred             cCc-CHHHHhhHhcccccCCHHHhCCCEEEEehHHHHHHHHHhhhccCCCccCCCCCCCccHHHHHHHHHHHHHHcCCCc
Confidence            999 9999999 677888 999999999999999999998876542    1   12456889999999999999999999


Q ss_pred             EEEEcCCCCcchhhhhHhhhhcCccccc------ccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHH
Q 007971           72 IFVSDGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEA  145 (583)
Q Consensus        72 IFVFDG~~P~~K~~t~~~R~~~r~~a~~------~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADA  145 (583)
                      +|||||..|++|..++.+|+++|.++..      +.++.+++.++.+....+++.++..++++|++|||||++|||||||
T Consensus        90 v~VFDg~~p~~K~~~~~~yK~~R~~~~e~l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~i~~lL~~~GIp~i~apgEADa  169 (363)
T 3ory_A           90 VYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEA  169 (363)
T ss_dssp             EEEECSSCGGGCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHTCCCCCCCHHHHHHHHHHHHHHTCCEEECSSCHHH
T ss_pred             EEEEcCCCccchHHHHHHHHHhhhhchHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEEeCccHHH
Confidence            9999999999999999999988876432      2345556666666666778899999999999999999999999999


Q ss_pred             HHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCC-------Cce----EEEEeHHHHHHHhCCChHHHHHHHHHhCC
Q 007971          146 QCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGE-------RGY----VVCYEMDDIERKLGFGRNSLITLALLLGS  214 (583)
Q Consensus       146 qcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~-------~~~----v~~y~~~~i~~~lgL~r~qli~laiL~G~  214 (583)
                      |||+|++.|++|+|+|+|+|+|+||+++|+++++...       +.+    +++|+.+.+.+.+|++++||+++|+|+||
T Consensus       170 qiA~La~~g~~~~I~S~D~D~l~fg~~~v~~~l~~~~~~~~p~~~~~v~~~~~~~~~~~v~~~~gl~~~q~id~~~L~Gs  249 (363)
T 3ory_A          170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGT  249 (363)
T ss_dssp             HHHHHHHTTSCSEEECSSSHHHHTTCSEEEESTTTCEEEECSSTTCEEEECCEEEEHHHHHHHHTCCHHHHHHHHHHHCB
T ss_pred             HHHHHHHCCCeEEEECCCcCccccCCCeEEEEeeccccccCCccccccccceEEEcHHHHHHHhCcCHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999876431       112    36899999999999999999999999999


Q ss_pred             CCCC-CCCCCCHHHHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCC
Q 007971          215 DYSQ-GVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETP  292 (583)
Q Consensus       215 DY~p-GvpGiG~ktA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP  292 (583)
                      ||+| ||||||+|||++||++||+++ +++++..                                      ..+  +||
T Consensus       250 Dy~p~GVpGIG~KtA~kLl~~~gsle~il~~~~~--------------------------------------~~~--~~~  289 (363)
T 3ory_A          250 DYNPDGFEGIGPKKALQLVKAYGGIEKIPKPILK--------------------------------------SPI--EVD  289 (363)
T ss_dssp             TTBTTCSTTCCHHHHHHHHHHHTSSTTSCGGGCC--------------------------------------CSS--CCC
T ss_pred             CCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhccc--------------------------------------ccC--CCC
Confidence            9999 999999999999999999863 4433321                                      011  478


Q ss_pred             cHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhHHHHHH
Q 007971          293 FSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDL  355 (583)
Q Consensus       293 ~~~Vi~~Yl~P~v~~~~~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l~e~~l  355 (583)
                      +.+|.++|++|.|.+ +.++.|+     ..+..+|++|+.+.++|+.+++++.+.|+.+.++-
T Consensus       290 ~~~~~~~f~~p~v~~-~~~~~w~-----~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~~  346 (363)
T 3ory_A          290 VIAIKKYFLQPQVTD-NYRIEWH-----TPDPDAVKRILVDEHDFSIDRVSTALERYVKAFKE  346 (363)
T ss_dssp             HHHHHHHHHSCCCCS-CCCCCCC-----CCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCC-CCCCCCC-----CCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhcc
Confidence            899999999999985 2333332     34778999999999999999999999999877654
>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
>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
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster} Back     alignment and structure
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo domain, mRNA turnover, RRN processing, RNA binding, DNA binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A Back     alignment and structure
>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex, exonuclease, hydrolase, mRNA proces nuclease, nucleus, rRNA processing, transcription; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>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
>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
>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
>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
>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
>2kvm_A Chromobox protein homolog 7; histone modification, lysine methylation, chromobox, polycom chromatin-binding; HET: MLY; NMR {Mus musculus} 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
>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
>2d9u_A Chromobox protein homolog 2 (isoform 2); chromobox homolog 2, chromo domain, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>1x3p_A Cpsrp43; chromo-2 domain, chloroplasts, LHCP, protein translocation, unknown function; NMR {Arabidopsis thaliana} SCOP: b.34.13.2 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3q6s_A Chromobox protein homolog 1; incenp, heterochromatin, centromere, cell cycle; 1.93A {Homo sapiens} SCOP: b.34.13.2 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
>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

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 583
d1ul1x2216 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc 7e-35
d1rxwa2217 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc 2e-34
d1a77a2207 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc 2e-33
d1b43a2219 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc 7e-28
d1rxwa1105 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu 1e-04
d1ul1x1140 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu 3e-04
d1b43a1120 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu 0.002
>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

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: Human (Homo sapiens) [TaxId: 9606]

 Score =  128 bits (323), Expect = 7e-35
 Identities = 43/216 (19%), Positives = 81/216 (37%), Gaps = 18/216 (8%)

Query: 2   GVKNLWDILES----CKKTLPLHHLQNKRVCIDLSCWIVQ-LQNVNKSYRPQTDKL---- 52
           G++ L  ++        +   +     ++V ID S  I Q L  V +      ++     
Sbjct: 1   GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETT 60

Query: 53  -FLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGS------EVTQDDKNLD 105
             L G+F+R   ++      ++V DG  P +K     +R    +      +  Q      
Sbjct: 61  SHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ 120

Query: 106 KMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSD 165
           ++    + +         E K L   +G+P L+   EAEA CA L          + D D
Sbjct: 121 EVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMD 180

Query: 166 IFLFGARTVYRDIWLGE--RGYVVCYEMDDIERKLG 199
              FG+  + R +   E  +  +  + +  I ++LG
Sbjct: 181 CLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELG 216
>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
>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
>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 ?
Query583
d1ul1x2216 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 100.0
d1a77a2207 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 100.0
d1rxwa2217 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 100.0
d1b43a2219 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 100.0
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr 99.71
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 99.6
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 99.59
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo 99.55
d1cmwa2164 5' to 3' exonuclease domain of DNA polymerase Taq 99.45
d1xo1a2167 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 99.1
d1tfra2169 T4 RNase H {Bacteriophage T4 [TaxId: 10665]} 98.98
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 98.9
d1cmwa1116 5' to 3' exonuclease domain of DNA polymerase Taq 98.65
d1q3la_52 Heterochromatin protein 1, HP1 {Fruit fly (Drosoph 96.76
d2dnva152 Chromobox protein homolog 8 {Mouse (Mus musculus) 96.34
d1pfba_55 Polycomb protein, Pc {Fruit fly (Drosophila melano 96.3
d1guwa_73 Heterochromatin protein 1, HP1 {Mouse (Mus musculu 96.22
d1g6za_70 Histone methyltransferase clr4, chromo domain {Fis 95.87
d2dnta166 Chromodomain protein, Y-like isoform {Human (Homo 95.76
d2dy8a169 ATP-dependent helicase CHD1 (Chromo domain protein 94.43
d1x3pa154 CpSRP43 {Thale cress (Arabidopsis thaliana) [TaxId 94.15
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 92.22
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 92.17
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 91.31
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 90.93
d2b2ya180 ATP-dependent helicase CHD1 (Chromo domain protein 90.63
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 90.61
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 89.93
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 89.84
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 81.96
>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} 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: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4e-41  Score=329.44  Aligned_cols=198  Identities=21%  Similarity=0.286  Sum_probs=153.5

Q ss_pred             CccchHHHHhhh----cccccccccCCCEEEeeHHHHHHHhhcccCCC------CCCCchhHHHHHHHHHHHHHHcCCEE
Q 007971            2 GVKNLWDILESC----KKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSY------RPQTDKLFLRGLFHRLRALIALNCGL   71 (583)
Q Consensus         2 GIkgL~~~L~~~----~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~------~g~~~~~~Lr~lf~rl~~Ll~~gI~P   71 (583)
                      ||+|||+||++.    .++.+|++|+|++||||||+|||+++.+++..      ..+.++.++.++|+++..|+++||+|
T Consensus         1 GIkgL~~~l~~~~~~~i~~~~l~~l~gk~vaIDas~~l~~~l~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~l~~~~I~p   80 (216)
T d1ul1x2           1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKP   80 (216)
T ss_dssp             CCTTHHHHHHTTCTTSCCEECGGGGTTCCEEEEHHHHHHHHHSCC-------------CCHHHHHHHHHHHHHHHTTCCE
T ss_pred             CcchHHHHHHHhCcCceEEecHHHcCCCEEEEEeHHHHHHHHHHhccccchhhccCCCCcHHHHHHHHHHHHHHHcCCeE
Confidence            999999999964    57899999999999999999999998765432      12456789999999999999999999


Q ss_pred             EEEEcCCCCcchhhhhHhhhhcCcccccc------cccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHH
Q 007971           72 IFVSDGSIPAIKLSTYRRRLNSGSEVTQD------DKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEA  145 (583)
Q Consensus        72 IFVFDG~~P~~K~~t~~~R~~~r~~a~~~------~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADA  145 (583)
                      ||||||.+|+.|..+..+|+.+|.++...      .++..++.++.+....++..+++.++++|+.+||||++|||||||
T Consensus        81 ifVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ll~~~gv~~i~Ap~EAda  160 (216)
T d1ul1x2          81 VYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEA  160 (216)
T ss_dssp             EEEECCSCCSCCCCCCCCC-----------------------------CCCCCCSCHHHHHHHHHHHTCCEEECSSCHHH
T ss_pred             EEEEcCCCCccccchhhhhhhhHHHhhhhHHhhhhcchHHHHHHhhccCeeccHHHHHHHHHHHHhcCeeeEeccchHHH
Confidence            99999999999999988887776554321      122233444444444566778899999999999999999999999


Q ss_pred             HHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCC--ceEEEEeHHHHHHHhC
Q 007971          146 QCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER--GYVVCYEMDDIERKLG  199 (583)
Q Consensus       146 qcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~--~~v~~y~~~~i~~~lg  199 (583)
                      |||+|++.|+||+|+|+|||+|+||++.||+++....+  ..+++|++++|++.||
T Consensus       161 q~A~L~~~g~vd~v~S~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~il~~LG  216 (216)
T d1ul1x2         161 SCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELG  216 (216)
T ss_dssp             HHHHHHHHTSSSEEECSCTHHHHTTCSEEEECSSCCC-CCCCEEEEEHHHHHHHHT
T ss_pred             HHHHHHhcCceEEEEccccceeccCCcEEEEecccccCCCCcEEEEEHHHHHHhcC
Confidence            99999999999999999999999999999999875432  3689999999999987
>d1a77a2 c.120.1.2 (A:2-208) 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
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>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
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>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
>d1g6za_ b.34.13.2 (A:) Histone methyltransferase clr4, chromo domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} 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
>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
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} 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
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>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
>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