Citrus Sinensis ID: 003386

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-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820----
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEEDLDMEEPSSTLETSDKQNVSSFPDGDGKQRGTRGVSPASPKREGKRKRGRPAGGSAKKRKSTVNLARRKRPHVRNKPSKIYQNESDESNASDETEKKEEINREENHEDREMDDEENLETRQTNVVEDLESLDRGKALQQEVVKDFGKEKQTVRAPDIEMRERYHSKDSETTDKQQVDAVQAMLLDMIPSLGMKNEKTTNPIPKEESSSAEPSAEPTKKKKVSYKDIASKLLKDW
cccccccccccHHHHHHHcccccccEEEEcccEEcccHHHHHHHHHHHHccccccEEEEEEEEcccHHHHHHHHHHHHHccccEEEEEcccccccccccccccEEEccccccccccccEEEEEEEccccccccccccEEEEEEEccccccccccEEEEEEEcccccHHHHHHHHHHHcccccccccccccccccEEEcccccccccEEEEccccEEEEEEEccccccccccccccccccccEEEEEEccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEcccccEEEEEEcccccHHHHHcccccEEEccHHHHHHHcccccccccccEEcccHHHHHHHHHHHHHccccccccccHHHHHHHHHHccccccccHHHHHHHHHccccccccccccEEEEEcccccccccHHHHHHHHHHHHHHHHHHcccEEEccccccEEEEEEcccccccccccHHHHHHHHHHHHccccccEEEcccHHHHHHHccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccHHcHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHccc
ccHHHHHHHHHHHHHccccEEEEEEEEEEEcccccccccHHHHHHHHHccccccEEEEEEEEEcccHHHHHHHHHHHHHccccEEEEEccccccccccccccEEEEcHHHccccccccEEEEEEEEccccccccEEEEEEEEEccccccccccEEEEEEEEcccccHHHHHHHHHHHccccccccccccccccEEEEcccccccccEEEccccccEEEEEEEEEcccccHHccccEEEEcccEEEEcccccHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHcccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEccccccEEEEEEcccEHHHHHccccccEEcHHHHHHHHHcccccccccccEEEccHHHHHHHHHHHccccccccccccHHHHHHHHHHccccccccHHHHHHHHcccHcccccccccEEEEEccccccccccccccHHHHHHHHHHHHHcccEEEccccccEEEEEEccccccccHHHHHHHHHHHHHHcccccccEEEcHHHHHHHHHccccccHHHEEEcccccEEcccccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccHHHccccccEccccccccccccccccHHHccccccccccccccccccccccccccEccccccccccccEEEcccccccccccccccEEEccccccccccccccccccHHHHHHHHHcHccccccccccccccHHccccccccccccccccEcHHHHHHHHHccc
MVFELFAQLMTLSVlhdkdnacnistvamndGICVCVHVYMLSQLRSQIMAadqtgepcwslVAHNVDEVEKFFKETIENrdegivlkdlgskwepgdrsgkwlklkpeyiragsdlDVLIIGgyygsgrrgGEVAQFLVALaerpapdtyprrfisfcrvgtglsdeELDAVVTKLKPyfrkyeypkrappsfyqvtnnskerpdvwiespeksIILSITSDIRTIRSevfsapyslrfpridrvrydkpwhdcldvqSFVELVhssngttqkgkeygglqddkpkqfrssrkgekknvsivpshflqtdvsdikgetsiFSDMVFYFvnvppaysldsLHKMVVENggtfsmnlNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCcsqkkllqlqpkyylhlsdSSKKKLQEEVDEFSDLYFWDLDLADIKQLLsnvdrsedpktidyykkkycpqdkwscfhgcciyfyhsteplspdWEVLLGLALRRLKLEISfhggkvcnnlaNATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQkseeyeyslkptgmqESYLELCEedldmeepsstletsdkqnvssfpdgdgkqrgtrgvspaspkregkrkrgrpaggsakkrKSTVNLarrkrphvrnkpskiyqnesdesnasdetekkEEINreenhedremddeenLETRQTNVVEDLESLDRGKALQQEVVKDFGkekqtvrapdiemreryhskdsettdKQQVDAVQAMLLDMipslgmknekttnpipkeesssaepsaeptkkkkvSYKDIASKLLKDW
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKetienrdegivlkdlgskwepgdrsgkwlklkpeyiragsdldVLIIGGYYGSGRRGGEVAQFLVALAerpapdtyprrFISFCRvgtglsdeelDAVVTKLKPYFrkyeypkrappsfyqvtnnskerpdvwiespekSIILSITSDIRTIRSevfsapyslrfpriDRVRYDKPWHDCLDVQSFVELVHSsngttqkgkeygglqddkpkqfrssrkgekknvsivpshflqtdvsdIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLlsnvdrsedpktiDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQkseeyeyslkptgmQESYLELCEEDLDMEEPSstletsdkqnvssfpdgdgkqrgtrgvspaspkregkrkrgrpaggsakkrkstvnlarrkrphvrnkpskiyqnesdesnasdetekkeeinreenhedremddeenletrqtnvvedlesldrGKALQQevvkdfgkekqtvrapdiemreryhskdsettdkqQVDAVQAMLLDMIPSLGMKNEKTtnpipkeesssaepsaeptkkkkvsykDIASKLLKDW
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIggyygsgrrggEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSqkkllqlqpkYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVllglalrrlklEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYlelceedldmeePSSTLETSDKQNVSSFPDGDGKQRGTRGVSPAspkregkrkrgrpaggsakkrkSTVNLARRKRPHVRNKPSKIYQNESDESNASdetekkeeinreenhedreMDDEENLETRQTNVVEDLESLDRGKALQQEVVKDFGKEKQTVRAPDIEMRERYHSKDSETTDKQQVDAVQAMLLDMIPSLGMKNEKTTNPIPKeesssaepsaepTKKKKVSYKDIASKLLKDW
**FELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQV********DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH***********************************IVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLS*********EVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLA*********************************************************************************************************************************************************************************************************************************************************************
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVEL*******************************************************SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQ******************KKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVN******************KKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG*****************************************************************************************************************************************************************************************QVDAVQAMLLDMIP**********************************YKDIASKLLKDW
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDK**************VSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEED*****************************************************************RRKRPHVRNKPSKI***************************************RQTNVVEDLESLDRGKALQQEVVKDFGKEKQTVRAPDIEMRE************QQVDAVQAMLLDMIPSLGMKNEKTT************************YKDIASKLLKDW
MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQ**************************************VSD*KGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYL********************************************************************************************************************************************ALQQEV**************************S****KQQVDAVQAMLLDMIPSLG*****************************VSYKDIASKLLKDW
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SSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVFELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEEDLDMEEPSSTLETSDKQNVSSFPDGDGKQRGTRGVSPASPKREGKRKRGRPAGGSAKKRKSTVNLARRKRPHVRNKPSKIYQxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxETRQTNVVEDLESLDRGKALQQEVVKDFGKEKQTVRAPDIEMRERYHSKDSETTDKQQVDAVQAMLLDMIPSLGMKNEKTTNPIPKEESSSAEPSAEPTKKKKVSYKDIASKLLKDW
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 ?
Query824 2.2.26 [Sep-21-2011]
Q9LL841219 DNA ligase 4 OS=Arabidops yes no 0.894 0.604 0.516 0.0
Q7X7E91322 Putative DNA ligase 4 OS= yes no 0.266 0.166 0.632 3e-88
Q5R6L3911 DNA ligase 4 OS=Pongo abe yes no 0.593 0.536 0.298 3e-59
P49917911 DNA ligase 4 OS=Homo sapi yes no 0.593 0.536 0.294 1e-58
Q8BTF7911 DNA ligase 4 OS=Mus muscu yes no 0.594 0.537 0.306 3e-58
Q90YB1912 DNA ligase 4 OS=Gallus ga yes no 0.594 0.537 0.304 6e-55
Q54CR91088 DNA ligase 4 OS=Dictyoste yes no 0.552 0.418 0.294 2e-48
Q2U6A11006 DNA ligase 4 OS=Aspergill yes no 0.574 0.470 0.268 1e-42
Q6C8A3956 DNA ligase 4 OS=Yarrowia yes no 0.449 0.387 0.300 5e-39
Q1DKE7985 DNA ligase 4 OS=Coccidioi N/A no 0.597 0.499 0.255 5e-38
>sp|Q9LL84|DNLI4_ARATH DNA ligase 4 OS=Arabidopsis thaliana GN=LIG4 PE=1 SV=1 Back     alignment and function desciption
 Score =  811 bits (2095), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/863 (51%), Positives = 573/863 (66%), Gaps = 126/863 (14%)

Query: 55   TGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAG 114
            +GEP WS+V H   +VE+FFKET+ENRDEGIVLKDL SKWEPGDRSGKW+KLKPEYIRAG
Sbjct: 390  SGEPSWSIVVHAAADVERFFKETVENRDEGIVLKDLESKWEPGDRSGKWMKLKPEYIRAG 449

Query: 115  SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 174
            +DLDVLIIGGYYGSGRRGGEVAQFLVALA+R   + YPRRF+SFCRVGTGLSD+EL+ VV
Sbjct: 450  ADLDVLIIGGYYGSGRRGGEVAQFLVALADRAEANVYPRRFMSFCRVGTGLSDDELNTVV 509

Query: 175  TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA 234
            +KLKPYFRK E+PK+APPSFYQVTN+SKERPDVWI+SPEKSIILSITSDIRTIRSEVF A
Sbjct: 510  SKLKPYFRKNEHPKKAPPSFYQVTNHSKERPDVWIDSPEKSIILSITSDIRTIRSEVFVA 569

Query: 235  PYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRK 294
            PYSLRFPRID+VRYDKPWH+CLDVQ+FVELV+SSNGTTQK KE    QD+ PK  +SS++
Sbjct: 570  PYSLRFPRIDKVRYDKPWHECLDVQAFVELVNSSNGTTQKQKESESTQDN-PKVNKSSKR 628

Query: 295  GEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSM 354
            GEKKNVS+VPS F+QTDVSDIKG+TSIFS+M+FYFVNVP ++SL++ HKMVVENGG FSM
Sbjct: 629  GEKKNVSLVPSQFIQTDVSDIKGKTSIFSNMIFYFVNVPRSHSLETFHKMVVENGGKFSM 688

Query: 355  NLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKK 414
            NLNNSVTHC+AA++ G+KY+AAKR+ DVIH+SWVLDCCS+ K+L L PKY+LHL+D+S+ 
Sbjct: 689  NLNNSVTHCIAAESSGIKYQAAKRQRDVIHFSWVLDCCSRNKMLPLLPKYFLHLTDASRT 748

Query: 415  KLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIY 474
            KLQ+++DEFSD Y+WDLDL  +KQ+LSN  +SED K+IDYYKKK CP+ +WSC   CC+Y
Sbjct: 749  KLQDDIDEFSDSYYWDLDLEGLKQVLSNAKQSEDSKSIDYYKKKLCPEKRWSCLLSCCVY 808

Query: 475  FYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLT 534
            FY  ++ LS + E LLG+  +RL LE+   GGKV NNLA+A+H+VVL++    ++F  ++
Sbjct: 809  FYPYSQTLSTEEEALLGIMAKRLMLEVLMAGGKVSNNLAHASHLVVLAMAEEPLDFTLVS 868

Query: 535  ESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEEDLDM 594
            +SF+  EK LL  K+LHVV S WLE+ L +E+K  E  Y+L+P  M+ES         D 
Sbjct: 869  KSFSEMEKRLLLKKRLHVVSSHWLEESLQREEKLCEDVYTLRPKYMEES---------DT 919

Query: 595  EEPSSTLETSDKQNVSSFPDGDGKQRGTRGVSPASPKREGKRKRGRPAGGSAKKRKSTVN 654
            EE   +    D   V+S      K+       PAS K      RGR    + K+ +S+ N
Sbjct: 920  EESDKS--EHDTTEVASQGSAQTKE-------PASSKIAITSSRGRSNTRAVKRGRSSTN 970

Query: 655  LARRKRPHVRNKPSKIYQNESDESNASDET------------------------------ 684
              +R +     +PSKI  +E++ES+AS+E                               
Sbjct: 971  SLQRVQRRRGKQPSKISGDETEESDASEEKVSTRLSDIAEETDSFGEAQRNSSRGKCAKR 1030

Query: 685  -----------------EKKEEINREENHEDREMDDE-----------------ENLETR 710
                             +K  +I  +E+ E+ E+D                   EN ETR
Sbjct: 1031 GKSRVGQTQRVQRSRRGKKAAKIGGDESDENDELDGNNNVSADAEEGNAAGRSVENEETR 1090

Query: 711  QTNVVEDLESLDRGKALQ-QEVVKDFGKEKQTVRAPDIEMRERYHSKDSETTDKQQVDAV 769
            + ++ +  ES  R   +  +E ++D    K      +++M+E+    +         D +
Sbjct: 1091 EPDIAKYTESQQRDNTVAVEEALQDSRNAK-----TEMDMKEKLQIHE---------DPL 1136

Query: 770  QAMLLDMIPSLGMKNEKTTNPIPKE----------------------ESSSAEPSAEP-- 805
            QAML+ M P    K  +T+N    E                      +++S    AE   
Sbjct: 1137 QAMLMKMFPIPSQKTTETSNRTTGEYRKANVSGECESSEKRKLDAETDNTSVNAGAESDV 1196

Query: 806  ----TKKKKVSYKDIASKLLKDW 824
                 KKKKVSY+D+A +LLKDW
Sbjct: 1197 VPPLVKKKKVSYRDVAGELLKDW 1219
Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair. May be involved for T-DNA integration even if not absolutely required. Seems to be dispensable under normal growth conditions.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 5EC: .EC: 1EC: .EC: 1
>sp|Q7X7E9|DNLI4_ORYSJ Putative DNA ligase 4 OS=Oryza sativa subsp. japonica GN=LIG4 PE=2 SV=2 Back     alignment and function description
>sp|Q5R6L3|DNLI4_PONAB DNA ligase 4 OS=Pongo abelii GN=DNL4 PE=2 SV=1 Back     alignment and function description
>sp|P49917|DNLI4_HUMAN DNA ligase 4 OS=Homo sapiens GN=LIG4 PE=1 SV=2 Back     alignment and function description
>sp|Q8BTF7|DNLI4_MOUSE DNA ligase 4 OS=Mus musculus GN=Lig4 PE=2 SV=2 Back     alignment and function description
>sp|Q90YB1|DNLI4_CHICK DNA ligase 4 OS=Gallus gallus GN=LIG4 PE=2 SV=2 Back     alignment and function description
>sp|Q54CR9|DNLI4_DICDI DNA ligase 4 OS=Dictyostelium discoideum GN=lig4 PE=3 SV=1 Back     alignment and function description
>sp|Q2U6A1|DNLI4_ASPOR DNA ligase 4 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=lig4 PE=3 SV=1 Back     alignment and function description
>sp|Q6C8A3|DNLI4_YARLI DNA ligase 4 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=LIG4 PE=3 SV=1 Back     alignment and function description
>sp|Q1DKE7|DNLI4_COCIM DNA ligase 4 OS=Coccidioides immitis (strain RS) GN=LIG4 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 ?
Query824
225445943 1162 PREDICTED: DNA ligase 4-like [Vitis vini 0.925 0.656 0.673 0.0
297735473 1163 unnamed protein product [Vitis vinifera] 0.925 0.656 0.673 0.0
224144326 1242 predicted protein [Populus trichocarpa] 0.923 0.612 0.604 0.0
356556242 1171 PREDICTED: DNA ligase 4-like [Glycine ma 0.923 0.649 0.617 0.0
112732548 1319 DNA ligase IV [Populus nigra] 0.928 0.579 0.555 0.0
357449599 1244 DNA ligase [Medicago truncatula] gi|3554 0.922 0.610 0.575 0.0
297796605 1221 ATLIG4 [Arabidopsis lyrata subsp. lyrata 0.907 0.612 0.537 0.0
449463583 1214 PREDICTED: DNA ligase 4-like [Cucumis sa 0.933 0.633 0.541 0.0
449516627918 PREDICTED: LOW QUALITY PROTEIN: DNA liga 0.933 0.837 0.540 0.0
30696835 1219 DNA ligase 4 [Arabidopsis thaliana] gi|7 0.894 0.604 0.516 0.0
>gi|225445943|ref|XP_002263967.1| PREDICTED: DNA ligase 4-like [Vitis vinifera] Back     alignment and taxonomy information
 Score = 1033 bits (2671), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 526/781 (67%), Positives = 628/781 (80%), Gaps = 18/781 (2%)

Query: 55   TGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAG 114
            +GEPCWSL+A++VD+VE+FFK+T+ENRDEGIVLKDLGSKWEP DRSGKWLKLKPEY+ AG
Sbjct: 389  SGEPCWSLIAYDVDDVERFFKKTVENRDEGIVLKDLGSKWEPSDRSGKWLKLKPEYVHAG 448

Query: 115  SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 174
            SDLDVLIIGGYYGSGRRGGEVAQFLV LA+   PDTYPRRFISFCRVGTGLSD+ELDAVV
Sbjct: 449  SDLDVLIIGGYYGSGRRGGEVAQFLVGLADHSGPDTYPRRFISFCRVGTGLSDDELDAVV 508

Query: 175  TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA 234
            TKLKPYFRK EYPK+APPSFYQVTNNSKERPD+WI+SPEKSIILSITSDIRTIRSEVF+A
Sbjct: 509  TKLKPYFRKNEYPKKAPPSFYQVTNNSKERPDIWIDSPEKSIILSITSDIRTIRSEVFAA 568

Query: 235  PYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRK 294
            PYSLRFPRID VRYDKPWH+CLDVQSF+ELVHSSNGTTQ+G +YG +QD KPK+ +SS+K
Sbjct: 569  PYSLRFPRIDCVRYDKPWHECLDVQSFMELVHSSNGTTQRGADYGRMQDSKPKRMKSSKK 628

Query: 295  GEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSM 354
            GE+K   +VPSHF+QTDV+++KGET IFS+M+FYFVN PP +SLDSLHK+VVENGGTFSM
Sbjct: 629  GEQKTAHVVPSHFMQTDVTNVKGETLIFSNMMFYFVNTPPTHSLDSLHKLVVENGGTFSM 688

Query: 355  NLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKK 414
            NLNNSVTHCVAA +KG+KY+AAK RGD+IH SWV DCCSQKKLL LQPKY+L LS+ SKK
Sbjct: 689  NLNNSVTHCVAAQSKGIKYQAAKLRGDIIHCSWVFDCCSQKKLLPLQPKYFLFLSEHSKK 748

Query: 415  KLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIY 474
            KLQEE+D+FSD Y+ DLD++DIKQLLSNVDRS++ KTIDYYK KYCP++KWS FH CCI 
Sbjct: 749  KLQEEIDKFSDSYYQDLDISDIKQLLSNVDRSDNSKTIDYYKNKYCPKEKWSRFHDCCIC 808

Query: 475  FYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLT 534
            F+ S +  + DWE+L  LALRR+KLE+S  GGKV NNL+ ATH+VV SV G+D++F+ + 
Sbjct: 809  FHSSIQSSNSDWELLSKLALRRMKLEVSMGGGKVGNNLSQATHLVVFSVPGFDLDFSDIM 868

Query: 535  ESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEEDLDM 594
            ESF+  EKHLL NKKLHVV  QWLE CL + ++ +E +YSLKP G++ES    C+ D+D+
Sbjct: 869  ESFSPAEKHLLCNKKLHVVGYQWLEGCLEEGRRLQEQKYSLKPEGLEESNFGECKHDIDV 928

Query: 595  EEPSSTLETSDKQNVSSFPDGDGKQRGTRGVSP-------ASPKREGKRKRGRPAGGSAK 647
            E P S L++ + QN+ SFPD +GKQ   RG +P       ASPKR+ KRKRGRPAG S K
Sbjct: 929  EAP-SVLDSVENQNLVSFPDKEGKQ--GRGKAPPESISILASPKRDEKRKRGRPAGPSTK 985

Query: 648  KRKSTVNLARRKRPHVRNKPSKIYQNESDESNASDETEKKEE--INREENHEDREMDDEE 705
            K K+  + ARR RP +  KP KIY+NESD   ASD  EK EE       NH    ++ +E
Sbjct: 986  KGKAGFSQARRTRPRI-GKPPKIYENESD---ASDSGEKMEEEGTKMGGNHAIHGVECKE 1041

Query: 706  NLETRQTNVVEDLESLDRGKALQQEVVKDFGKEKQTVRAPDIEMRERYHSKDSETTDKQQ 765
              E ++T +VED ES  RGK  ++EV  D  +EK   RA DIE+       +S+ T+K +
Sbjct: 1042 CPEIQETEIVEDSESSQRGKTEEKEVALDNVREKWLDRAQDIELDSENKVDNSKKTEKLE 1101

Query: 766  --VDAVQAMLLDMIPSLGMKNEKTTNPIPKEESSSAEPSAEPTKKKKVSYKDIASKLLKD 823
              VD VQAMLLDMIPSLG+K  ++TNPI  +E    E  AEP KKKKVSYKD+A  LLKD
Sbjct: 1102 VMVDPVQAMLLDMIPSLGVKKAESTNPIIDDEKPPVEQGAEPVKKKKVSYKDVAGALLKD 1161

Query: 824  W 824
            W
Sbjct: 1162 W 1162

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297735473|emb|CBI17913.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224144326|ref|XP_002325262.1| predicted protein [Populus trichocarpa] gi|222866696|gb|EEF03827.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356556242|ref|XP_003546435.1| PREDICTED: DNA ligase 4-like [Glycine max] Back     alignment and taxonomy information
>gi|112732548|dbj|BAF03051.1| DNA ligase IV [Populus nigra] Back     alignment and taxonomy information
>gi|357449599|ref|XP_003595076.1| DNA ligase [Medicago truncatula] gi|355484124|gb|AES65327.1| DNA ligase [Medicago truncatula] Back     alignment and taxonomy information
>gi|297796605|ref|XP_002866187.1| ATLIG4 [Arabidopsis lyrata subsp. lyrata] gi|297312022|gb|EFH42446.1| ATLIG4 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449463583|ref|XP_004149513.1| PREDICTED: DNA ligase 4-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449516627|ref|XP_004165348.1| PREDICTED: LOW QUALITY PROTEIN: DNA ligase 4-like, partial [Cucumis sativus] Back     alignment and taxonomy information
>gi|30696835|ref|NP_568851.2| DNA ligase 4 [Arabidopsis thaliana] gi|75174554|sp|Q9LL84.1|DNLI4_ARATH RecName: Full=DNA ligase 4; AltName: Full=DNA ligase IV; AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4 gi|9651815|gb|AAF91284.1|AF233527_1 DNA ligase IV [Arabidopsis thaliana] gi|332009474|gb|AED96857.1| DNA ligase 4 [Arabidopsis thaliana] 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 ?
Query824
TAIR|locus:21755441219 ATLIG4 [Arabidopsis thaliana ( 0.640 0.433 0.659 5.8e-200
UNIPROTKB|E2R0G7911 LIG4 "DNA ligase" [Canis lupus 0.591 0.534 0.285 1.5e-48
ZFIN|ZDB-GENE-070820-10909 lig4 "ligase IV, DNA, ATP-depe 0.584 0.530 0.280 5.5e-48
UNIPROTKB|Q5R6L3911 DNL4 "DNA ligase 4" [Pongo abe 0.593 0.536 0.277 7.9e-48
MGI|MGI:1335098911 Lig4 "ligase IV, DNA, ATP-depe 0.595 0.538 0.281 6.4e-47
UNIPROTKB|P49917911 LIG4 "DNA ligase 4" [Homo sapi 0.592 0.535 0.274 8.5e-47
RGD|1304639911 Lig4 "ligase IV, DNA, ATP-depe 0.594 0.537 0.277 3.4e-45
UNIPROTKB|F1P275912 LIG4 "DNA ligase" [Gallus gall 0.589 0.532 0.279 6e-45
UNIPROTKB|Q90YB1912 LIG4 "DNA ligase 4" [Gallus ga 0.589 0.532 0.279 7.9e-45
UNIPROTKB|F1MB07911 LIG4 "DNA ligase" [Bos taurus 0.592 0.535 0.261 5e-42
TAIR|locus:2175544 ATLIG4 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1871 (663.7 bits), Expect = 5.8e-200, Sum P(2) = 5.8e-200
 Identities = 349/529 (65%), Positives = 427/529 (80%)

Query:    55 TGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAG 114
             +GEP WS+V H   +VE+FFKET+ENRDEGIVLKDL SKWEPGDRSGKW+KLKPEYIRAG
Sbjct:   390 SGEPSWSIVVHAAADVERFFKETVENRDEGIVLKDLESKWEPGDRSGKWMKLKPEYIRAG 449

Query:   115 SDLDVLIIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 174
             +DLDVLII           EVAQFLVALA+R   + YPRRF+SFCRVGTGLSD+EL+ VV
Sbjct:   450 ADLDVLIIGGYYGSGRRGGEVAQFLVALADRAEANVYPRRFMSFCRVGTGLSDDELNTVV 509

Query:   175 TKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA 234
             +KLKPYFRK E+PK+APPSFYQVTN+SKERPDVWI+SPEKSIILSITSDIRTIRSEVF A
Sbjct:   510 SKLKPYFRKNEHPKKAPPSFYQVTNHSKERPDVWIDSPEKSIILSITSDIRTIRSEVFVA 569

Query:   235 PYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRK 294
             PYSLRFPRID+VRYDKPWH+CLDVQ+FVELV+SSNGTTQK KE    QD+ PK  +SS++
Sbjct:   570 PYSLRFPRIDKVRYDKPWHECLDVQAFVELVNSSNGTTQKQKESESTQDN-PKVNKSSKR 628

Query:   295 GEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSM 354
             GEKKNVS+VPS F+QTDVSDIKG+TSIFS+M+FYFVNVP ++SL++ HKMVVENGG FSM
Sbjct:   629 GEKKNVSLVPSQFIQTDVSDIKGKTSIFSNMIFYFVNVPRSHSLETFHKMVVENGGKFSM 688

Query:   355 NLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSXXXXXXXXXXYYLHLSDSSKK 414
             NLNNSVTHC+AA++ G+KY+AAKR+ DVIH+SWVLDCCS          Y+LHL+D+S+ 
Sbjct:   689 NLNNSVTHCIAAESSGIKYQAAKRQRDVIHFSWVLDCCSRNKMLPLLPKYFLHLTDASRT 748

Query:   415 KLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIY 474
             KLQ+++DEFSD Y+WDLDL  +KQ+LSN  +SED K+IDYYKKK CP+ +WSC   CC+Y
Sbjct:   749 KLQDDIDEFSDSYYWDLDLEGLKQVLSNAKQSEDSKSIDYYKKKLCPEKRWSCLLSCCVY 808

Query:   475 FYHSTEPLSPDWEVXXXXXXXXXXXEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLT 534
             FY  ++ LS + E            E+   GGKV NNLA+A+H+VVL++    ++F  ++
Sbjct:   809 FYPYSQTLSTEEEALLGIMAKRLMLEVLMAGGKVSNNLAHASHLVVLAMAEEPLDFTLVS 868

Query:   535 ESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQES 583
             +SF+  EK LL  K+LHVV S WLE+ L +E+K  E  Y+L+P  M+ES
Sbjct:   869 KSFSEMEKRLLLKKRLHVVSSHWLEESLQREEKLCEDVYTLRPKYMEES 917
GO:0003677 "DNA binding" evidence=IEA
GO:0003909 "DNA ligase activity" evidence=IEA
GO:0003910 "DNA ligase (ATP) activity" evidence=IEA;IDA
GO:0005524 "ATP binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0006260 "DNA replication" evidence=IEA
GO:0006266 "DNA ligation" evidence=IBA
GO:0006281 "DNA repair" evidence=IEA
GO:0006310 "DNA recombination" evidence=IEA
GO:0032807 "DNA ligase IV complex" evidence=IBA
GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA
GO:0005515 "protein binding" evidence=IPI
GO:0006974 "response to DNA damage stimulus" evidence=IMP
GO:0010165 "response to X-ray" evidence=IMP
GO:0015074 "DNA integration" evidence=IMP
GO:0000723 "telomere maintenance" evidence=IMP
GO:0006302 "double-strand break repair" evidence=IMP
GO:0009506 "plasmodesma" evidence=IDA
GO:0048046 "apoplast" evidence=IDA
UNIPROTKB|E2R0G7 LIG4 "DNA ligase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-070820-10 lig4 "ligase IV, DNA, ATP-dependent" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q5R6L3 DNL4 "DNA ligase 4" [Pongo abelii (taxid:9601)] Back     alignment and assigned GO terms
MGI|MGI:1335098 Lig4 "ligase IV, DNA, ATP-dependent" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|P49917 LIG4 "DNA ligase 4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|1304639 Lig4 "ligase IV, DNA, ATP-dependent" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1P275 LIG4 "DNA ligase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q90YB1 LIG4 "DNA ligase 4" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1MB07 LIG4 "DNA ligase" [Bos taurus (taxid:9913)] 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) ?
Q9LL84DNLI4_ARATH6, ., 5, ., 1, ., 10.51680.89440.6045yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
4th Layer6.5.1.10.824
3rd Layer6.5.10.766

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 ?
Query824
cd07968140 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/ol 5e-55
TIGR00574514 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1 3e-35
PRK01109590 PRK01109, PRK01109, ATP-dependent DNA ligase; Prov 3e-29
cd07893129 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligo 1e-25
COG1793444 COG1793, CDC9, ATP-dependent DNA ligase [DNA repli 1e-25
PLN03113744 PLN03113, PLN03113, DNA ligase 1; Provisional 4e-21
cd07969144 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oli 5e-19
cd07903225 cd07903, Adenylation_DNA_ligase_IV, Adenylation do 7e-18
pfam0467995 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligas 4e-14
cd07972122 cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleo 8e-14
cd07967139 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/o 1e-13
pfam0053377 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain 2e-11
cd07901207 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenyla 4e-11
smart0029278 smart00292, BRCT, breast cancer carboxy-terminal d 6e-11
PRK09632764 PRK09632, PRK09632, ATP-dependent DNA ligase; Revi 1e-10
TIGR02779298 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, l 6e-10
pfam1273863 pfam12738, PTCB-BRCT, twin BRCT domain 1e-09
pfam01068195 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligas 2e-09
cd07898201 cd07898, Adenylation_DNA_ligase, Adenylation domai 2e-09
PRK03180508 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed 3e-09
cd0002772 cd00027, BRCT, Breast Cancer Suppressor Protein (B 3e-09
TIGR02776552 TIGR02776, NHEJ_ligase_prk, DNA ligase D 4e-09
cd07900219 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation 9e-09
cd07906190 cd07906, Adenylation_DNA_ligase_LigD_LigC, Adenyla 1e-07
PRK09125282 PRK09125, PRK09125, DNA ligase; Provisional 1e-06
cd08040108 cd08040, OBF_DNA_ligase_family, The Oligonucleotid 1e-06
PHA02587488 PHA02587, 30, DNA ligase; Provisional 1e-04
cd07971115 cd07971, OBF_DNA_ligase_LigD, The Oligonucleotide/ 1e-04
cd07896174 cd07896, Adenylation_kDNA_ligase_like, Adenylation 2e-04
pfam0053377 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain 3e-04
TIGR04120526 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent 5e-04
PRK09633610 PRK09633, ligD, ATP-dependent DNA ligase; Reviewed 0.001
PRK05972860 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed 0.003
>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information 
 Score =  185 bits (473), Expect = 5e-55
 Identities = 73/146 (50%), Positives = 101/146 (69%), Gaps = 7/146 (4%)

Query: 114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPD-TYPRRFISFCRVGTGLSDEELDA 172
           G DLD+LIIGGYYG GRRGG+V+ FL  +AE   P+   P  F SFC+VG+G SDEELD 
Sbjct: 1   GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEELDE 60

Query: 173 VVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVF 232
           +  KLKP+++   + K+APPS   +    KE+PDVWIE P+ S++L + +    + S+ +
Sbjct: 61  IRRKLKPHWKP--FDKKAPPSS--LLKFGKEKPDVWIE-PKDSVVLEVKAAEI-VPSDSY 114

Query: 233 SAPYSLRFPRIDRVRYDKPWHDCLDV 258
              Y+LRFPR +++RYDK WHDCL +
Sbjct: 115 KTGYTLRFPRCEKIRYDKDWHDCLTL 140

ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Length = 140
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>gnl|CDD|234900 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|153435 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|215584 PLN03113, PLN03113, DNA ligase 1; Provisional Back     alignment and domain information
>gnl|CDD|153438 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA Ligase IV Back     alignment and domain information
>gnl|CDD|218210 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligase C terminal region Back     alignment and domain information
>gnl|CDD|153441 cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|153436 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain Back     alignment and domain information
>gnl|CDD|185711 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of archaeal and bacterial LigB-like DNA ligases Back     alignment and domain information
>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain Back     alignment and domain information
>gnl|CDD|236599 PRK09632, PRK09632, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|234009 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase domain Back     alignment and domain information
>gnl|CDD|193214 pfam12738, PTCB-BRCT, twin BRCT domain Back     alignment and domain information
>gnl|CDD|216280 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain Back     alignment and domain information
>gnl|CDD|185709 cd07898, Adenylation_DNA_ligase, Adenylation domain of ATP-dependent DNA Ligases Back     alignment and domain information
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|237994 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain Back     alignment and domain information
>gnl|CDD|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D Back     alignment and domain information
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of eukaryotic DNA Ligase I Back     alignment and domain information
>gnl|CDD|185715 cd07906, Adenylation_DNA_ligase_LigD_LigC, Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>gnl|CDD|181662 PRK09125, PRK09125, DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|153442 cd08040, OBF_DNA_ligase_family, The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>gnl|CDD|222893 PHA02587, 30, DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|153440 cd07971, OBF_DNA_ligase_LigD, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>gnl|CDD|185707 cd07896, Adenylation_kDNA_ligase_like, Adenylation domain of kDNA ligases and similar proteins Back     alignment and domain information
>gnl|CDD|215978 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain Back     alignment and domain information
>gnl|CDD|234477 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent, PP_1105 family Back     alignment and domain information
>gnl|CDD|182006 PRK09633, ligD, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|235658 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 824
KOG0966881 consensus ATP-dependent DNA ligase IV [Replication 100.0
PLN03113744 DNA ligase 1; Provisional 100.0
PRK01109590 ATP-dependent DNA ligase; Provisional 100.0
KOG0967714 consensus ATP-dependent DNA ligase I [Replication, 100.0
PRK03180508 ligB ATP-dependent DNA ligase; Reviewed 100.0
TIGR00574514 dnl1 DNA ligase I, ATP-dependent (dnl1). All prote 100.0
PRK09247539 ATP-dependent DNA ligase; Validated 100.0
TIGR02779298 NHEJ_ligase_lig DNA polymerase LigD, ligase domain 100.0
PRK09632764 ATP-dependent DNA ligase; Reviewed 100.0
PRK05972860 ligD ATP-dependent DNA ligase; Reviewed 100.0
TIGR02776552 NHEJ_ligase_prk DNA ligase D. Members of this prot 100.0
COG1793444 CDC9 ATP-dependent DNA ligase [DNA replication, re 100.0
PRK08224350 ligC ATP-dependent DNA ligase; Reviewed 100.0
PRK09633610 ligD ATP-dependent DNA ligase; Reviewed 100.0
cd07967139 OBF_DNA_ligase_III The Oligonucleotide/oligosaccha 99.97
PHA02587488 30 DNA ligase; Provisional 99.96
cd07968140 OBF_DNA_ligase_IV The Oligonucleotide/oligosacchar 99.96
PRK07636275 ligB ATP-dependent DNA ligase; Reviewed 99.95
cd07969144 OBF_DNA_ligase_I The Oligonucleotide/oligosacchari 99.95
PRK09125282 DNA ligase; Provisional 99.94
cd07972122 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligo 99.93
cd07893129 OBF_DNA_ligase The Oligonucleotide/oligosaccharide 99.92
PHA00454315 ATP-dependent DNA ligase 99.91
cd07971115 OBF_DNA_ligase_LigD The Oligonucleotide/oligosacch 99.84
PF0467997 DNA_ligase_A_C: ATP dependent DNA ligase C termina 99.79
cd08040108 OBF_DNA_ligase_family The Oligonucleotide/oligosac 99.78
cd07970122 OBF_DNA_ligase_LigC The Oligonucleotide/oligosacch 99.75
cd07900219 Adenylation_DNA_ligase_I_Euk Adenylation domain of 99.65
cd07897207 Adenylation_DNA_ligase_Bac1 Adenylation domain of 99.59
cd08039235 Adenylation_DNA_ligase_Fungal Adenylation domain o 99.58
cd07901207 Adenylation_DNA_ligase_Arch_LigB Adenylation domai 99.56
cd07898201 Adenylation_DNA_ligase Adenylation domain of ATP-d 99.54
cd07902213 Adenylation_DNA_ligase_III Adenylation domain of D 99.53
cd07903225 Adenylation_DNA_ligase_IV Adenylation domain of DN 99.51
cd07905194 Adenylation_DNA_ligase_LigC Adenylation domain of 99.47
cd07906190 Adenylation_DNA_ligase_LigD_LigC Adenylation domai 99.45
cd07896174 Adenylation_kDNA_ligase_like Adenylation domain of 99.4
PF01068202 DNA_ligase_A_M: ATP dependent DNA ligase domain; I 99.33
PF0053378 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP 99.26
smart0029280 BRCT breast cancer carboxy-terminal domain. 99.09
cd0804177 OBF_kDNA_ligase_like The Oligonucleotide/oligosacc 98.98
cd06846182 Adenylation_DNA_ligase_like Adenylation domain of 98.94
cd0002772 BRCT Breast Cancer Suppressor Protein (BRCA1), car 98.92
KOG1929 811 consensus Nucleotide excision repair factor NEF2, 98.92
PF0053378 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IP 98.8
KOG3524 850 consensus Predicted guanine nucleotide exchange fa 98.73
smart0029280 BRCT breast cancer carboxy-terminal domain. 98.65
KOG3226508 consensus DNA repair protein [Replication, recombi 98.63
PF1273863 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W 98.58
cd07895215 Adenylation_mRNA_capping Adenylation domain of GTP 98.52
cd0002772 BRCT Breast Cancer Suppressor Protein (BRCA1), car 98.41
KOG35481176 consensus DNA damage checkpoint protein RHP9/CRB2/ 98.27
PF1141136 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 98.18
KOG2481570 consensus Protein required for normal rRNA process 98.17
KOG2481570 consensus Protein required for normal rRNA process 98.08
KOG1929 811 consensus Nucleotide excision repair factor NEF2, 97.98
COG5163591 NOP7 Protein required for biogenesis of the 60S ri 97.89
PLN03122 815 Poly [ADP-ribose] polymerase; Provisional 97.81
COG5163591 NOP7 Protein required for biogenesis of the 60S ri 97.66
PF1474366 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2 97.58
PF1273863 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2W 97.56
cd07894342 Adenylation_RNA_ligase Adenylation domain of RNA c 97.3
KOG3226508 consensus DNA repair protein [Replication, recombi 97.21
PLN03123981 poly [ADP-ribose] polymerase; Provisional 97.1
KOG4362684 consensus Transcriptional regulator BRCA1 [Replica 96.91
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 96.42
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 96.32
PLN03122 815 Poly [ADP-ribose] polymerase; Provisional 96.3
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 96.19
PRK06195309 DNA polymerase III subunit epsilon; Validated 96.03
PRK06063313 DNA polymerase III subunit epsilon; Provisional 95.98
PLN03123 981 poly [ADP-ribose] polymerase; Provisional 95.95
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 95.73
KOG2093 1016 consensus Translesion DNA polymerase - REV1 deoxyc 95.58
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain 95.21
COG5275276 BRCT domain type II [General function prediction o 95.01
KOG2043896 consensus Signaling protein SWIFT and related BRCT 93.21
KOG2043896 consensus Signaling protein SWIFT and related BRCT 93.04
KOG35481176 consensus DNA damage checkpoint protein RHP9/CRB2/ 90.89
KOG0966881 consensus ATP-dependent DNA ligase IV [Replication 89.23
KOG4362684 consensus Transcriptional regulator BRCA1 [Replica 83.31
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=1.7e-77  Score=680.70  Aligned_cols=509  Identities=35%  Similarity=0.594  Sum_probs=389.0

Q ss_pred             CccEEEEEccHHHH-------------HHHHHHhhcCCCCc----eEEecCCHHHHHHHHHHHHhCCCceEEEeCCCCCC
Q 003386           32 GICVCVHVYMLSQL-------------RSQIMAADQTGEPC----WSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW   94 (824)
Q Consensus        32 ~~~v~~~~FDll~l-------------r~~L~~l~~~~~~~----~~~~~~~~~di~~~~~~ai~~g~EGIV~K~~dS~Y   94 (824)
                      ...+||.+||||++             ++.|..++-+....    ....++..++++++|++||++|.||||+|+++|.|
T Consensus       344 ~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y  423 (881)
T KOG0966|consen  344 SQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIVRSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSY  423 (881)
T ss_pred             CCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEeehhhcccHHHHHHHHHHHHhcCCCceEEeccCccc
Confidence            56899999999975             56677777665433    34467889999999999999999999999999999


Q ss_pred             cCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHH
Q 003386           95 EPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV  173 (824)
Q Consensus        95 ~pg~Rs~~WiKiK~~y~~-~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L  173 (824)
                      .||.|+++|||+||+|+. +|+++|++|||||||+|+++|.+.+|+||+.++..++.+|.+|.+||+||+|+|..++..|
T Consensus       424 ~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~g~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v  503 (881)
T KOG0966|consen  424 VPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGRGDRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTV  503 (881)
T ss_pred             CccccCCCcEeecHHHHhhcCccccEEEEecccCCCCCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHH
Confidence            999999999999999999 6999999999999999999999999999999987777889999999999999999999999


Q ss_pred             HHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEecCCCcc
Q 003386          174 VTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWH  253 (824)
Q Consensus       174 ~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~  253 (824)
                      +.+|++||.++ ..+.+|++|+..+   +..|++||+ |..|+|++|++ .+++.+..|.++|||||||+.++|.||+|+
T Consensus       504 ~~klr~~w~~~-~~~apP~s~l~~t---k~~Pd~wI~-P~~SiIlqika-a~i~~s~~f~tn~tLrfPr~ekvR~DK~W~  577 (881)
T KOG0966|consen  504 REKLRGHWKPT-SLEAPPESFLFGT---KKIPDVWID-PDNSIILQIKA-AEIVPSSNFVTNYTLRFPRIEKVRLDKPWH  577 (881)
T ss_pred             HHhhhhhcccc-cccCCCHHHHhcc---cCCCceeEC-CCCceEEEeeh-heeeecccccccceeecceeeeeecCCcHH
Confidence            99999999982 4444444455443   347999999 99999999995 456789999999999999999999999999


Q ss_pred             CcCCHHHHHHHHHhcCCccccccccCCCCCCCCcccccccccccccccccCCccccCCcccccCCCCCccCeEEEEEcCC
Q 003386          254 DCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP  333 (824)
Q Consensus       254 e~~t~~el~el~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~~k~~~~~~~~~~~~~~~s~~~~~s~lF~Gl~FcV~~~~  333 (824)
                      ||+|+++|.+|...+.       ++.+.+. ++++ ...+++++.+..   -+......+.+.+.+++|.|+.|||+++.
T Consensus       578 ec~tl~~l~~l~~~~~-------~d~~~~~-kk~~-~t~~~~k~~~~~---i~~~~~~~~~~~~~s~if~gl~f~Vlsgt  645 (881)
T KOG0966|consen  578 ECLTLNELGDLVNVSK-------SDVEDKE-KKKR-DTLKVRKRTRKA---IHDSAPNRSKVAKISNIFDGLEFCVLSGT  645 (881)
T ss_pred             HHhhHHHHHHHhcccc-------CCcchhh-hhcc-cchhhhhhhhhh---hcccccchhcccchhhhhcCeeEEEecCC
Confidence            9999999999985321       1111111 1111 111111111111   12233445567788999999999999875


Q ss_pred             -CCCCHHHHHHHHHHcCCEEEecCCCCceEEEE-ecC--CChhHHhHhcCCCeeecchHHHHHhcCccCCCCccccccCC
Q 003386          334 -PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA-ADN--KGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLS  409 (824)
Q Consensus       334 -~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia-~~~--~t~K~~~a~~~~dIV~p~WV~DCI~~~~lLp~eP~~ll~~S  409 (824)
                       ...++.+|+++|++|||++++|++++.|+||+ ++.  .+++++++.+.++||+|+||+||+...+++||.|+++|+++
T Consensus       646 ~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldcc~~~~l~p~~P~~~fh~~  725 (881)
T KOG0966|consen  646 SETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDCCKKQRLLPWLPRDLFHAT  725 (881)
T ss_pred             cccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHHHhhhhccccccHHHHhhC
Confidence             46679999999999999999999998999995 333  34566666665699999999999999999999999999999


Q ss_pred             hhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeEEEEccCCCCCCCchHHH
Q 003386          410 DSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVL  489 (824)
Q Consensus       410 ~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~~YL~g~~~~~~~d~~~i  489 (824)
                      +..++.++..+|+|||||++|++.+.|+.+++.+..+.+............+...+.+|.-|..+|+......+.+    
T Consensus       726 e~~~~~~a~~~D~~gdSy~~di~l~~l~~~ls~~k~S~ds~~~~~~~~~~~~e~r~~~~~~~~~~f~~~~~~~~se----  801 (881)
T KOG0966|consen  726 EKGREKLAKEVDCLGDSYENDIDLEQLKKVLSGIKKSQDSLPPMGASEKDSLERRFSLFLSSLRMFYVLRRKLSSE----  801 (881)
T ss_pred             chHHHHHHHHHhhhcchhhhhccHHHHHHHHhhhhhcccccCchhhhhhhcHHHhhccccccceeeecccccccHH----
Confidence            9999999999999999999999999999999988876654322211111111112222222223333333233322    


Q ss_pred             HHHHHHHHHHHHHhcCCEEEccCC-------CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEecccHHHHHH
Q 003386          490 LGLALRRLKLEISFHGGKVCNNLA-------NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCL  562 (824)
Q Consensus       490 ~~~~l~~L~~~I~~~GG~V~~~ls-------~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~~~IVt~~WLedCi  562 (824)
                          .......+..+||.+++.-.       .+||+|+.... ..  ..  +.+.  ........++ +||.+.||.+|+
T Consensus       802 ----~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~-~~--h~--~~~~--~~~~~lt~~r-kv~~~~wv~~s~  869 (881)
T KOG0966|consen  802 ----EVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCID-ED--HE--KIKE--QKKASLTIKR-KVVAPSWVDHSI  869 (881)
T ss_pred             ----HHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecc-hH--HH--HHHH--HHHHHhcccc-cccCHHHHHHhh
Confidence                23445678889999987553       37999986322 11  11  1111  1111122344 999999999999


Q ss_pred             HhCCccCCCCCC
Q 003386          563 AKEQKSEEYEYS  574 (824)
Q Consensus       563 ~~g~~l~Ee~Y~  574 (824)
                      .++.++||++|.
T Consensus       870 ~~~~~~~e~~~~  881 (881)
T KOG0966|consen  870 NENCLLPEEDFP  881 (881)
T ss_pred             cccccCccccCC
Confidence            999999999995

>PLN03113 DNA ligase 1; Provisional Back     alignment and domain information
>PRK01109 ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair] Back     alignment and domain information
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain Back     alignment and domain information
>PRK09632 ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>TIGR02776 NHEJ_ligase_prk DNA ligase D Back     alignment and domain information
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PHA02587 30 DNA ligase; Provisional Back     alignment and domain information
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PRK09125 DNA ligase; Provisional Back     alignment and domain information
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>PHA00454 ATP-dependent DNA ligase Back     alignment and domain information
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases Back     alignment and domain information
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I Back     alignment and domain information
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases Back     alignment and domain information
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins Back     alignment and domain information
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases Back     alignment and domain information
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases Back     alignment and domain information
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III Back     alignment and domain information
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV Back     alignment and domain information
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins Back     alignment and domain information
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1 Back     alignment and domain information
>smart00292 BRCT breast cancer carboxy-terminal domain Back     alignment and domain information
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit Back     alignment and domain information
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases Back     alignment and domain information
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain Back     alignment and domain information
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair] Back     alignment and domain information
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1 Back     alignment and domain information
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms] Back     alignment and domain information
>smart00292 BRCT breast cancer carboxy-terminal domain Back     alignment and domain information
>KOG3226 consensus DNA repair protein [Replication, recombination and repair] Back     alignment and domain information
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A Back     alignment and domain information
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes Back     alignment and domain information
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain Back     alignment and domain information
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair] Back     alignment and domain information
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining Back     alignment and domain information
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification] Back     alignment and domain information
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification] Back     alignment and domain information
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair] Back     alignment and domain information
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PLN03122 Poly [ADP-ribose] polymerase; Provisional Back     alignment and domain information
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A Back     alignment and domain information
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A Back     alignment and domain information
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins Back     alignment and domain information
>KOG3226 consensus DNA repair protein [Replication, recombination and repair] Back     alignment and domain information
>PLN03123 poly [ADP-ribose] polymerase; Provisional Back     alignment and domain information
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription] Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PLN03122 Poly [ADP-ribose] polymerase; Provisional Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PLN03123 poly [ADP-ribose] polymerase; Provisional Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair] Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>COG5275 BRCT domain type II [General function prediction only] Back     alignment and domain information
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair] Back     alignment and domain information
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair] Back     alignment and domain information
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair] Back     alignment and domain information
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair] Back     alignment and domain information
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription] 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 ?
Query824
2hiv_A621 Atp-Dependent Dna Ligase From S. Solfataricus Lengt 3e-14
3rr5_A570 Dna Ligase From The Archaeon Thermococcus Sp. 1519 5e-13
4eq5_A571 Dna Ligase From The Archaeon Thermococcus Sibiricus 3e-12
2cfm_A561 Atp-Dependent Dna Ligase From Pyrococcus Furiosus L 3e-12
1x9n_A688 Crystal Structure Of Human Dna Ligase I Bound To 5' 7e-10
3ii6_X263 Structure Of Human Xrcc4 In Complex With The Tandem 8e-10
3l2p_A579 Human Dna Ligase Iii Recognizes Dna Ends By Dynamic 8e-08
3gde_A558 The Closed Conformation Of Atp-Dependent Dna Ligase 4e-04
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus Length = 621 Back     alignment and structure 
Iteration: 1

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/209 (29%), Positives = 102/209 (48%), Gaps = 23/209 (11%)
Query: 64  AHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEYIRAGSD-LDVL 120
           A+NV++++ FF   I    EG+++K +G  + ++ G R   W+KLK +Y    +D +D++
Sbjct: 410 ANNVEDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLWIKLKRDYQSEMADTVDLV 469
Query: 121 IIXXXXXXXXXXXEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPY 180
           ++           +++  L+A A  P  D+    F S C+V +G SDE+LD +  KL   
Sbjct: 470 VVGGFYGKGKRGGKISSLLMA-AYNPKTDS----FESVCKVASGFSDEQLDELQKKLMEI 524
Query: 181 FRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILS---ITSDIRTIRSEVFS--AP 235
            R  ++P+           NSK  PD+W+E    + I+      S + T   +V    A 
Sbjct: 525 KRDVKHPR----------VNSKMEPDIWVEPVYVAEIIGSEITISPLHTCCQDVVEKDAG 574
Query: 236 YSLRFPRIDRVRYDKPWHDCLDVQSFVEL 264
            S+RFPR  R R DK   D       +E+
Sbjct: 575 LSIRFPRFIRWRDDKSPEDATTTDEILEM 603
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519 Length = 570 Back     alignment and structure
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus Length = 571 Back     alignment and structure
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus Length = 561 Back     alignment and structure
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To 5'-Adenylated, Nicked Dna Length = 688 Back     alignment and structure
>pdb|3II6|X Chain X, Structure Of Human Xrcc4 In Complex With The Tandem Brct Domains Of Dna Ligaseiv. Length = 263 Back     alignment and structure
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic Switching Between Two Dna Bound States Length = 579 Back     alignment and structure
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From Archaeoglobus Fulgidus Length = 558 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 ?
Query824
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 5e-56
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 5e-54
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 7e-53
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 2e-52
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 1e-50
3ii6_X263 DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter 6e-43
1z56_C264 DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA 8e-42
1vs0_A310 Putative DNA ligase-like protein RV0938/MT0965; OB 1e-28
1a0i_A348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 1e-23
1wf6_A132 Similar to S.pombe -RAD4+/CUT5+product (A40727); B 2e-17
1wf6_A132 Similar to S.pombe -RAD4+/CUT5+product (A40727); B 6e-09
2d8m_A129 DNA-repair protein XRCC1; parallel beta-sheet, DNA 5e-17
2d8m_A129 DNA-repair protein XRCC1; parallel beta-sheet, DNA 6e-05
2ebw_A97 DNA repair protein REV1; A/B/A 3 layers, parallel 5e-15
2ebw_A97 DNA repair protein REV1; A/B/A 3 layers, parallel 1e-07
3olc_X298 DNA topoisomerase 2-binding protein 1; BRCT domain 1e-14
3olc_X298 DNA topoisomerase 2-binding protein 1; BRCT domain 5e-10
1fvi_A297 Chlorella virus DNA ligase-adenylate; adenylated D 3e-13
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-09
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-04
2cou_A109 ECT2 protein; BRCT domain, RHO GTPase, structural 8e-11
2cou_A109 ECT2 protein; BRCT domain, RHO GTPase, structural 2e-07
1l0b_A229 BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu 1e-10
3al2_A235 DNA topoisomerase 2-binding protein 1; BRCT domain 2e-10
1t15_A214 Breast cancer type 1 susceptibility protein; prote 2e-10
3pc6_A104 DNA repair protein XRCC1; BRCT domain, protein:pro 4e-10
3pc6_A104 DNA repair protein XRCC1; BRCT domain, protein:pro 4e-07
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleo 6e-10
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleo 7e-08
3pa6_A107 Microcephalin; BRCT domain, cell cycle; HET: MSE; 8e-10
3pa6_A107 Microcephalin; BRCT domain, cell cycle; HET: MSE; 2e-04
3l3e_A107 DNA topoisomerase 2-binding protein 1; BRCT domain 9e-10
3l3e_A107 DNA topoisomerase 2-binding protein 1; BRCT domain 5e-06
2jw5_A106 DNA polymerase lambda; BRCT domain, family X polym 4e-09
2jw5_A106 DNA polymerase lambda; BRCT domain, family X polym 2e-06
2nte_A210 BARD-1, BRCA1-associated ring domain protein 1; BR 5e-09
3sqd_A219 PAX-interacting protein 1; tandem BRCT domains, ce 1e-07
3sqd_A219 PAX-interacting protein 1; tandem BRCT domains, ce 3e-04
3u3z_A199 Microcephalin; DNA repair, cell cycle regulation, 3e-07
3l41_A220 BRCT-containing protein 1; BRC1, BRCT domain, tand 5e-06
3l41_A220 BRCT-containing protein 1; BRC1, BRCT domain, tand 4e-04
3ef0_A372 RNA polymerase II subunit A C-terminal domain phos 5e-06
3ef0_A372 RNA polymerase II subunit A C-terminal domain phos 2e-05
2etx_A209 Mediator of DNA damage checkpoint protein 1; tande 1e-05
3ef1_A442 RNA polymerase II subunit A C-terminal domain phos 2e-05
3ef1_A442 RNA polymerase II subunit A C-terminal domain phos 5e-04
2vxb_A241 DNA repair protein RHP9; BRCT, nucleus, cell cycle 2e-04
2coe_A120 Deoxynucleotidyltransferase, terminal variant; BRC 6e-04
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Length = 579 Back     alignment and structure
 Score =  201 bits (514), Expect = 5e-56
 Identities = 56/227 (24%), Positives = 98/227 (43%), Gaps = 14/227 (6%)

Query: 45  LRSQIMAADQTGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWL 104
           L   ++                  ++       I+   EG+VLKD+   +EPG R   WL
Sbjct: 363 LHDNMVEIPNRIMFSEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWL 420

Query: 105 KLKPEYIRAGS---DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRV 161
           K+K +Y+  G+     D++++G +YG G +GG ++ FL+   +   P +  +++ +  + 
Sbjct: 421 KVKKDYLNEGAMADTADLVVLGAFYGQGSKGGMMSIFLMGCYD---PGS--QKWCTVTKC 475

Query: 162 GTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT 221
             G  D  L  +  +L     K        PS+ +V  N    PD  +  P+K+ +  IT
Sbjct: 476 AGGHDDATLARLQNELDMV--KISKDPSKIPSWLKV--NKIYYPDFIVPDPKKAAVWEIT 531

Query: 222 SDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 268
               +      +   S+RFPR  R+R DK W    ++    EL   S
Sbjct: 532 GAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLS 578
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Length = 561 Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Length = 558 Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Length = 621 Back     alignment and structure
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Length = 688 Back     alignment and structure
>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A* Length = 263 Back     alignment and structure
>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae} Length = 264 Back     alignment and structure
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis} Length = 310 Back     alignment and structure
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1 Length = 348 Back     alignment and structure
>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5 Length = 132 Back     alignment and structure
>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5 Length = 132 Back     alignment and structure
>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 129 Back     alignment and structure
>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 129 Back     alignment and structure
>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens} Length = 97 Back     alignment and structure
>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens} Length = 97 Back     alignment and structure
>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Length = 298 Back     alignment and structure
>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Length = 298 Back     alignment and structure
>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A* Length = 297 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>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
>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 109 Back     alignment and structure
>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 109 Back     alignment and structure
>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3 Length = 229 Back     alignment and structure
>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A* Length = 235 Back     alignment and structure
>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A Length = 214 Back     alignment and structure
>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} PDB: 3pc8_A* 3qvg_B* 1cdz_A Length = 104 Back     alignment and structure
>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} PDB: 3pc8_A* 3qvg_B* 1cdz_A Length = 104 Back     alignment and structure
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Length = 112 Back     alignment and structure
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Length = 112 Back     alignment and structure
>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Length = 107 Back     alignment and structure
>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Length = 107 Back     alignment and structure
>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens} Length = 106 Back     alignment and structure
>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens} Length = 106 Back     alignment and structure
>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A Length = 210 Back     alignment and structure
>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens} Length = 219 Back     alignment and structure
>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens} Length = 219 Back     alignment and structure
>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A* Length = 199 Back     alignment and structure
>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A* Length = 220 Back     alignment and structure
>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A* Length = 220 Back     alignment and structure
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Length = 372 Back     alignment and structure
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Length = 372 Back     alignment and structure
>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A Length = 209 Back     alignment and structure
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Length = 442 Back     alignment and structure
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Length = 442 Back     alignment and structure
>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A* Length = 241 Back     alignment and structure
>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query824
3ii6_X263 DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter 100.0
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 100.0
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 100.0
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 100.0
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 100.0
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 100.0
1vs0_A310 Putative DNA ligase-like protein RV0938/MT0965; OB 100.0
1z56_C264 DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA 100.0
1a0i_A348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 99.96
1fvi_A297 Chlorella virus DNA ligase-adenylate; adenylated D 99.95
3olc_X298 DNA topoisomerase 2-binding protein 1; BRCT domain 99.87
1kzy_C259 Tumor suppressor P53-binding protein 1; tandem-BRC 99.82
1l0b_A229 BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu 99.81
1t15_A214 Breast cancer type 1 susceptibility protein; prote 99.78
2vxb_A241 DNA repair protein RHP9; BRCT, nucleus, cell cycle 99.77
3u3z_A199 Microcephalin; DNA repair, cell cycle regulation, 99.77
2nte_A210 BARD-1, BRCA1-associated ring domain protein 1; BR 99.75
2etx_A209 Mediator of DNA damage checkpoint protein 1; tande 99.72
1p16_A395 GTP--RNA, mRNA capping enzyme alpha subunit; guany 99.65
2ebw_A97 DNA repair protein REV1; A/B/A 3 layers, parallel 99.58
3al2_A235 DNA topoisomerase 2-binding protein 1; BRCT domain 99.54
3sqd_A219 PAX-interacting protein 1; tandem BRCT domains, ce 99.52
1wf6_A132 Similar to S.pombe -RAD4+/CUT5+product (A40727); B 99.48
4id3_A92 DNA repair protein REV1; BRCT domain, protein bind 99.47
2d8m_A129 DNA-repair protein XRCC1; parallel beta-sheet, DNA 99.42
2ep8_A100 Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r 99.41
3l3e_A107 DNA topoisomerase 2-binding protein 1; BRCT domain 99.4
2cou_A109 ECT2 protein; BRCT domain, RHO GTPase, structural 99.39
3pc6_A104 DNA repair protein XRCC1; BRCT domain, protein:pro 99.38
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleo 99.38
3pc6_A104 DNA repair protein XRCC1; BRCT domain, protein:pro 99.36
3pa6_A107 Microcephalin; BRCT domain, cell cycle; HET: MSE; 99.35
4id3_A92 DNA repair protein REV1; BRCT domain, protein bind 99.35
2coe_A120 Deoxynucleotidyltransferase, terminal variant; BRC 99.34
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleo 99.33
1ckm_A330 MRNA capping enzyme; nucleotidyltransferase; HET: 99.33
2jw5_A106 DNA polymerase lambda; BRCT domain, family X polym 99.31
2cou_A109 ECT2 protein; BRCT domain, RHO GTPase, structural 99.29
3l41_A220 BRCT-containing protein 1; BRC1, BRCT domain, tand 99.28
1wf6_A132 Similar to S.pombe -RAD4+/CUT5+product (A40727); B 99.27
2ebw_A97 DNA repair protein REV1; A/B/A 3 layers, parallel 99.25
2d8m_A129 DNA-repair protein XRCC1; parallel beta-sheet, DNA 99.21
3olc_X298 DNA topoisomerase 2-binding protein 1; BRCT domain 99.17
3l3e_A107 DNA topoisomerase 2-binding protein 1; BRCT domain 99.15
2ep8_A100 Pescadillo homolog 1; A/B/A 3 layers, nucleolus, r 99.15
3pa6_A107 Microcephalin; BRCT domain, cell cycle; HET: MSE; 99.01
3pc7_A88 DNA ligase 3; DNA repair, BRCT domain, protein:pro 98.99
3pc7_A88 DNA ligase 3; DNA repair, BRCT domain, protein:pro 98.96
2dun_A133 POL MU, DNA polymerase MU; layers A/B/A, parallel 98.91
3ef0_A372 RNA polymerase II subunit A C-terminal domain phos 98.88
3ef1_A442 RNA polymerase II subunit A C-terminal domain phos 98.83
3u3z_A199 Microcephalin; DNA repair, cell cycle regulation, 98.76
1t15_A214 Breast cancer type 1 susceptibility protein; prote 98.69
2jw5_A106 DNA polymerase lambda; BRCT domain, family X polym 98.68
3ef0_A372 RNA polymerase II subunit A C-terminal domain phos 98.66
2nte_A210 BARD-1, BRCA1-associated ring domain protein 1; BR 98.62
3ef1_A442 RNA polymerase II subunit A C-terminal domain phos 98.58
1l0b_A229 BRCA1; TANDEM-BRCT, three-helix bundle, unknown fu 98.57
1l7b_A92 DNA ligase; BRCT, autostructure, structural genomi 98.53
2coe_A120 Deoxynucleotidyltransferase, terminal variant; BRC 98.51
3sqd_A219 PAX-interacting protein 1; tandem BRCT domains, ce 98.47
3ii6_X263 DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alter 98.42
2etx_A209 Mediator of DNA damage checkpoint protein 1; tande 98.4
2k6g_A109 Replication factor C subunit 1; protein, BRCT, DNA 98.38
1z56_C264 DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA 98.36
3kyh_C461 MRNA-capping enzyme subunit alpha; 5' modification 98.33
2ebu_A112 Replication factor C subunit 1; A/B/A 3 layers, pa 98.3
2cok_A113 Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r 98.3
1kzy_C259 Tumor suppressor P53-binding protein 1; tandem-BRC 98.24
2dun_A133 POL MU, DNA polymerase MU; layers A/B/A, parallel 98.22
2vxb_A241 DNA repair protein RHP9; BRCT, nucleus, cell cycle 98.19
3al2_A235 DNA topoisomerase 2-binding protein 1; BRCT domain 98.15
1ik9_C37 DNA ligase IV; DNA END joining, double-strand brea 98.11
3l41_A220 BRCT-containing protein 1; BRC1, BRCT domain, tand 98.01
2l42_A106 DNA-binding protein RAP1; BRCT domain, protein bin 97.72
3rtx_A343 MRNA-capping enzyme; guanylyltransferase, RNA poly 97.7
2l42_A106 DNA-binding protein RAP1; BRCT domain, protein bin 97.66
3t7k_A256 RTT107, regulator of TY1 transposition protein 107 97.47
1l7b_A92 DNA ligase; BRCT, autostructure, structural genomi 96.87
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 96.3
2k6g_A109 Replication factor C subunit 1; protein, BRCT, DNA 96.16
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 95.9
2ebu_A112 Replication factor C subunit 1; A/B/A 3 layers, pa 95.83
2cok_A113 Poly [ADP-ribose] polymerase-1; BRCT domain, DNA r 95.5
3qwu_A370 DNA ligase; structural genomics, PSI-2, midwest ce 93.65
2vug_A389 PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transfe 93.36
4gns_A290 Chitin biosynthesis protein CHS5; FN3, BRCT, tetra 92.45
3huf_A325 DNA repair and telomere maintenance protein NBS1; 92.15
3vnn_A139 DNA ligase 4; non-homologous END joining, DNA repa 88.82
3qbz_A160 DDK kinase regulatory subunit DBF4; FHA domain,RAD 87.3
3t7k_A256 RTT107, regulator of TY1 transposition protein 107 86.41
3oq0_A151 DBF4, protein DNA52; DDK, BRCT, RAD53, replication 84.02
3oq4_A134 DBF4, protein DNA52; DDK, BRCT, RAD53, replication 82.4
>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A* Back     alignment and structure
Probab=100.00  E-value=1e-44  Score=385.54  Aligned_cols=248  Identities=25%  Similarity=0.439  Sum_probs=203.6

Q ss_pred             CCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC--CeeecchHHHHHhc
Q 003386          317 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG--DVIHYSWVLDCCSQ  394 (824)
Q Consensus       317 ~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~--dIV~p~WV~DCI~~  394 (824)
                      ++++||+|+.|||+++....++++|+++|.+|||++++|+++ .||||++++.+.|++.+++++  +||+|+||+||+++
T Consensus         6 ~~s~lF~G~~f~V~sg~~~~~k~~L~~lI~~~GG~v~~n~~~-~t~~iIa~~~~~k~~~~~~~g~~~IV~p~Wv~Dci~~   84 (263)
T 3ii6_X            6 KISNIFEDVEFCVMSGTDSQPKPDLENRIAEFGGYIVQNPGP-DTYCVIAGSENIRVKNIILSNKHDVVKPAWLLECFKT   84 (263)
T ss_dssp             CCCCTTTTCEEEECCCC--CCHHHHHHHHHHTTCEECSSCCT-TEEEEECSSCCHHHHHHHHSCSCCEECHHHHHHHHHH
T ss_pred             cCcccCCCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCC-CEEEEEeCCCCHHHHHHHhcCCCCEeehHHHHHHHhc
Confidence            578999999999999888889999999999999999999985 577777788889999998864  99999999999999


Q ss_pred             CccCCCCccccccCChhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCc------chhHHHhhhcCCC-CCCCC
Q 003386          395 KKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDP------KTIDYYKKKYCPQ-DKWSC  467 (824)
Q Consensus       395 ~~lLp~eP~~ll~~S~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~------~~i~~l~~~~~~~-~~~~l  467 (824)
                      +++||++|+|++++++++++.+++++|+|||||+.++|+++|+.+|++|+.....      ..+++++.+++.+ .++.|
T Consensus        85 ~~llp~~p~~~~~~~~~~~~~~~~~~D~~GDsy~~~~~~~~l~~ll~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l  164 (263)
T 3ii6_X           85 KSFVPWQPRFMIHMCPSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNSNEQTPEEMASLIADLEYRYSWDCSPLSM  164 (263)
T ss_dssp             TSCCCCCGGGEEECCHHHHHHTTTTBCTTSCBSSSCCCHHHHHHHHHSCCCCCSCCHHHHHHHHHHHHHHHTCTTCGGGT
T ss_pred             CCcCCCCHHHHhhCCHHHHHHHHHhccccCCccCCcCCHHHHHHHHHhCcccccCCchhhHHHHHHHHHhhcccCCcchh
Confidence            9999999999999999999999999999999999999999999999999764322      2356677666654 58899


Q ss_pred             CCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCC-ceEEEEecCCCcccchhhhHHHHHHHhhhhcc
Q 003386          468 FHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLAN-ATHVVVLSVLGYDVNFNSLTESFTAREKHLLW  546 (824)
Q Consensus       468 F~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls~-vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~  546 (824)
                      |+||+|||++++.. +.+...+....+++++.+|+++||++++.+++ ||||||.+..++...++.+++         ..
T Consensus       165 F~~~~vy~~~~~~~-~~~~~~i~~~~l~~~~~~i~~~GG~v~~~l~~~vTHVVv~~~~~r~~~~~~~~~---------~~  234 (263)
T 3ii6_X          165 FRRHTVYLDSYAVI-NDLSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGEDHSRVADFKAFRR---------TF  234 (263)
T ss_dssp             TTTCEEEECCBSST-TCGGGBCCSSHHHHHHHHHHHTTCEEESSCCTTCCEEEECSCCTTHHHHHHHHH---------TC
T ss_pred             hCCeEEEEeccccc-CCcccccchhHHHHHHHHHHccCCEEecCCCCCceEEEECCCCccHHHHHHHHh---------hc
Confidence            99999999987532 22222233345678899999999999999994 999999864322111222221         12


Q ss_pred             CCccEEecccHHHHHHHhCCccCCCCCCC
Q 003386          547 NKKLHVVRSQWLEDCLAKEQKSEEYEYSL  575 (824)
Q Consensus       547 ~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v  575 (824)
                      .+.++||+++||++||++|+++||++|.|
T Consensus       235 ~~~~~iV~~~Wv~dci~~~~~l~E~~Y~i  263 (263)
T 3ii6_X          235 KRKFKILKESWVTDSIDKCELQEENQYLI  263 (263)
T ss_dssp             SSCCEEEETHHHHHHHHTTSCCCGGGTBC
T ss_pred             CCCCEEeChHHHHHHHHcCCcCCHhhCCC
Confidence            46799999999999999999999999975
>3l2p_A DNA ligase 3; DNA ligase, DNA repair, ATP-binding, cell cycle, cell divisi damage; HET: DNA AMP; 3.00A {Homo sapiens} Back     alignment and structure
>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP: a.235.1.1 b.40.4.6 d.142.2.1 Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Back     alignment and structure
>3gde_A DNA ligase; DNA-binding domain, adenylation domain, OB-fold domain, ATP-binding, cell cycle, cell division, DNA damage, DNA recombination; HET: DNA; 2.30A {Archaeoglobus fulgidus} Back     alignment and structure
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle, cell division, DNA damage, DNA recombination, DNA repair, DNA replication; HET: AMP; 1.8A {Pyrococcus furiosus} PDB: 3rr5_A* Back     alignment and structure
>1vs0_A Putative DNA ligase-like protein RV0938/MT0965; OB fold, nucleotidyl transferase, structural genomic protein structure initiative; HET: APK MSE; 2.40A {Mycobacterium tuberculosis} Back     alignment and structure
>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae} Back     alignment and structure
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria phage T7} SCOP: b.40.4.6 d.142.2.1 Back     alignment and structure
>1fvi_A Chlorella virus DNA ligase-adenylate; adenylated DNA ligase; HET: AMP; 2.00A {Chlorella virus} SCOP: b.40.4.6 d.142.2.1 PDB: 2q2t_A* 2q2u_A* 1p8l_A* Back     alignment and structure
>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Back     alignment and structure
>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B Back     alignment and structure
>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3 Back     alignment and structure
>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A Back     alignment and structure
>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A* Back     alignment and structure
>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A* Back     alignment and structure
>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A Back     alignment and structure
>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A Back     alignment and structure
>1p16_A GTP--RNA, mRNA capping enzyme alpha subunit; guanylyltransferase, transcription, capping, CTD, mRNA; HET: SEP G GTP; 2.70A {Candida albicans} SCOP: b.40.4.6 d.142.2.3 Back     alignment and structure
>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A* Back     alignment and structure
>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens} Back     alignment and structure
>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5 Back     alignment and structure
>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C} Back     alignment and structure
>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ep8_A Pescadillo homolog 1; A/B/A 3 layers, nucleolus, ribosome biogenesis, DNA damage, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Back     alignment and structure
>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} SCOP: c.15.1.1 PDB: 3pc8_A* 3qvg_B* 1cdz_A Back     alignment and structure
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Back     alignment and structure
>3pc6_A DNA repair protein XRCC1; BRCT domain, protein:protein interactions, DNA L III-alpha BRCT2 domain, DNA binding protein; HET: DNA; 1.90A {Mus musculus} SCOP: c.15.1.1 PDB: 3pc8_A* 3qvg_B* 1cdz_A Back     alignment and structure
>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Back     alignment and structure
>4id3_A DNA repair protein REV1; BRCT domain, protein binding; HET: DNA; 1.97A {Saccharomyces cerevisiae S288C} Back     alignment and structure
>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Back     alignment and structure
>1ckm_A MRNA capping enzyme; nucleotidyltransferase; HET: GTP; 2.50A {Paramecium bursaria chlorella virus 1} SCOP: b.40.4.6 d.142.2.3 PDB: 1ckn_A* 1cko_A* 1ckn_B* Back     alignment and structure
>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>2cou_A ECT2 protein; BRCT domain, RHO GTPase, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Back     alignment and structure
>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A* Back     alignment and structure
>1wf6_A Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, topoisomerase II binding protein, checkpoint; NMR {Homo sapiens} SCOP: c.15.1.5 Back     alignment and structure
>2ebw_A DNA repair protein REV1; A/B/A 3 layers, parallel beta-sheet, DNA replication, translession synthesis, TLS, DNA polymerase zeta, PCNA; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>2d8m_A DNA-repair protein XRCC1; parallel beta-sheet, DNA ligase III, poly(ADP-ribose) polymerase-1, DNA polymerase beta, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3olc_X DNA topoisomerase 2-binding protein 1; BRCT domain, DNA repair, RAD9, DNA binding protein; HET: DNA; 2.40A {Homo sapiens} PDB: 2xnk_A* 2xnh_A* Back     alignment and structure
>2ep8_A Pescadillo homolog 1; A/B/A 3 layers, nucleolus, ribosome biogenesis, DNA damage, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3pa6_A Microcephalin; BRCT domain, cell cycle; HET: MSE; 1.50A {Homo sapiens} PDB: 3ktf_A* 2wt8_A* Back     alignment and structure
>3pc7_A DNA ligase 3; DNA repair, BRCT domain, protein:protein interactions, XRCC1 domain, DNA binding protein; HET: DNA MSE; 1.65A {Homo sapiens} SCOP: c.15.1.2 PDB: 3pc8_C* 1imo_A* 1in1_A* 3qvg_A* Back     alignment and structure
>3pc7_A DNA ligase 3; DNA repair, BRCT domain, protein:protein interactions, XRCC1 domain, DNA binding protein; HET: DNA MSE; 1.65A {Homo sapiens} SCOP: c.15.1.2 PDB: 3pc8_C* 1imo_A* 1in1_A* 3qvg_A* Back     alignment and structure
>2dun_A POL MU, DNA polymerase MU; layers A/B/A, parallel beta-sheet of 4 strands, non- homologous END jonting, somatic hypermutation, V(D)J recombination; HET: DNA; NMR {Homo sapiens} PDB: 2htf_A* Back     alignment and structure
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Back     alignment and structure
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Back     alignment and structure
>3u3z_A Microcephalin; DNA repair, cell cycle regulation, cell cycle; HET: SEP PTR; 1.50A {Homo sapiens} PDB: 3szm_A* 3t1n_A* 3sht_A 3shv_A* Back     alignment and structure
>1t15_A Breast cancer type 1 susceptibility protein; protein-peptide complex, antitumor protein; HET: SEP; 1.85A {Homo sapiens} SCOP: c.15.1.3 c.15.1.3 PDB: 1jnx_X* 1t29_A* 1t2v_A* 1y98_A* 3coj_X* 3k0h_A* 3k0k_A* 3pxe_A* 3pxb_A 3pxc_X 1t2u_A 1n5o_X 3pxa_A 3k15_A* 3k16_A* 3pxd_A 2ing_X 1oqa_A Back     alignment and structure
>2jw5_A DNA polymerase lambda; BRCT domain, family X polymerase, nonhomologous END joining (NHEJ), DNA damage, DNA repair, DNA replication, DNA synthesis; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Back     alignment and structure
>2nte_A BARD-1, BRCA1-associated ring domain protein 1; BRCT, ring finger, zinc-binding protein, ubiquitin LI antitumor protein; 1.90A {Homo sapiens} PDB: 3fa2_A 2r1z_A Back     alignment and structure
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Back     alignment and structure
>1l0b_A BRCA1; TANDEM-BRCT, three-helix bundle, unknown function; 2.30A {Rattus norvegicus} SCOP: c.15.1.3 c.15.1.3 Back     alignment and structure
>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2 Back     alignment and structure
>2coe_A Deoxynucleotidyltransferase, terminal variant; BRCT domain, DNA polymerase, teminal deoxynucleotidyltransferase, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3sqd_A PAX-interacting protein 1; tandem BRCT domains, cell cycle; HET: SEP; 2.15A {Homo sapiens} Back     alignment and structure
>3ii6_X DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternative splicing, coiled coil, DNA damage, DNA recombination, isopeptide bond, nucleus; HET: DNA; 2.40A {Homo sapiens} PDB: 2e2w_A* Back     alignment and structure
>2etx_A Mediator of DNA damage checkpoint protein 1; tandem BRCT domains histone gamma-H2AX, cell cycle; 1.33A {Homo sapiens} PDB: 2azm_A* 3k05_A* 2ado_A Back     alignment and structure
>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A Back     alignment and structure
>1z56_C DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae} Back     alignment and structure
>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure
>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A Back     alignment and structure
>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4 c.15.1.4 PDB: 1gzh_B Back     alignment and structure
>2dun_A POL MU, DNA polymerase MU; layers A/B/A, parallel beta-sheet of 4 strands, non- homologous END jonting, somatic hypermutation, V(D)J recombination; HET: DNA; NMR {Homo sapiens} PDB: 2htf_A* Back     alignment and structure
>2vxb_A DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA damage, DNA replication inhibitor, phosphoprotein, checkpoint signalling; HET: DNA; 2.3A {Schizosaccharomyces pombe} PDB: 2vxc_A* Back     alignment and structure
>3al2_A DNA topoisomerase 2-binding protein 1; BRCT domain, protein binding, DNA binding protein; HET: DNA MSE; 2.00A {Homo sapiens} PDB: 3al3_A* Back     alignment and structure
>1ik9_C DNA ligase IV; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} Back     alignment and structure
>3l41_A BRCT-containing protein 1; BRC1, BRCT domain, tandem BRCT repeat, phosphoserine binding domain, DNA repair, cell division, mitosis; HET: SEP; 1.45A {Schizosaccharomyces pombe} PDB: 3l40_A* Back     alignment and structure
>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3rtx_A MRNA-capping enzyme; guanylyltransferase, RNA polymerase II CTD, lysyl-N-GMP, NUC mRNA capping, transferase; HET: SEP GUN; 2.81A {Mus musculus} PDB: 3s24_A Back     alignment and structure
>2l42_A DNA-binding protein RAP1; BRCT domain, protein binding; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3t7k_A RTT107, regulator of TY1 transposition protein 107; BRCT, DNA repair, phospho-peptide, protein binding; HET: SEP; 2.03A {Saccharomyces cerevisiae} PDB: 3t7j_A* 3t7i_A Back     alignment and structure
>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2 Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A Back     alignment and structure
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2le0_A Back     alignment and structure
>3qwu_A DNA ligase; structural genomics, PSI-2, midwest center for structural GE MCSG; HET: DNA ADN; 2.35A {Aquifex aeolicus} Back     alignment and structure
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP; 2.9A {Pyrococcus abyssi GE5} Back     alignment and structure
>4gns_A Chitin biosynthesis protein CHS5; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae} Back     alignment and structure
>3huf_A DNA repair and telomere maintenance protein NBS1; NBS1, FHA domain, BRCT domain, phosphoprotein binding, phosp binding, DNA repair; HET: DNA TPO; 2.15A {Schizosaccharomyces pombe} PDB: 3hue_A* 3i0m_A* 3i0n_A* Back     alignment and structure
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens} Back     alignment and structure
>3qbz_A DDK kinase regulatory subunit DBF4; FHA domain,RAD53, replication checkpoint, cell cycle; 2.69A {Saccharomyces cerevisiae} Back     alignment and structure
>3t7k_A RTT107, regulator of TY1 transposition protein 107; BRCT, DNA repair, phospho-peptide, protein binding; HET: SEP; 2.03A {Saccharomyces cerevisiae} PDB: 3t7j_A* 3t7i_A Back     alignment and structure
>3oq0_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.70A {Saccharomyces cerevisiae} Back     alignment and structure
>3oq4_A DBF4, protein DNA52; DDK, BRCT, RAD53, replication checkpoint, FHA domain, regula subunit of DDK, CDC7, phosphorylation, nuclear; 2.40A {Saccharomyces cerevisiae} 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 824
d1x9na2148 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (H 5e-29
d1wf6a_132 c.15.1.5 (A:) DNA topoisomerase II binding protein 4e-14
d1in1a_88 c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sa 6e-13
d1in1a_88 c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sa 6e-05
d1cdza_96 c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Hom 2e-11
d1cdza_96 c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Hom 0.003
d1x9na3220 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human ( 4e-09
d1t15a2102 c.15.1.3 (A:1758-1859) Breast cancer associated pr 5e-09
d1t15a2102 c.15.1.3 (A:1758-1859) Breast cancer associated pr 0.003
d1a0ia2239 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-te 5e-08
d1fvia2188 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-te 2e-07
d1t15a1109 c.15.1.3 (A:1649-1757) Breast cancer associated pr 1e-06
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 148 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  110 bits (277), Expect = 5e-29
 Identities = 39/161 (24%), Positives = 61/161 (37%), Gaps = 18/161 (11%)

Query: 114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 173
           G  LD+++IG Y G G+R G    FL+A     + D       + C++GTG SDEEL+  
Sbjct: 1   GDTLDLVVIGAYLGRGKRAGRYGGFLLA-----SYDEDSEELQAICKLGTGFSDEELEEH 55

Query: 174 VTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL--SITSDIRT---IR 228
                 +         +P  + ++  +    PD W++      +    ++          
Sbjct: 56  ------HQSLKALVLPSPRPYVRI--DGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARG 107

Query: 229 SEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSN 269
                   SLRFPR  RVR DK             L    +
Sbjct: 108 LVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQS 148
>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]} Length = 132 Back     information, alignment and structure
>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 96 Back     information, alignment and structure
>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 96 Back     information, alignment and structure
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 220 Back     information, alignment and structure
>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102 Back     information, alignment and structure
>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102 Back     information, alignment and structure
>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]} Length = 239 Back     information, alignment and structure
>d1fvia2 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Length = 188 Back     information, alignment and structure
>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 109 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 ?
Query824
d1x9na2148 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 99.96
d1cdza_96 DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta 99.56
d1x9na3220 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 99.52
d1wf6a_132 DNA topoisomerase II binding protein 1, TopBP1 {Hu 99.45
d1wf6a_132 DNA topoisomerase II binding protein 1, TopBP1 {Hu 99.42
d1cdza_96 DNA-repair protein XRCC1 {Human (Homo sapiens) [Ta 99.41
d1t15a2102 Breast cancer associated protein, BRCA1 {Human (Ho 99.34
d1in1a_88 DNA ligase III alpha {Human (Homo sapiens) [TaxId: 99.33
d1a0ia2239 ATP-dependent DNA ligase, N-terminal domain {Bacte 99.2
d1t15a2102 Breast cancer associated protein, BRCA1 {Human (Ho 99.19
d1in1a_88 DNA ligase III alpha {Human (Homo sapiens) [TaxId: 99.09
d1fvia2188 ATP-dependent DNA ligase, N-terminal domain {Chlor 99.04
d1t15a1109 Breast cancer associated protein, BRCA1 {Human (Ho 98.98
d1t15a1109 Breast cancer associated protein, BRCA1 {Human (Ho 98.9
d1kzyc1153 53BP1 {Human (Homo sapiens) [TaxId: 9606]} 98.69
d1l7ba_92 NAD+-dependent DNA ligase, domain 4 {Thermus therm 98.58
d1l0ba297 Breast cancer associated protein, BRCA1 {Rat (Ratt 97.91
d1kzyc1153 53BP1 {Human (Homo sapiens) [TaxId: 9606]} 97.82
d1ckma2228 RNA guanylyltransferase (mRNA capping enzyme), N-t 97.46
d1a0ia1109 ATP-dependent DNA ligase {Bacteriophage T7 [TaxId: 97.37
d1l0ba297 Breast cancer associated protein, BRCA1 {Rat (Ratt 97.2
d1fvia1104 ATP-dependent DNA ligase {Chlorella virus PBCV-1 [ 97.17
d1l7ba_92 NAD+-dependent DNA ligase, domain 4 {Thermus therm 97.13
d1p16a2245 mRNA capping enzyme alpha subunit {Yeast (Candida 96.74
d1kzyc2106 53BP1 {Human (Homo sapiens) [TaxId: 9606]} 95.83
d1s68a_233 RNA ligase 2, N-terminal domain {Bacteriophage T4 95.21
d1kzyc2106 53BP1 {Human (Homo sapiens) [TaxId: 9606]} 94.34
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA ligase/mRNA capping enzyme postcatalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=9.4e-30  Score=245.87  Aligned_cols=138  Identities=30%  Similarity=0.566  Sum_probs=116.0

Q ss_pred             CCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCc
Q 003386          114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS  193 (824)
Q Consensus       114 ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~  193 (824)
                      ||++||||||||||+|+|+|.+++||||+++++.     ++|+++|+||+|||++++++|.+.|.+++..      .+|.
T Consensus         1 gdtlDlVViG~~~g~G~r~~~~~slllg~~~~~~-----~~l~~vg~VgtGfs~~~~~~l~~~l~~~~~~------~~~~   69 (148)
T d1x9na2           1 GDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDS-----EELQAICKLGTGFSDEELEEHHQSLKALVLP------SPRP   69 (148)
T ss_dssp             CEEEEEEEEEEEEBCTTSBTSEEEEEEEEEETTT-----TEEEEEEEECCSCCHHHHHHHHHHHHHTEES------SCCT
T ss_pred             CCCEeEEEEeeEeCCCCCCCceeeEEEEEEcCCC-----CEEEEEEEEcCcChHHHHHHHHhhccccccC------CCCc
Confidence            6899999999999999999999999999998653     3899999999999999999999999999876      2333


Q ss_pred             ccccCCCCCCCCcEEEeCCcceEEEEEEeccccccccccc---------CCceeeccEEeeEecCCCccCcCCHHHHHHH
Q 003386          194 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVEL  264 (824)
Q Consensus       194 ~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~---------~g~tLRfPr~~~iR~DK~~~e~~t~~el~el  264 (824)
                      +....  ...+|++||+ |.  +|+||+++.. +.+..|+         .+++||||||++||+||+|+||+|+++|.+|
T Consensus        70 ~~~~~--~~~~~~~wv~-P~--~V~Ev~~~~i-t~s~~~~~~~~~~~~~~g~sLRfPr~~riR~DK~~~e~~t~~~l~~l  143 (148)
T d1x9na2          70 YVRID--GAVIPDHWLD-PS--AVWEVKCADL-SLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACL  143 (148)
T ss_dssp             TEECS--SSCCCSEEEC-SC--CEEEEEESEE-EEESSCCTTTTTSCSSCEEEEESCEEEEECTTCCGGGSCBHHHHHHH
T ss_pred             ceecc--CccCCcEEec-cc--eEEEEEeeee-eeccceeeccccccCCCceEEEcCEEEEEeCCCChHHCcCHHHHHHH
Confidence            44432  3578999998 86  5899997543 3455554         4689999999999999999999999999999


Q ss_pred             HHhc
Q 003386          265 VHSS  268 (824)
Q Consensus       265 ~~~~  268 (824)
                      ++++
T Consensus       144 ~~~Q  147 (148)
T d1x9na2         144 YRKQ  147 (148)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            8643
>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wf6a_ c.15.1.5 (A:) DNA topoisomerase II binding protein 1, TopBP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cdza_ c.15.1.1 (A:) DNA-repair protein XRCC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1a0ia2 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-terminal domain {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1t15a2 c.15.1.3 (A:1758-1859) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1in1a_ c.15.1.2 (A:) DNA ligase III alpha {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fvia2 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Back     information, alignment and structure
>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1t15a1 c.15.1.3 (A:1649-1757) Breast cancer associated protein, BRCA1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein, BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1kzyc1 c.15.1.4 (C:1714-1866) 53BP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ckma2 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain {Chlorella virus PBCV-1 [TaxId: 10506]} Back     information, alignment and structure
>d1a0ia1 b.40.4.6 (A:241-349) ATP-dependent DNA ligase {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein, BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1fvia1 b.40.4.6 (A:190-293) ATP-dependent DNA ligase {Chlorella virus PBCV-1 [TaxId: 10506]} Back     information, alignment and structure
>d1l7ba_ c.15.1.2 (A:) NAD+-dependent DNA ligase, domain 4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]} Back     information, alignment and structure
>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1s68a_ d.142.2.4 (A:) RNA ligase 2, N-terminal domain {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure