Citrus Sinensis ID: 006003

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-----
MTKTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFCIL
ccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHcccEEEEEEcccccEEEEEEEccEEEEEEccccccccccccHHHHHHHccccccEEEEEEEEEEEcccccEEcccHHHHHHHHHcccccccccEEEEEEEEEEEccEEcccccHHHHHHHHHHHcccccccEEEEccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEccccccccccccccccEEEccccccccccccEEEEEEEEcccccccccccEEEEEEEccccccccccEEEEEEEcccccHHHHHHHHHHHcccEEEcccccccccccEEEcccccccccEEEEccccEEEEEEEccccccccccccccEEEcccEEEEEEccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEc
ccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccccccHHHHHEHccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHcccccccHcccccHHHHHHHHHccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccccccccccccccccHHccccccHHHHHHHccccEEEEEEEEcccEEEEEEcccEEEEEEccccccccccccHHHHHHHcccccEEEEEEEEEEEccccccEccHcHHcHHHHHcccHHHcccEEEEEEEEEEEEcccccccccHHHHHHHHHHHccccccEEEEEEcccccccccccccccccEcccccHHHHHHHHHHHHHccccEEEEEccccccccccccccEEEEcHHHHccccccEEEEEEEEcccccccccHHHHHHHHccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHccccccccccccccEEEEEcccccccEEEcccccEEEEEEEEccccccHHHHcccEEEEcccEEEEcccccHHHcccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEEccHHcccccccccccccccHccEEEEEc
MTKTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPsldrergsyglkeSVLANCLIDalgmskdsADAVRLINwrkggaapnagnfPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLklgiseksifhefhpdaedlfNVTCDLKLVCEKLKDRNqrhkrqdievgkavRPQLAMRIGDAHAAWRKLHGKEVVIeckfdgdriqihkngseihyfsrsfldhseyghAMSKIIEQNVLVDRCILDGEMLVWDTSLNrfaefgsnQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKvvkpskgrletlvpdhglnshvrpqgepcwslvaHNVDEVEKFFKETIENrdegivlkdlgskwepgdrsgkwlklkpeyiragsdlDVLIIGgyygsgrrgGEVAQFLVALaerpapdtyprrfisfcrvgtglsdeELDAVVTKLKPyfrkyeypkrappsfyqvtnnskerpdvwiespeksIILSITSDIRTIRSevfsapyslrfpridrvrydkpwhdcldvqSFVELVhssngttqkgkeygglqddkpkqfrssrkgekknvsivpshflqtdvsdikgetsiFSDMVFCIL
MTKTEETEVIVLVslfnwiqktkpaakkrskfrKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRkggaapnagNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLkdrnqrhkrqdievgkavrpqLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKetienrdegivlkdlgskwepgdrsgkwlklkpeyiragsdldVLIIGGYYGSGRRGGEVAQFLVALAerpapdtyprrFISFCRvgtglsdeelDAVVTKLKPYFrkyeypkrappsfyqvtnnskerpdvwiespekSIILSITSDIRTIRSevfsapyslrfpriDRVRYDKPWHDCLDVQSFVELVHSsngttqkgkeygglqddkpkqfrssrkgekknvsivpshflqtdvsdikgetsifsDMVFCIL
MTKTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIggyygsgrrggEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFCIL
*******EVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLA******EKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKD*********IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVV********TLV***GLN*HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQV********DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVH************************************VPSHFLQTDVSDIKGETSIFSDMVFCI*
****EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVA****************IKELNDL******************TLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQR***QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGS***********LSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVE*********************************************************IFSDMVFCIL
MTKTEETEVIVLVSLFNWIQK*********KFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDK**************VSIVPSHFLQTDVSDIKGETSIFSDMVFCIL
****EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGT***************************NV**VPSHFLQTDVSDIKGETSIFSDMVFCIL
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MTKTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTxxxxxxxxxxxxxxxxxxxxxSVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFCIL
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 ?
Query665 2.2.26 [Sep-21-2011]
Q9LL84 1219 DNA ligase 4 OS=Arabidops yes no 0.987 0.538 0.823 0.0
Q7X7E9 1322 Putative DNA ligase 4 OS= yes no 0.902 0.453 0.656 0.0
Q5R6L3 911 DNA ligase 4 OS=Pongo abe yes no 0.938 0.684 0.353 1e-107
P49917 911 DNA ligase 4 OS=Homo sapi yes no 0.938 0.684 0.351 1e-107
Q90YB1 912 DNA ligase 4 OS=Gallus ga yes no 0.936 0.683 0.352 1e-104
Q8BTF7 911 DNA ligase 4 OS=Mus muscu yes no 0.938 0.684 0.347 1e-104
Q54CR9 1088 DNA ligase 4 OS=Dictyoste yes no 0.870 0.532 0.335 1e-101
Q6C8A3 956 DNA ligase 4 OS=Yarrowia yes no 0.932 0.648 0.323 8e-84
A8N936 1025 DNA ligase 4 OS=Coprinops N/A no 0.845 0.548 0.346 1e-83
Q7Z7W5 1025 DNA ligase 4 OS=Coprinops N/A no 0.845 0.548 0.346 1e-83
>sp|Q9LL84|DNLI4_ARATH DNA ligase 4 OS=Arabidopsis thaliana GN=LIG4 PE=1 SV=1 Back     alignment and function desciption
 Score = 1117 bits (2890), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 545/662 (82%), Positives = 605/662 (91%), Gaps = 5/662 (0%)

Query: 4   TEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSY 63
           TEE +  VLVSLFNWIQK+K +++KRSKFRKFLDTYC   DYF A+RLI+PSLDRERGSY
Sbjct: 2   TEEIKFSVLVSLFNWIQKSKTSSQKRSKFRKFLDTYCKPSDYFVAVRLIIPSLDRERGSY 61

Query: 64  GLKESVLANCLIDALGMSKDSADAVRLINWRKGG---AAPNAGNFPMVAAEVLQRRQGMI 120
           GLKESVLA CLIDALG+S+D+ DAVRL+NWRKGG   A  NAGNF ++AAEVLQRRQGM 
Sbjct: 62  GLKESVLATCLIDALGISRDAPDAVRLLNWRKGGTAKAGANAGNFSLIAAEVLQRRQGMA 121

Query: 121 SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKS 180
           SGGLTIKELNDLLDRLASSENRAEK  VLSTLI+KTNAQEMKW+I IILKDLKLG+SEKS
Sbjct: 122 SGGLTIKELNDLLDRLASSENRAEKTLVLSTLIQKTNAQEMKWVIRIILKDLKLGMSEKS 181

Query: 181 IFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWR 240
           IF EFHPDAEDLFNVTCDLKLVCEKL+DR+QRHKRQDIEVGKAVRPQLAMRIGD +AAW+
Sbjct: 182 IFQEFHPDAEDLFNVTCDLKLVCEKLRDRHQRHKRQDIEVGKAVRPQLAMRIGDVNAAWK 241

Query: 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILD 300
           KLHGK+VV ECKFDGDRIQIHKNG++IHYFSR+FLDHSEY HAMS +I QN+LVD+CILD
Sbjct: 242 KLHGKDVVAECKFDGDRIQIHKNGTDIHYFSRNFLDHSEYAHAMSDLIVQNILVDKCILD 301

Query: 301 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERH 360
           GEMLVWDTSLNRFAEFGSNQEIAKAAR+GL S +QLCY AFDVLYVGDTSVIHQSLKERH
Sbjct: 302 GEMLVWDTSLNRFAEFGSNQEIAKAAREGLDSHKQLCYVAFDVLYVGDTSVIHQSLKERH 361

Query: 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420
           ELL+KVVKP KGRLE LVP+ GLN H RP GEP WS+V H   +VE+FFKET+ENRDEGI
Sbjct: 362 ELLKKVVKPLKGRLEVLVPEGGLNVH-RPSGEPSWSIVVHAAADVERFFKETVENRDEGI 420

Query: 421 VLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAER 480
           VLKDL SKWEPGDRSGKW+KLKPEYIRAG+DLDVLIIGGYYGSGRRGGEVAQFLVALA+R
Sbjct: 421 VLKDLESKWEPGDRSGKWMKLKPEYIRAGADLDVLIIGGYYGSGRRGGEVAQFLVALADR 480

Query: 481 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540
              + YPRRF+SFCRVGTGLSD+EL+ VV+KLKPYFRK E+PK+APPSFYQVTN+SKERP
Sbjct: 481 AEANVYPRRFMSFCRVGTGLSDDELNTVVSKLKPYFRKNEHPKKAPPSFYQVTNHSKERP 540

Query: 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600
           DVWI+SPEKSIILSITSDIRTIRSEVF APYSLRFPRID+VRYDKPWH+CLDVQ+FVELV
Sbjct: 541 DVWIDSPEKSIILSITSDIRTIRSEVFVAPYSLRFPRIDKVRYDKPWHECLDVQAFVELV 600

Query: 601 HSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDM 660
           +SSNGTTQK KE    QD+ PK  +SS++GEKKNVS+VPS F+QTDVSDIKG+TSIFS+M
Sbjct: 601 NSSNGTTQKQKESESTQDN-PKVNKSSKRGEKKNVSLVPSQFIQTDVSDIKGKTSIFSNM 659

Query: 661 VF 662
           +F
Sbjct: 660 IF 661
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|Q90YB1|DNLI4_CHICK DNA ligase 4 OS=Gallus gallus GN=LIG4 PE=2 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|Q54CR9|DNLI4_DICDI DNA ligase 4 OS=Dictyostelium discoideum 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|A8N936|DNLI4_COPC7 DNA ligase 4 OS=Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) GN=LIG4 PE=3 SV=2 Back     alignment and function description
>sp|Q7Z7W5|DNLI4_COPCI DNA ligase 4 OS=Coprinopsis cinerea GN=LIG4 PE=2 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 ?
Query665
224144326 1242 predicted protein [Populus trichocarpa] 0.989 0.529 0.832 0.0
225445943 1162 PREDICTED: DNA ligase 4-like [Vitis vini 0.987 0.565 0.831 0.0
112732548 1319 DNA ligase IV [Populus nigra] 0.992 0.500 0.825 0.0
297735473 1163 unnamed protein product [Vitis vinifera] 0.987 0.564 0.829 0.0
30696835 1219 DNA ligase 4 [Arabidopsis thaliana] gi|7 0.987 0.538 0.823 0.0
297796605 1221 ATLIG4 [Arabidopsis lyrata subsp. lyrata 0.987 0.538 0.819 0.0
356556242 1171 PREDICTED: DNA ligase 4-like [Glycine ma 0.989 0.561 0.813 0.0
357449599 1244 DNA ligase [Medicago truncatula] gi|3554 0.990 0.529 0.771 0.0
449463583 1214 PREDICTED: DNA ligase 4-like [Cucumis sa 0.990 0.542 0.794 0.0
255573570 850 DNA ligase IV, putative [Ricinus communi 0.948 0.742 0.793 0.0
>gi|224144326|ref|XP_002325262.1| predicted protein [Populus trichocarpa] gi|222866696|gb|EEF03827.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score = 1130 bits (2923), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 551/662 (83%), Positives = 605/662 (91%), Gaps = 4/662 (0%)

Query: 4   TEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSY 63
           T  T+  +LVSLFNWI KTK +++KRSKFRKF+DT+C   DYFSA+RLILP+LDRERG+Y
Sbjct: 10  TAHTKFSILVSLFNWISKTKTSSRKRSKFRKFIDTFCSPSDYFSAVRLILPNLDRERGTY 69

Query: 64  GLKESVLANCLIDALGMSKDSADAVRLINWRKGGA---APNAGNFPMVAAEVLQRRQGMI 120
           GLKESVLA  LI+ALGMS+DS DA++LINWRKGGA     NAGNF +VAAEVLQRRQG +
Sbjct: 70  GLKESVLAVSLIEALGMSRDSPDALKLINWRKGGANATGANAGNFSLVAAEVLQRRQGTV 129

Query: 121 SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKS 180
           SGGLTI+ELN LLD+LASSENR EK +VL+ LI KTN QEMKWIIMIILKDLKLG+SEKS
Sbjct: 130 SGGLTIEELNGLLDKLASSENRGEKTAVLAALINKTNTQEMKWIIMIILKDLKLGMSEKS 189

Query: 181 IFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWR 240
           +FHEFHPDAEDLFNVTCDLKLVCEKL+DRNQRHKRQDIEVGKAVRPQLAMR+ DAHAAW+
Sbjct: 190 VFHEFHPDAEDLFNVTCDLKLVCEKLRDRNQRHKRQDIEVGKAVRPQLAMRVSDAHAAWK 249

Query: 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILD 300
           KLHGKEVV+ECKFDGDRIQIHKNG+E+HYFSR+FLDHSEY H MS II QNVL +RCILD
Sbjct: 250 KLHGKEVVVECKFDGDRIQIHKNGAEVHYFSRNFLDHSEYAHGMSDIIVQNVLDERCILD 309

Query: 301 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERH 360
           GEMLVWDTSLNRFAEFGSNQEIAKAARDGL SDRQLCY AFD+LYVGDTSVIHQ+LKERH
Sbjct: 310 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLDSDRQLCYVAFDILYVGDTSVIHQTLKERH 369

Query: 361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420
           ELL+KVVKP KGRLE LVP+ GLN+H  P GEP  SL+A+NVD++EKFFKETIENRDEGI
Sbjct: 370 ELLRKVVKPVKGRLEILVPNGGLNAHRLP-GEPYCSLIAYNVDDIEKFFKETIENRDEGI 428

Query: 421 VLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAER 480
           VLKDLGSKWEP DRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFL+ LAER
Sbjct: 429 VLKDLGSKWEPSDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLLGLAER 488

Query: 481 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540
           PA +TYPRRFISFCRVG GLSDEELD VV+KLKPYFRK EYPK +PPSFYQVTNNSKERP
Sbjct: 489 PASNTYPRRFISFCRVGNGLSDEELDTVVSKLKPYFRKNEYPKNSPPSFYQVTNNSKERP 548

Query: 541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600
           DVWIE+P+KSIILSITSDIRTI SEVFSAPYSLRFPRIDRVRYDKPWH+CLDVQSFVELV
Sbjct: 549 DVWIENPDKSIILSITSDIRTISSEVFSAPYSLRFPRIDRVRYDKPWHECLDVQSFVELV 608

Query: 601 HSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDM 660
           HSSNGTTQKGK YG +QD KP   +SSRKGEKK+VS+VPSH +QTD+SDIKGET IFS+M
Sbjct: 609 HSSNGTTQKGKGYGYVQDSKPTHIKSSRKGEKKSVSVVPSHLIQTDISDIKGETLIFSNM 668

Query: 661 VF 662
           +F
Sbjct: 669 MF 670

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225445943|ref|XP_002263967.1| PREDICTED: DNA ligase 4-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|112732548|dbj|BAF03051.1| DNA ligase IV [Populus nigra] Back     alignment and taxonomy information
>gi|297735473|emb|CBI17913.3| unnamed protein product [Vitis vinifera] 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
>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|356556242|ref|XP_003546435.1| PREDICTED: DNA ligase 4-like [Glycine max] 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|449463583|ref|XP_004149513.1| PREDICTED: DNA ligase 4-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255573570|ref|XP_002527709.1| DNA ligase IV, putative [Ricinus communis] gi|223532899|gb|EEF34668.1| DNA ligase IV, putative [Ricinus communis] 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 ?
Query665
TAIR|locus:2175544 1219 ATLIG4 [Arabidopsis thaliana ( 0.987 0.538 0.806 1.1e-291
DICTYBASE|DDB_G0292760 1088 lig4 "BRCT domain-containing p 0.643 0.393 0.311 1.9e-89
UNIPROTKB|Q5R6L3 911 DNL4 "DNA ligase 4" [Pongo abe 0.899 0.656 0.348 5.9e-89
UNIPROTKB|P49917 911 LIG4 "DNA ligase 4" [Homo sapi 0.899 0.656 0.346 2e-88
UNIPROTKB|F1RLP1 910 LIG4 "DNA ligase" [Sus scrofa 0.890 0.650 0.343 4.3e-86
UNIPROTKB|E2R0G7 911 LIG4 "DNA ligase" [Canis lupus 0.897 0.655 0.343 6.9e-86
UNIPROTKB|F1MB07 911 LIG4 "DNA ligase" [Bos taurus 0.897 0.655 0.343 1.8e-85
RGD|1304639 911 Lig4 "ligase IV, DNA, ATP-depe 0.899 0.656 0.334 4.4e-84
UNIPROTKB|Q90YB1 912 LIG4 "DNA ligase 4" [Gallus ga 0.738 0.538 0.361 9e-77
UNIPROTKB|F1P275 912 LIG4 "DNA ligase" [Gallus gall 0.738 0.538 0.361 1.1e-76
TAIR|locus:2175544 ATLIG4 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 2788 (986.5 bits), Expect = 1.1e-291, Sum P(2) = 1.1e-291
 Identities = 534/662 (80%), Positives = 594/662 (89%)

Query:     4 TEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSY 63
             TEE +  VLVSLFNWIQK+K +++KRSKFRKFLDTYC   DYF A+RLI+PSLDRERGSY
Sbjct:     2 TEEIKFSVLVSLFNWIQKSKTSSQKRSKFRKFLDTYCKPSDYFVAVRLIIPSLDRERGSY 61

Query:    64 GLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAP---NAGNFPMVAAEVLQRRQGMI 120
             GLKESVLA CLIDALG+S+D+ DAVRL+NWRKGG A    NAGNF ++AAEVLQRRQGM 
Sbjct:    62 GLKESVLATCLIDALGISRDAPDAVRLLNWRKGGTAKAGANAGNFSLIAAEVLQRRQGMA 121

Query:   121 SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKS 180
             SGGLTIKELNDLLDRLASSENRAEK  VLSTLI+KTNAQEMKW+I IILKDLKLG+SEKS
Sbjct:   122 SGGLTIKELNDLLDRLASSENRAEKTLVLSTLIQKTNAQEMKWVIRIILKDLKLGMSEKS 181

Query:   181 IFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAHAAWR 240
             IF EFHPDAEDLFNVTCDLKLVCEKL+DR+QRHKRQDIEVGKAVRPQLAMRIGD +AAW+
Sbjct:   182 IFQEFHPDAEDLFNVTCDLKLVCEKLRDRHQRHKRQDIEVGKAVRPQLAMRIGDVNAAWK 241

Query:   241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILD 300
             KLHGK+VV ECKFDGDRIQIHKNG++IHYFSR+FLDHSEY HAMS +I QN+LVD+CILD
Sbjct:   242 KLHGKDVVAECKFDGDRIQIHKNGTDIHYFSRNFLDHSEYAHAMSDLIVQNILVDKCILD 301

Query:   301 GEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERH 360
             GEMLVWDTSLNRFAEFGSNQEIAKAAR+GL S +QLCY AFDVLYVGDTSVIHQSLKERH
Sbjct:   302 GEMLVWDTSLNRFAEFGSNQEIAKAAREGLDSHKQLCYVAFDVLYVGDTSVIHQSLKERH 361

Query:   361 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGI 420
             ELL+KVVKP KGRLE LVP+ GLN H RP GEP WS+V H   +VE+FFKET+ENRDEGI
Sbjct:   362 ELLKKVVKPLKGRLEVLVPEGGLNVH-RPSGEPSWSIVVHAAADVERFFKETVENRDEGI 420

Query:   421 VLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIXXXXXXXXXXXEVAQFLVALAER 480
             VLKDL SKWEPGDRSGKW+KLKPEYIRAG+DLDVLII           EVAQFLVALA+R
Sbjct:   421 VLKDLESKWEPGDRSGKWMKLKPEYIRAGADLDVLIIGGYYGSGRRGGEVAQFLVALADR 480

Query:   481 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERP 540
                + YPRRF+SFCRVGTGLSD+EL+ VV+KLKPYFRK E+PK+APPSFYQVTN+SKERP
Sbjct:   481 AEANVYPRRFMSFCRVGTGLSDDELNTVVSKLKPYFRKNEHPKKAPPSFYQVTNHSKERP 540

Query:   541 DVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 600
             DVWI+SPEKSIILSITSDIRTIRSEVF APYSLRFPRID+VRYDKPWH+CLDVQ+FVELV
Sbjct:   541 DVWIDSPEKSIILSITSDIRTIRSEVFVAPYSLRFPRIDKVRYDKPWHECLDVQAFVELV 600

Query:   601 HSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDM 660
             +SSNGTTQK KE    QD+ PK  +SS++GEKKNVS+VPS F+QTDVSDIKG+TSIFS+M
Sbjct:   601 NSSNGTTQKQKESESTQDN-PKVNKSSKRGEKKNVSLVPSQFIQTDVSDIKGKTSIFSNM 659

Query:   661 VF 662
             +F
Sbjct:   660 IF 661
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
DICTYBASE|DDB_G0292760 lig4 "BRCT domain-containing protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|Q5R6L3 DNL4 "DNA ligase 4" [Pongo abelii (taxid:9601)] Back     alignment and assigned GO terms
UNIPROTKB|P49917 LIG4 "DNA ligase 4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RLP1 LIG4 "DNA ligase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E2R0G7 LIG4 "DNA ligase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F1MB07 LIG4 "DNA ligase" [Bos taurus (taxid:9913)] 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|Q90YB1 LIG4 "DNA ligase 4" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1P275 LIG4 "DNA ligase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9LL84DNLI4_ARATH6, ., 5, ., 1, ., 10.82320.98790.5389yesno

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 Layer6.5.1.10.914
3rd Layer6.5.10.921

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 ?
Query665
TIGR00574514 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1 1e-104
cd07903225 cd07903, Adenylation_DNA_ligase_IV, Adenylation do 3e-82
PRK01109590 PRK01109, PRK01109, ATP-dependent DNA ligase; Prov 5e-62
cd07968140 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/ol 2e-55
COG1793444 COG1793, CDC9, ATP-dependent DNA ligase [DNA repli 3e-52
pfam01068195 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligas 1e-40
cd07901207 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenyla 1e-38
cd07900219 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation 3e-36
cd07898201 cd07898, Adenylation_DNA_ligase, Adenylation domai 9e-36
pfam04675177 pfam04675, DNA_ligase_A_N, DNA ligase N terminus 1e-32
PLN03113744 PLN03113, PLN03113, DNA ligase 1; Provisional 1e-31
PRK03180508 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed 2e-31
cd07906190 cd07906, Adenylation_DNA_ligase_LigD_LigC, Adenyla 3e-28
cd07902213 cd07902, Adenylation_DNA_ligase_III, Adenylation d 1e-26
cd07893129 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligo 2e-25
TIGR02779298 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, l 3e-24
PRK09632764 PRK09632, PRK09632, ATP-dependent DNA ligase; Revi 7e-20
cd08039235 cd08039, Adenylation_DNA_ligase_Fungal, Adenylatio 3e-19
cd07969144 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oli 4e-19
TIGR02776 552 TIGR02776, NHEJ_ligase_prk, DNA ligase D 3e-15
PRK05972 860 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed 2e-14
cd07967139 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/o 9e-14
pfam0467995 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligas 2e-13
cd07972122 cd07972, OBF_DNA_ligase_Arch_LigB, The Oligonucleo 2e-13
cd06846182 cd06846, Adenylation_DNA_ligase_like, Adenylation 1e-11
cd07905194 cd07905, Adenylation_DNA_ligase_LigC, Adenylation 1e-11
PRK07636275 PRK07636, ligB, ATP-dependent DNA ligase; Reviewed 3e-11
PRK09633 610 PRK09633, ligD, ATP-dependent DNA ligase; Reviewed 2e-10
PHA02587488 PHA02587, 30, DNA ligase; Provisional 2e-10
TIGR04120526 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent 1e-09
cd07897207 cd07897, Adenylation_DNA_ligase_Bac1, Adenylation 6e-09
PRK09125282 PRK09125, PRK09125, DNA ligase; Provisional 9e-09
PRK09247539 PRK09247, PRK09247, ATP-dependent DNA ligase; Vali 4e-08
cd07896174 cd07896, Adenylation_kDNA_ligase_like, Adenylation 8e-08
cd08040108 cd08040, OBF_DNA_ligase_family, The Oligonucleotid 3e-06
cd07971115 cd07971, OBF_DNA_ligase_LigD, The Oligonucleotide/ 4e-04
pfam04675177 pfam04675, DNA_ligase_A_N, DNA ligase N terminus 0.003
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information 
 Score =  326 bits (837), Expect = e-104
 Identities = 175/558 (31%), Positives = 267/558 (47%), Gaps = 66/558 (11%)

Query: 63  YGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMIS- 121
           YG+ E +L   +   LG+ KD  +   L +   G              E L  +Q   S 
Sbjct: 2   YGIGEKLLIKAISSILGIPKDEIEEKVLEDGDLG-----------EVIEGLFSKQKQTSF 50

Query: 122 --GGLTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGI 176
               LT+KE+ ++L  +A      ++ +KI +L +L+K+    E K++I +IL DL++GI
Sbjct: 51  FPAPLTVKEVYEVLKFIARLSGEGSQDKKIKLLKSLLKRATPLEAKYLIRLILGDLRIGI 110

Query: 177 SEKSIFHEFH-------PDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQ 227
           +EK+I            PD E  FN+T DL  V + L +   R   +D  I++G   +P 
Sbjct: 111 AEKTILDALAKAFLLSPPDVERAFNLTNDLGKVAKILLEEGLRGLDKDLSIQLGIPFKPM 170

Query: 228 LAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSK 286
           LA R      A +K       +E K+DG+R+Q+HK+G +   FSR   +++  Y    ++
Sbjct: 171 LAERAKSIEEALKKKGNG-FYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYAYPEIFTE 229

Query: 287 -IIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIA-KAARDGLSSDRQLCYFAFDVL 344
            I E    +  CILDGEM+  D    +   F +      K     +     +C F FD+L
Sbjct: 230 FIKEAFPGIKSCILDGEMVAIDPETGKPLPFQTLLRRKRKYDIKAMEQKVPVCLFVFDIL 289

Query: 345 YVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDE 404
           Y+   S+I + L ER E+L+ ++KP   R+E +                    +  NV+E
Sbjct: 290 YLNGESLIDEPLIERREILESILKPIPNRIE-IAE----------------MKIVSNVEE 332

Query: 405 VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLIIGGYYGS 463
           +EKF  E I    EG++LKDL S +EPG R   WLK+KPEY+   G  LD+++IG YYG 
Sbjct: 333 LEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKVKPEYLEGMGDTLDLVVIGAYYGK 392

Query: 464 GRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 523
           G RGG    FL+A       D     F +  +VGTG +D +L  +  KL P     + P 
Sbjct: 393 GSRGGMYGSFLLACY-----DPESEEFKTITKVGTGFTDADLQELGKKLPPL--WIDPPG 445

Query: 524 RAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFSAPYSLRFPRIDRVR 582
              PS         + PD+W   P+ +I+  +T ++I T      +   SLRFPR  R+R
Sbjct: 446 SRVPSI------LPDEPDIW---PDPAIVWEVTGAEI-TKSPAYKANGISLRFPRFSRIR 495

Query: 583 YDKPWHDCLDVQSFVELV 600
            DK   D   ++   EL 
Sbjct: 496 DDKGPEDATTIEQIKELY 513

All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 514
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA Ligase IV Back     alignment and domain information
>gnl|CDD|234900 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>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
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication, recombination, and repair] 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|185711 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of archaeal and bacterial LigB-like DNA ligases 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|185709 cd07898, Adenylation_DNA_ligase, Adenylation domain of ATP-dependent DNA Ligases Back     alignment and domain information
>gnl|CDD|218206 pfam04675, DNA_ligase_A_N, DNA ligase N terminus Back     alignment and domain information
>gnl|CDD|215584 PLN03113, PLN03113, DNA ligase 1; Provisional Back     alignment and domain information
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed 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|185712 cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA Ligase III 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|234009 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase domain Back     alignment and domain information
>gnl|CDD|236599 PRK09632, PRK09632, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|185716 cd08039, Adenylation_DNA_ligase_Fungal, Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins 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|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D Back     alignment and domain information
>gnl|CDD|235658 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed 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|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|185704 cd06846, Adenylation_DNA_ligase_like, Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases Back     alignment and domain information
>gnl|CDD|185714 cd07905, Adenylation_DNA_ligase_LigC, Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases Back     alignment and domain information
>gnl|CDD|236070 PRK07636, ligB, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|182006 PRK09633, ligD, ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>gnl|CDD|222893 PHA02587, 30, DNA ligase; Provisional 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|185708 cd07897, Adenylation_DNA_ligase_Bac1, Adenylation domain of putative bacterial ATP-dependent DNA ligases Back     alignment and domain information
>gnl|CDD|181662 PRK09125, PRK09125, DNA ligase; Provisional Back     alignment and domain information
>gnl|CDD|236428 PRK09247, PRK09247, ATP-dependent DNA ligase; Validated 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|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|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|218206 pfam04675, DNA_ligase_A_N, DNA ligase N terminus Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 665
KOG0966 881 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
TIGR00574514 dnl1 DNA ligase I, ATP-dependent (dnl1). All prote 100.0
PRK09247539 ATP-dependent DNA ligase; Validated 100.0
PRK03180508 ligB ATP-dependent DNA ligase; Reviewed 100.0
PHA02587488 30 DNA ligase; Provisional 100.0
COG1793444 CDC9 ATP-dependent DNA ligase [DNA replication, re 100.0
TIGR02779298 NHEJ_ligase_lig DNA polymerase LigD, ligase domain 100.0
PRK09632764 ATP-dependent DNA ligase; Reviewed 100.0
PRK08224350 ligC ATP-dependent DNA ligase; Reviewed 100.0
PRK05972 860 ligD ATP-dependent DNA ligase; Reviewed 100.0
PRK09633 610 ligD ATP-dependent DNA ligase; Reviewed 100.0
PRK07636275 ligB ATP-dependent DNA ligase; Reviewed 100.0
cd07900219 Adenylation_DNA_ligase_I_Euk Adenylation domain of 100.0
TIGR02776 552 NHEJ_ligase_prk DNA ligase D. Members of this prot 100.0
cd07903225 Adenylation_DNA_ligase_IV Adenylation domain of DN 100.0
cd07902213 Adenylation_DNA_ligase_III Adenylation domain of D 100.0
cd07901207 Adenylation_DNA_ligase_Arch_LigB Adenylation domai 100.0
PRK09125282 DNA ligase; Provisional 100.0
PHA00454315 ATP-dependent DNA ligase 100.0
cd07898201 Adenylation_DNA_ligase Adenylation domain of ATP-d 100.0
cd07897207 Adenylation_DNA_ligase_Bac1 Adenylation domain of 100.0
cd08039235 Adenylation_DNA_ligase_Fungal Adenylation domain o 100.0
cd07905194 Adenylation_DNA_ligase_LigC Adenylation domain of 100.0
PF01068202 DNA_ligase_A_M: ATP dependent DNA ligase domain; I 100.0
cd07906190 Adenylation_DNA_ligase_LigD_LigC Adenylation domai 100.0
cd07967139 OBF_DNA_ligase_III The Oligonucleotide/oligosaccha 100.0
cd07896174 Adenylation_kDNA_ligase_like Adenylation domain of 100.0
cd06846182 Adenylation_DNA_ligase_like Adenylation domain of 99.97
PF04675177 DNA_ligase_A_N: DNA ligase N terminus; InterPro: I 99.97
cd07968140 OBF_DNA_ligase_IV The Oligonucleotide/oligosacchar 99.97
cd07969144 OBF_DNA_ligase_I The Oligonucleotide/oligosacchari 99.96
cd07895215 Adenylation_mRNA_capping Adenylation domain of GTP 99.95
cd07972122 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligo 99.95
KOG4437482 consensus ATP-dependent DNA ligase III [Replicatio 99.94
cd07893129 OBF_DNA_ligase The Oligonucleotide/oligosaccharide 99.94
cd07971115 OBF_DNA_ligase_LigD The Oligonucleotide/oligosacch 99.84
PF0467997 DNA_ligase_A_C: ATP dependent DNA ligase C termina 99.8
cd08040108 OBF_DNA_ligase_family The Oligonucleotide/oligosac 99.79
cd07894342 Adenylation_RNA_ligase Adenylation domain of RNA c 99.74
cd07970122 OBF_DNA_ligase_LigC The Oligonucleotide/oligosacch 99.72
PF01331192 mRNA_cap_enzyme: mRNA capping enzyme, catalytic do 99.3
COG5226404 CEG1 mRNA capping enzyme, guanylyltransferase (alp 99.18
cd0804177 OBF_kDNA_ligase_like The Oligonucleotide/oligosacc 99.12
COG1423382 ATP-dependent DNA ligase, homolog of eukaryotic li 98.85
TIGR01209374 RNA ligase, Pab1020 family. Members of this family 98.83
cd09232186 Snurportin-1_C C-terminal m3G cap-binding domain o 98.56
PF1474366 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2 98.2
smart00532441 LIGANc Ligase N family. 97.87
cd00114307 LIGANc NAD+ dependent DNA ligase adenylation domai 97.85
PF01653315 DNA_ligase_aden: NAD-dependent DNA ligase adenylat 97.75
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 97.66
TIGR00575 652 dnlj DNA ligase, NAD-dependent. The member of this 97.64
PRK14351 689 ligA NAD-dependent DNA ligase LigA; Provisional 97.55
PRK07956 665 ligA NAD-dependent DNA ligase LigA; Validated 97.51
PRK14350 669 ligA NAD-dependent DNA ligase LigA; Provisional 97.2
PF09414186 RNA_ligase: RNA ligase; InterPro: IPR021122 This e 96.98
TIGR02307325 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of t 96.92
PRK01109590 ATP-dependent DNA ligase; Provisional 96.84
COG0272 667 Lig NAD-dependent DNA ligase (contains BRCT domain 96.63
PHA02142366 putative RNA ligase 95.74
KOG3132325 consensus m3G-cap-specific nuclear import receptor 94.47
TIGR02306341 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The me 93.24
PRK09247539 ATP-dependent DNA ligase; Validated 89.77
KOG2386393 consensus mRNA capping enzyme, guanylyltransferase 89.41
PF04675177 DNA_ligase_A_N: DNA ligase N terminus; InterPro: I 87.46
PRK03180508 ligB ATP-dependent DNA ligase; Reviewed 83.98
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=1.8e-131  Score=1081.33  Aligned_cols=624  Identities=46%  Similarity=0.776  Sum_probs=545.1

Q ss_pred             CCCCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC----chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHh
Q 006003            3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL   78 (665)
Q Consensus         3 ~~~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~----~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~   78 (665)
                      ||+++.|+.+|++|+.|+.+.....|++++++++++|+.+    +|+||+|||+||++||+|+.|||||..||++|+++|
T Consensus         1 ~~~~~~F~~~~~~f~~i~~t~~~~~k~~~~~k~~~s~~~~~e~~sd~y~~lRL~lp~lDReR~~Yglket~La~l~i~~l   80 (881)
T KOG0966|consen    1 MASPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESWCRPCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL   80 (881)
T ss_pred             CCCccccchHHHHHHHHHHhhhhHhHHHHHhhccccccccccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999999865    999999999999999999999999999999999999


Q ss_pred             CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhccCCCC-CCCCHHHHHHHHHHHHhhhhHHhHH-HHHHHHHHhC
Q 006003           79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMIS-GGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT  156 (665)
Q Consensus        79 ~~~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r~~~~~-~~lTi~eV~~~Ld~la~~~~~~~k~-~~l~~ll~~~  156 (665)
                      +++++|.||++|+||+.++..+  |||+.++++++++|+...+ +.|||.|||++||.||+......+. ..|..++++|
T Consensus        81 ~lprds~Da~rL~nwr~~~~~~--Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~~~~~~~~~l~~lv~~~  158 (881)
T KOG0966|consen   81 HLPRDSADAVRLKNWRASTGAR--GDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPSEDGKKFKKLSQLVEQC  158 (881)
T ss_pred             cCCCCcHHHHHHHhhccCCCcC--ccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCchhhhhhhHHHHHHHHhC
Confidence            9999999999999999987655  9999999999999987654 4599999999999999887765554 8999999999


Q ss_pred             CHHHHHHHHHHHHhhhccCCcccccccccCcCHHHHHhhhCCHHHHHHHHhhhhhccccCC--ccCCCccccccccccCC
Q 006003          157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD  234 (665)
Q Consensus       157 t~~E~k~l~RiilkdlriG~~e~til~~~hp~a~~~~~~~~dL~~v~~~l~~~~~~~~~~~--i~~g~~~~PmLA~~~~~  234 (665)
                      ||.|+|||+|||||++++|++|++||.+|||||+++||+|+||+.||+.|.||+.+++..+  |++|..|+||||++.+.
T Consensus       159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA~dl~~vtsDLk~Vc~~L~Dp~~~l~~~~~~i~lfsa~~PqLa~~~~~  238 (881)
T KOG0966|consen  159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDAQDLYNVTSDLKAVCKKLYDPSVGLKELDEDIELFSAFRPQLAQKQKL  238 (881)
T ss_pred             CHHHHHHHHHHHHHhhhcCCccchhhhhcCccHHHHHHHhhhHHHHHHHhcCCccCccccccceeehhhcCHHHHhhhcc
Confidence            9999999999999999999999999999999999999999999999999999999998877  99999999999999876


Q ss_pred             HH-HHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCcch-h----h-hHHHHHhhc--cccceeeeceEEE
Q 006003          235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYG-H----A-MSKIIEQNV--LVDRCILDGEMLV  305 (665)
Q Consensus       235 ~~-~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~~~-p----~-l~~~~~~~~--~~~~~ILDGElv~  305 (665)
                      .. +++++|++++|++|+|+||||+|+|++|+.++||||||.|||..| .    + +...+...+  ....||||||||+
T Consensus       239 ~~~~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSRNg~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~  318 (881)
T KOG0966|consen  239 GDWAIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSRNGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMT  318 (881)
T ss_pred             chHHHHHHhcCCceEEEeeccCceEEEEecCCEEEEEecCCcchhhhcCcccccccccHHHHhhhhhcchheEecceEEE
Confidence            55 689999999999999999999999999999999999999999422 1    1 222222212  3789999999999


Q ss_pred             eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 006003          306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS  385 (665)
Q Consensus       306 ~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~  385 (665)
                      ||+.+.++.|||+++++......  +...++||+|||+||+||++|.+.||.+|++.|+.++.+.+++++++.       
T Consensus       319 wD~~~~~f~~~G~~~dik~~~~~--~~~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~~-------  389 (881)
T KOG0966|consen  319 WDTKTKRFCPFGSNSDIKELSSR--DGSQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIVR-------  389 (881)
T ss_pred             eecchhhhccCCchhhHHHhhcc--ccCCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEee-------
Confidence            99999999999999988765432  356789999999999999999999999999999999999999987752       


Q ss_pred             cccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEcccccc-CCCcceEEEEEEEecCC
Q 006003          386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSG  464 (665)
Q Consensus       386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~-~g~~~DlvVIG~~~G~g  464 (665)
                                +..+++.++++++|++|+++|.||||+|.++|.|.||.|+++|+|+||+|+. +|+++|++|||||||+|
T Consensus       390 ----------~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~g  459 (881)
T KOG0966|consen  390 ----------SEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGRG  459 (881)
T ss_pred             ----------hhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCccccCCCcEeecHHHHhhcCccccEEEEecccCCC
Confidence                      4567899999999999999999999999999999999999999999999999 59999999999999999


Q ss_pred             CCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcEEE
Q 006003          465 RRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWI  544 (665)
Q Consensus       465 ~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~wi  544 (665)
                      +|+|++.+|+||+.++..++.+|.+|.++|+||+|+|++|+..+.++++++|.+ .++..+|+.++..+   ...||+||
T Consensus       460 ~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~-~~~~apP~s~l~~t---k~~Pd~wI  535 (881)
T KOG0966|consen  460 DRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKP-TSLEAPPESFLFGT---KKIPDVWI  535 (881)
T ss_pred             CCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhccc-ccccCCCHHHHhcc---cCCCceeE
Confidence            999999999999998877777889999999999999999999999999999987 34444444444432   34799999


Q ss_pred             eCCCceEEEEEeeeceecccCccCCCeeeeccEEEEEecCCCccCCCCHHHHHHHHHccCCCcccCCccCCCCCCCcccc
Q 006003          545 ESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQF  624 (665)
Q Consensus       545 ~~P~~s~v~ev~a~~~~~~s~~~~~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~  624 (665)
                      + |..|+|++|++. +++++..|.++|||||||+.++|+||+|+||+|+.+|.++...+.       ++.+.   +.+++
T Consensus       536 ~-P~~SiIlqikaa-~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~---~~kk~  603 (881)
T KOG0966|consen  536 D-PDNSIILQIKAA-EIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVED---KEKKK  603 (881)
T ss_pred             C-CCCceEEEeehh-eeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcch---hhhhc
Confidence            9 999999999953 345789999999999999999999999999999999999985321       11011   11111


Q ss_pred             ccccccccccceecCCcccCCCcCCcccccCccCCceEEEC
Q 006003          625 RSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFCIL  665 (665)
Q Consensus       625 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~g~~f~v~  665 (665)
                      +...+  .+++....-|-..++.+.+.+.|++|+|++|||+
T Consensus       604 ~~t~~--~~k~~~~~i~~~~~~~~~~~~~s~if~gl~f~Vl  642 (881)
T KOG0966|consen  604 RDTLK--VRKRTRKAIHDSAPNRSKVAKISNIFDGLEFCVL  642 (881)
T ss_pred             ccchh--hhhhhhhhhcccccchhcccchhhhhcCeeEEEe
Confidence            11111  1111112344556677889999999999999996

>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
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1) Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PHA02587 30 DNA ligase; Provisional Back     alignment and domain information
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair] 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
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I Back     alignment and domain information
>TIGR02776 NHEJ_ligase_prk DNA ligase D Back     alignment and domain information
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV Back     alignment and domain information
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III 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
>PRK09125 DNA ligase; Provisional Back     alignment and domain information
>PHA00454 ATP-dependent DNA ligase Back     alignment and domain information
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases 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
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases 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
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases 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
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins 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
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 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
>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
>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
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes 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
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair] 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
>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
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins 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
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate Back     alignment and domain information
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification] 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
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01209 RNA ligase, Pab1020 family Back     alignment and domain information
>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1 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
>smart00532 LIGANc Ligase N family Back     alignment and domain information
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain Back     alignment and domain information
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>PRK14351 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
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain Back     alignment and domain information
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family Back     alignment and domain information
>PRK01109 ATP-dependent DNA ligase; Provisional 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
>PHA02142 putative RNA ligase Back     alignment and domain information
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification] Back     alignment and domain information
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification] Back     alignment and domain information
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 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
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed 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 ?
Query665
4hto_A240 Crystal Structure Of The Dbd Domain Of Human Dna Li 1e-38
2hiv_A621 Atp-Dependent Dna Ligase From S. Solfataricus Lengt 4e-33
3l2p_A579 Human Dna Ligase Iii Recognizes Dna Ends By Dynamic 3e-31
3rr5_A570 Dna Ligase From The Archaeon Thermococcus Sp. 1519 9e-30
4eq5_A571 Dna Ligase From The Archaeon Thermococcus Sibiricus 3e-29
2cfm_A561 Atp-Dependent Dna Ligase From Pyrococcus Furiosus L 6e-29
1x9n_A688 Crystal Structure Of Human Dna Ligase I Bound To 5' 3e-25
3gde_A558 The Closed Conformation Of Atp-Dependent Dna Ligase 6e-20
3vnn_A139 Crystal Structure Of A Sub-Domain Of The Nucleotidy 2e-17
1vs0_A310 Crystal Structure Of The Ligase Domain From M. Tube 3e-07
>pdb|4HTO|A Chain A, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv Apo Form Length = 240 Back     alignment and structure 
Iteration: 1

 Score =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 92/213 (43%), Positives = 137/213 (64%), Gaps = 17/213 (7%)
Query: 12  LVSLFNWIQKTKPAAKKRSKFRKFLDT-----------YCDSVD-YFSALRLILPSLDRE 59
           L S    IQK+K  A+K   FR+FLD+           + D  D ++ A+RLILP L+RE
Sbjct: 19  LCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDVTDSFYPAMRLILPQLERE 78
Query: 60  RGSYGLKESVLANCLIDALGMSKDSADAVRLINWRK-GGAAPNAGNFPMVAAEVLQRRQG 118
           R +YG+KE++LA   I+ L + +D  DA++L+N+R   G   +AG+F M+A  VL+ R  
Sbjct: 79  RMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHGDAGDFAMIAYFVLKPR-C 137
Query: 119 MISGGLTIKELNDLLDRLASSENRAEKISV---LSTLIKKTNAQEMKWIIMIILKDLKLG 175
           +  G LTI+++NDLLD +AS+ +   K  +   L  LI +++A E KW+I +I+KDLKLG
Sbjct: 138 LQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSALEQKWLIRMIIKDLKLG 197
Query: 176 ISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKD 208
           +S+++IF  FH DA +L NVT DL+ VC +L D
Sbjct: 198 VSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHD 230
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus Length = 621 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|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|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From Archaeoglobus Fulgidus Length = 558 Back     alignment and structure
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The Nucleotidyltransferase (Adenylation) Domain Of Human Dna Ligase Iv Length = 139 Back     alignment and structure
>pdb|1VS0|A Chain A, Crystal Structure Of The Ligase Domain From M. Tuberculosis Ligd At 2.4a Length = 310 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 ?
Query665
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 1e-149
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 1e-144
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 1e-142
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 1e-137
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 1e-133
1vs0_A310 Putative DNA ligase-like protein RV0938/MT0965; OB 7e-54
1a0i_A348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 1e-40
3vnn_A139 DNA ligase 4; non-homologous END joining, DNA repa 6e-38
1fvi_A297 Chlorella virus DNA ligase-adenylate; adenylated D 3e-21
2vug_A389 PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transfe 1e-09
3qwu_A370 DNA ligase; structural genomics, PSI-2, midwest ce 8e-07
3kyh_C461 MRNA-capping enzyme subunit alpha; 5' modification 3e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-04
1ckm_A330 MRNA capping enzyme; nucleotidyltransferase; HET: 8e-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 =  444 bits (1144), Expect = e-149
 Identities = 139/613 (22%), Positives = 234/613 (38%), Gaps = 67/613 (10%)

Query: 12  LVSLFNWIQKTKPAAKKRSKFRKFLDTYCD----SVDYFSALRLILPSLDRERGSYGLKE 67
              L   +        K    + FL           D +  ++L+LP     +  Y L +
Sbjct: 12  FRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLP--GVIKTVYNLND 69

Query: 68  SVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGL 124
             +          + D                   G+         ++ +         L
Sbjct: 70  KQIVKLFSRIFNCNPDDMARDL-----------EQGDVSETIRVFFEQSKSFPPAAKSLL 118

Query: 125 TIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHE 184
           TI+E+++ L RL+      E+   L  +  +  A ++K II +I  DLK+    K +   
Sbjct: 119 TIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDA 178

Query: 185 FHPDAEDLFNVTCDLKLVCEKLKDRNQR---------HKRQDIEVGKAVRPQLAMRIGDA 235
             P+A + F  + +L+ V E++    Q                 +   V+P LA      
Sbjct: 179 LDPNAYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSV 238

Query: 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE--YGHAMSKIIEQNVL 293
             A +K     +  E K+DG+R+Q+HKNG    YFSRS          H    I +    
Sbjct: 239 EYAMKKCPNG-MFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPG 297

Query: 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIH 353
               ILD E+L+ D    +   FG+     KAA      D  +C F FD +Y  D S++ 
Sbjct: 298 GHSMILDSEVLLIDNKTGKPLPFGTLGVHKKAAFQ----DANVCLFVFDCIYFNDVSLMD 353

Query: 354 QSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI 413
           + L ER + L   +     R+                             ++       I
Sbjct: 354 RPLCERRKFLHDNMVEIPNRIM-FSE----------------MKRVTKALDLADMITRVI 396

Query: 414 ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGS---DLDVLIIGGYYGSGRRGGEV 470
           +   EG+VLKD+   +EPG R   WLK+K +Y+  G+     D++++G +YG G +GG +
Sbjct: 397 QEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKGGMM 454

Query: 471 AQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 530
           + FL+   +   P +  +++ +  +   G  D  L  +  +L     K        PS+ 
Sbjct: 455 SIFLMGCYD---PGS--QKWCTVTKCAGGHDDATLARLQNELDMV--KISKDPSKIPSWL 507

Query: 531 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 590
           +V  N    PD  +  P+K+ +  IT    +      +   S+RFPR  R+R DK W   
Sbjct: 508 KV--NKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHTADGISIRFPRCTRIRDDKDWKSA 565

Query: 591 LDVQSFVELVHSS 603
            ++    EL   S
Sbjct: 566 TNLPQLKELYQLS 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
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* Length = 621 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
>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
>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
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens} Length = 139 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
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP; 2.9A {Pyrococcus abyssi GE5} Length = 389 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} Length = 370 Back     alignment and structure
>3kyh_C MRNA-capping enzyme subunit alpha; 5' modification, triphosphatase, guanylyltransferase, complex, hydrolase, mRNA processing, nucleus; 3.00A {Saccharomyces cerevisiae} Length = 461 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
>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* Length = 330 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query665
3l2p_A579 DNA ligase 3; DNA ligase, DNA repair, ATP-binding, 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
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 100.0
1vs0_A310 Putative DNA ligase-like protein RV0938/MT0965; OB 100.0
1a0i_A348 DNA ligase; DNA replication; HET: DNA ATP; 2.60A { 100.0
1fvi_A297 Chlorella virus DNA ligase-adenylate; adenylated D 100.0
4htp_A240 DNA ligase 4; helical domain, DNA binding domain, 100.0
1p16_A395 GTP--RNA, mRNA capping enzyme alpha subunit; guany 100.0
1ckm_A330 MRNA capping enzyme; nucleotidyltransferase; HET: 99.97
3vnn_A139 DNA ligase 4; non-homologous END joining, DNA repa 99.95
3kyh_C461 MRNA-capping enzyme subunit alpha; 5' modification 99.9
3rtx_A343 MRNA-capping enzyme; guanylyltransferase, RNA poly 99.9
2vug_A389 PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transfe 99.52
3qwu_A370 DNA ligase; structural genomics, PSI-2, midwest ce 99.42
1ta8_A332 DNA ligase, NAD-dependent; nucleotidyl transferase 98.1
1s68_A249 RNA ligase 2; ribonucleic acid ligase, RNA repair; 98.03
2hvq_A335 ORF1, hypothetical 37.6 kDa protein in GP24-HOC in 98.02
1b04_A318 Protein (DNA ligase); DNA replication; 2.80A {Geob 97.96
4glw_A305 DNA ligase; inhibitor, ligase-ligase inhibitor com 97.65
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 97.58
3uq8_A322 DNA ligase; adenylated protein, ATP-grAsp, rossman 97.51
1zau_A328 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacteriu 97.46
1xk5_A204 Snurportin-1; protein-RNA-complex, transport prote 97.41
3jsl_A318 DNA ligase; NAD+-dependent, DNA damage, DNA repair 97.37
3gjx_B365 Snurportin-1; transport, cytoplasm, nucleus, RNA-b 97.19
1xdn_A277 RNA editing ligase MP52; HET: MSE ATP; 1.20A {Tryp 97.02
2owo_A 671 DNA ligase; protein-DNA complex, ligase-DNA comple 97.01
2c5u_A375 RNA ligase, T4 RNA ligase 1; nucleotidyl transfera 96.84
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 96.71
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 96.48
4e6n_A427 Metallophosphoesterase; RNA repair, RNA ligase, li 96.19
2hiv_A621 Thermostable DNA ligase; ATP-dependent, open confo 94.07
2cfm_A561 Thermostable DNA ligase; protein-nucleotide comple 89.55
3gde_A558 DNA ligase; DNA-binding domain, adenylation domain 89.34
1x9n_A688 DNA ligase I; 5'-adenylated nicked DNA, protein-DN 85.81
>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
Probab=100.00  E-value=1.2e-107  Score=923.30  Aligned_cols=553  Identities=25%  Similarity=0.415  Sum_probs=451.0

Q ss_pred             CCCCcHHHHHHHHHHHHhcCChhHHHHHHHHHhhhcCCC----chHhhhHhhcCCCCCCCccccCCCHHHHHHHHHHHhC
Q 006003            4 TEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALG   79 (665)
Q Consensus         4 ~~~~~F~~l~~~~e~i~~~~~~~~k~~~l~~~~~~~~~~----~~~~~~lrLllp~~d~~r~~yglke~~L~k~~~~~~~   79 (665)
                      .++|+|++||++|++|++++++.+|+++|++||.+|..+    .++||++|+|+|+.|+  ++|||+|++|+|+|++++|
T Consensus         4 ~~d~~F~~f~~l~~~ie~~s~r~~k~~il~~~~~~~~~~~~~~~~~y~~~~~l~P~~~~--~~~gi~ek~l~k~~~~~~g   81 (579)
T 3l2p_A            4 HKDCLLREFRKLCAMVADNPSYNTKTQIIQDFLRKGSAGDGFHGDVYLTVKLLLPGVIK--TVYNLNDKQIVKLFSRIFN   81 (579)
T ss_dssp             SGGGBHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCC-------CCHHHHHHHHCTTTSC--CCCSCCHHHHHHHHHHHHT
T ss_pred             cccCcHHHHHHHHHHHHhccChHHHHHHHHHHHHhcCCcccccchHHHHHHHhCCCccC--cccCCcHHHHHHHHHHHHC
Confidence            457999999999999999999999999999999998543    5899999999999974  6999999999999999999


Q ss_pred             CCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhc--cCC-CCCCCCHHHHHHHHHHHHhhhhHHhHHHHHHHHHHhC
Q 006003           80 MSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRR--QGM-ISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT  156 (665)
Q Consensus        80 ~~~~~~~~~~L~~wk~~~~~~~~gD~~~~~~~v~~~r--~~~-~~~~lTi~eV~~~Ld~la~~~~~~~k~~~l~~ll~~~  156 (665)
                      ++.++  ..++  |       ..||||.+|..++..+  +.. .+++|||.|||+.|++||+.++...+.++|+.|+.+|
T Consensus        82 ~~~~~--~~~~--~-------~~GD~~~~~~~~~~~~~~~~~~~~~~LTv~~V~~~L~~ia~~~g~~sq~~~l~~l~~~~  150 (579)
T 3l2p_A           82 CNPDD--MARD--L-------EQGDVSETIRVFFEQSKSFPPAAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRC  150 (579)
T ss_dssp             SCHHH--HHHH--G-------GGSCHHHHHHHHHHSCSSSCCCSSCCCBHHHHHHHHHHHHTCCSHHHHHHHHHHHHTTC
T ss_pred             cCHHH--HHHH--H-------HcCCHHHHHHHHHhcccCCCCCCCCCccHHHHHHHHHHHHhccCcHHHHHHHHHHHHhC
Confidence            98753  3333  3       2599999988776543  322 3579999999999999999999888889999999999


Q ss_pred             CHHHHHHHHHHHHhhhccCCcccccccccCcCHHHHHhhhCCHHHHHHHHhhhhh---------ccccCCccCCCccccc
Q 006003          157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQ---------RHKRQDIEVGKAVRPQ  227 (665)
Q Consensus       157 t~~E~k~l~RiilkdlriG~~e~til~~~hp~a~~~~~~~~dL~~v~~~l~~~~~---------~~~~~~i~~g~~~~Pm  227 (665)
                      ||.|+|||+|+|+++||+|++++||+.+|||+|.++|++++||+.||+.+.+...         .+....+.+|.||+||
T Consensus       151 ~~~E~k~l~R~i~~~lriG~~e~~vl~a~~~~a~~~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~PM  230 (579)
T 3l2p_A          151 TANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPM  230 (579)
T ss_dssp             CSHHHHHHHHHHTTCCSSSCCHHHHHHTTCTTHHHHHHHSCCHHHHHHHHHHHHHSCC--------CCCCCCTTSCCCCC
T ss_pred             CHHHHHHHHHHHHhhhhcccchhHHHHHhCHHHHHHHhhcCCHHHHHHHHHhhchhhhcccccccccccccCCCCCCCCc
Confidence            9999999999999999999999999999999999999999999999988764321         1223457889999999


Q ss_pred             cccccCCHHHHHHHhcCCceEEEEeeceeEEEEEEeCCEEEEEecCCCCCCc-chhhhHHHHHhhc-cccceeeeceEEE
Q 006003          228 LAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNV-LVDRCILDGEMLV  305 (665)
Q Consensus       228 LA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~g~~v~~~SR~g~d~t~-~~p~l~~~~~~~~-~~~~~ILDGElv~  305 (665)
                      ||+++.+++++++++.+ .|++|+||||+|||+|++|+++++|||||++++. ..+.+.+.+...+ ...++|||||||+
T Consensus       231 LA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~g~~v~l~SR~g~~~~p~~~~~l~~~l~~~~~~~~~~iLDGElv~  309 (579)
T 3l2p_A          231 LAEACKSVEYAMKKCPN-GMFSEIKYDGERVQVHKNGDHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMILDSEVLL  309 (579)
T ss_dssp             EEEECCCHHHHHHHCTT-CEEEEECCCSEEEEEEEETTEEEEECTTSCBCCGGGTTTGGGTHHHHSTTCSEEEEEEEEEE
T ss_pred             cCCcCCCHHHHHhhCCC-CeEEEEccCcEEEEEEEECCEEEEECCCCCccChhHHHHHHHHHHHhcCcCCceEEEeEEEE
Confidence            99999999888888754 7999999999999999999999999999999842 2223333332223 2468999999999


Q ss_pred             eeCCCCccccccchHHHHHHhhcCCCCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCCCcceecccCCCCCc
Q 006003          306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNS  385 (665)
Q Consensus       306 ~d~~~~~~~~F~~lq~~~~~~~~~~~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~p~~~~~~  385 (665)
                      ||+.+++++||+.++...+..    ..+.+++|++|||||+||+++++.||.+||++|++++.+.++++.+..       
T Consensus       310 ~d~~~g~~~~F~~L~~~~~~~----~~~~~v~~~vFDlL~l~G~~L~~~Pl~eRr~~L~~~~~~~~~~i~~~~-------  378 (579)
T 3l2p_A          310 IDNKTGKPLPFGTLGVHKKAA----FQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSE-------  378 (579)
T ss_dssp             BCTTTCCBCCGGGGSHHHHHH----CSSCCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHCCCBTTTEEECC-------
T ss_pred             EeCCCCcccCHHHHHHHhhhh----cccCCeEEEEEEeeccCCCccccCCHHHHHHHHHHHhhcCCCeEEEee-------
Confidence            998778889999987543322    124689999999999999999999999999999999987766654321       


Q ss_pred             cccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEeecCCCCCccCCCCCCeEEEccccccC---CCcceEEEEEEEec
Q 006003          386 HVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRA---GSDLDVLIIGGYYG  462 (665)
Q Consensus       386 ~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K~~~s~Y~~GkRs~~WlKiK~~y~~~---g~~~DlvVIG~~~G  462 (665)
                                +..+.+.+++.++|++++++|+||||+|+++|+|+||+|  +|+|+|++|+++   ++++|+||||+++|
T Consensus       379 ----------~~~~~~~~~~~~~~~~a~~~g~EGlv~K~~ds~Y~~Grr--~WlK~K~~y~~~g~~~~t~D~vViG~~~G  446 (579)
T 3l2p_A          379 ----------MKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYG  446 (579)
T ss_dssp             ----------EEEECSHHHHHHHHHHHHHTTCCCEEEEESSCCCCTTCE--EEEEECTTTCC---CCEEEEEEEEEEECC
T ss_pred             ----------eEEcCCHHHHHHHHHHHHHhCCCceEEecCcCCCCCCCe--eeEEEechhhccccccccccEEEEEEEeC
Confidence                      223467889999999999999999999999999999988  899999999974   57999999999999


Q ss_pred             CCCCCCccceEEEEEeeCCCCCCCCcceEEEEEeccCCCHHHHHHHHHhhccccccccCCCCCCCCceeecCCCCCCCcE
Q 006003          463 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV  542 (665)
Q Consensus       463 ~g~r~g~~~sfllg~~d~~~~~~~~~~~~~~~kVgsG~s~~~~~~l~~~l~~~~~~~~~~~~~pp~~~~~~~~~~~~pd~  542 (665)
                      +|+++|.+|+|+||++|+++     ++|+++||||||||++++++|.+.|.+++...  +...+|.|+...  ....||+
T Consensus       447 ~Gkr~g~~g~lllg~~d~~~-----~~l~~vgkvgtGftd~~l~~l~~~l~~~~~~~--~~~~~~~~~~~~--~~~~pd~  517 (579)
T 3l2p_A          447 QGSKGGMMSIFLMGCYDPGS-----QKWCTVTKCAGGHDDATLARLQNELDMVKISK--DPSKIPSWLKVN--KIYYPDF  517 (579)
T ss_dssp             CTTSCSSCCEEEEEEECTTT-----SSEEEEEEECTTCCHHHHHHTTTSSCCCCCCC-----------------------
T ss_pred             CCCCCCceeEEEEEEEeCCC-----CeEEEecCccCCCCHHHHHHHHHHhhcccccc--CCccCCceeecC--CCCCCcE
Confidence            99999999999999998653     37999999999999999999999999987542  112245676553  3568999


Q ss_pred             EEeCCCceEEEEEeeeceecccCccC-CCeeeeccEEEEEecCCCccCCCCHHHHHHHHHcc
Q 006003          543 WIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS  603 (665)
Q Consensus       543 wi~~P~~s~v~ev~a~~~~~~s~~~~-~g~sLRfPr~~riR~DK~~~d~~t~~el~~l~~~~  603 (665)
                      |+..|+.++|+||+++..+ .|+.|+ .|++||||||.|+|+||+|+||+|++++.+||+.+
T Consensus       518 ~~~~P~~~~V~Ei~~~~i~-~S~~~~~~G~sLRFPR~~riR~DK~~~ea~t~~~l~~l~~~~  578 (579)
T 3l2p_A          518 IVPDPKKAAVWEITGAEFS-KSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLS  578 (579)
T ss_dssp             -------CEEEEEEESCEE-ECTTSSSTTEEESSCEECCCCSSCCSSSSCBHHHHHHHHHTC
T ss_pred             EEecCCCCeEEEEEeeEEe-ecCCcccCCEEEECCeEEEEeCCCChHHCCCHHHHHHHHhhc
Confidence            9844888899999965443 567665 79999999999999999999999999999999754
>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
>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
>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
>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
>4htp_A DNA ligase 4; helical domain, DNA binding domain, DNA, ligase-HYD complex; HET: DNA; 2.25A {Homo sapiens} PDB: 4hto_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
>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
>3vnn_A DNA ligase 4; non-homologous END joining, DNA repair, XRCC4; HET: DNA; 2.90A {Homo sapiens} 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
>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
>2vug_A PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; HET: ANP; 2.9A {Pyrococcus abyssi GE5} 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
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A* Back     alignment and structure
>1s68_A RNA ligase 2; ribonucleic acid ligase, RNA repair; HET: AMP; 1.90A {Enterobacteria phage T4} SCOP: d.142.2.4 Back     alignment and structure
>2hvq_A ORF1, hypothetical 37.6 kDa protein in GP24-HOC intergenic region; RNA, ligase, lysine adenylate; HET: APK; 2.40A {Enterobacteria phage T4} PDB: 2hvr_A* 2hvs_A* Back     alignment and structure
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Geobacillus stearothermophilus} SCOP: d.142.2.2 Back     alignment and structure
>4glw_A DNA ligase; inhibitor, ligase-ligase inhibitor complex; HET: DNA 0XT NMN; 2.00A {Streptococcus pneumoniae} Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>3uq8_A DNA ligase; adenylated protein, ATP-grAsp, rossman fold, adenylation; HET: DNA NAD AMP; 1.70A {Haemophilus influenzae} PDB: 3pn1_A* 3bac_A* Back     alignment and structure
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Back     alignment and structure
>1xk5_A Snurportin-1; protein-RNA-complex, transport protein; HET: TPG; 2.40A {Homo sapiens} Back     alignment and structure
>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} SCOP: d.142.2.2 PDB: 3jsn_A* Back     alignment and structure
>3gjx_B Snurportin-1; transport, cytoplasm, nucleus, RNA-binding, acetylation, GTP-binding, HOST-virus interaction, nucleotide-binding, phosphoprotein; HET: GTP; 2.50A {Homo sapiens} PDB: 3nby_B* 3nbz_B* 3nc0_B* 3gb8_B 2qna_B Back     alignment and structure
>1xdn_A RNA editing ligase MP52; HET: MSE ATP; 1.20A {Trypanosoma brucei} SCOP: d.142.2.4 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
>2c5u_A RNA ligase, T4 RNA ligase 1; nucleotidyl transferase, ATP-binding; HET: APC; 2.21A {Bacteriophage T4} Back     alignment and structure
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} 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
>4e6n_A Metallophosphoesterase; RNA repair, RNA ligase, ligase-activating, protein binding; HET: AMP; 2.39A {Clostridium thermocellum} PDB: 4drf_A* 3ty9_A* 3ty8_A* 3ty5_A* Back     alignment and structure
>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A {Sulfolobus solfataricus} PDB: 2hix_A* 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
>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
>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

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 665
d1x9na3220 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human ( 6e-36
d1x9na2148 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (H 9e-29
d1a0ia2239 d.142.2.1 (A:2-240) ATP-dependent DNA ligase, N-te 1e-21
d1x9na1272 a.235.1.1 (A:262-533) DNA ligase I (LIG1) {Human ( 1e-17
d1fvia2188 d.142.2.1 (A:2-189) ATP-dependent DNA ligase, N-te 3e-16
d1s68a_233 d.142.2.4 (A:) RNA ligase 2, N-terminal domain {Ba 2e-14
d1p16a2245 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subu 2e-12
d1ckma2228 d.142.2.3 (A:11-238) RNA guanylyltransferase (mRNA 2e-09
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 220 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  132 bits (333), Expect = 6e-36
 Identities = 57/234 (24%), Positives = 105/234 (44%), Gaps = 22/234 (9%)

Query: 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLD 276
           +  G  ++P LA          ++        E K+DG R QIH   G E+  FSR+  D
Sbjct: 1   LSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQED 60

Query: 277 HSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDR 334
           ++     +   I +  L  V   ILD E + WD    +   F       +   D      
Sbjct: 61  NTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQV 120

Query: 335 QLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPC 394
           Q+C +AFD++Y+   S++ + L  R +LL++    ++G                      
Sbjct: 121 QVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEF-----------------VFA 163

Query: 395 WSLVAHNVDEVEKFFKETIENRDEGIVLK--DLGSKWEPGDRSGKWLKLKPEYI 446
            SL   +++++ +F ++++++  EG+++K  D+ + +E   RS  WLKLK +Y+
Sbjct: 164 TSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYL 217
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 148 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
>d1x9na1 a.235.1.1 (A:262-533) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Length = 272 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
>d1s68a_ d.142.2.4 (A:) RNA ligase 2, N-terminal domain {Bacteriophage T4 [TaxId: 10665]} Length = 233 Back     information, alignment and structure
>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]} Length = 245 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]} Length = 228 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 ?
Query665
d1x9na3220 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 100.0
d1x9na2148 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 99.97
d1a0ia2239 ATP-dependent DNA ligase, N-terminal domain {Bacte 99.97
d1fvia2188 ATP-dependent DNA ligase, N-terminal domain {Chlor 99.96
d1x9na1272 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 99.96
d1ckma2228 RNA guanylyltransferase (mRNA capping enzyme), N-t 99.79
d1p16a2245 mRNA capping enzyme alpha subunit {Yeast (Candida 99.78
d1s68a_233 RNA ligase 2, N-terminal domain {Bacteriophage T4 99.45
d1a0ia1109 ATP-dependent DNA ligase {Bacteriophage T7 [TaxId: 98.21
d1fvia1104 ATP-dependent DNA ligase {Chlorella virus PBCV-1 [ 97.96
d1b04a_312 Adenylation domain of NAD+-dependent DNA ligase {B 97.46
d1ta8a_313 Adenylation domain of NAD+-dependent DNA ligase {E 97.33
d1xdna_265 RNA editing ligase MP52 {Trypanosoma brucei [TaxId 96.25
d1dgsa3314 Adenylation domain of NAD+-dependent DNA ligase {T 96.17
d1x9na1272 DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 92.37
>d1x9na3 d.142.2.1 (A:534-753) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: ATP-grasp
superfamily: DNA ligase/mRNA capping enzyme, catalytic domain
family: ATP-dependent DNA ligase catalytic domain
domain: DNA ligase I (LIG1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.5e-46  Score=371.69  Aligned_cols=210  Identities=27%  Similarity=0.533  Sum_probs=175.9

Q ss_pred             ccCCCccccccccccCCHHHHHHHhcCCceEEEEeeceeEEEEEE-eCCEEEEEecCCCCCCcchhhhHHHHHhhc--cc
Q 006003          218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKIIEQNV--LV  294 (665)
Q Consensus       218 i~~g~~~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~qih~-~g~~v~~~SR~g~d~t~~~p~l~~~~~~~~--~~  294 (665)
                      |+||.|++||||+++.+.++.++++.+.+|++|+||||+|||+|+ ++++|++|||+|+++|..+|++.+.+....  ..
T Consensus         1 ~~pg~P~~PMLA~~~~~~~~~~~~~~~~~~~~e~K~DG~R~~i~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~~~~~~~~   80 (220)
T d1x9na3           1 LSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSV   80 (220)
T ss_dssp             CCTTSCCCCCEEEEESSHHHHHHHTTTSCEEEEEEESSEEEEEEECTTSCEEEECTTSCBCTTTCHHHHHTSGGGBCTTC
T ss_pred             CCCCCCCCCeeCCCCCChHHHHhhcCCCcEEEEEeECcEEEEEEEECCCEEEEEeCCCccccccchhHHHHHHHhhcCCC
Confidence            589999999999999988888899988999999999999999998 578999999999999999999876543322  24


Q ss_pred             cceeeeceEEEeeCCCCccccccchHHHHHHhhcCC---CCCCceEEEEEEEEeeCCccccCCCHHHHHHHHHhhcCCCC
Q 006003          295 DRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL---SSDRQLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK  371 (665)
Q Consensus       295 ~~~ILDGElv~~d~~~~~~~~F~~lq~~~~~~~~~~---~~~~~~~~~vFDiL~lng~~l~~~pl~eRr~~L~~~~~~~~  371 (665)
                      .++|||||||+||.....+.+|   +.+....+...   ....+++|+|||||++||+++++.||.+|+++|++++.+.+
T Consensus        81 ~~~iLDGEl~~~d~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~~~~~p~~eR~~~L~~~~~~~~  157 (220)
T d1x9na3          81 TSFILDTEAVAWDREKKQIQPF---QVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETE  157 (220)
T ss_dssp             CCEEEEEEEEEECTTTCSBCCH---HHHTTSCSSCCCGGGCCSEEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBCCBT
T ss_pred             cceeeeeeeEEecCCCCccchH---HHHhhhhhcccchhhhccccceEEEEEEEECCcchhhhhHHHHHHHHHHHhccCC
Confidence            6899999999999876655555   33322222111   12357999999999999999999999999999999998877


Q ss_pred             CcceecccCCCCCccccCCCCCccccccCCHHHHHHHHHHHHHcCCceEEee--cCCCCCccCCCCCCeEEEcccccc
Q 006003          372 GRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLK--DLGSKWEPGDRSGKWLKLKPEYIR  447 (665)
Q Consensus       372 ~~~~~~~p~~~~~~~v~~~~~~~~~~~~~~~~~i~~~~~~ai~~g~EGlV~K--~~~s~Y~~GkRs~~WlKiK~~y~~  447 (665)
                      +++.++.                 ...+++.+++.+++++++++|.||||+|  +++|+|++|+||.+|+|+||+|++
T Consensus       158 ~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGim~K~~~~~s~Y~~GkRs~~w~K~K~ey~d  218 (220)
T d1x9na3         158 GEFVFAT-----------------SLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD  218 (220)
T ss_dssp             TTEEECC-----------------EECCCCHHHHHHHHHHHHHTSEEEEEEEESSSSCSSCTTTCSEEEEEEEHHHHH
T ss_pred             CeEEEEE-----------------eeccCCHHHHHHHHHHHHHCCCceEEEeccCCCCCeecCCcCCCeEEEcccccC
Confidence            6654321                 3456789999999999999999999999  579999999999999999999975
>d1x9na2 b.40.4.6 (A:754-901) DNA ligase I (LIG1) {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
>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
>d1x9na1 a.235.1.1 (A:262-533) DNA ligase I (LIG1) {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
>d1p16a2 d.142.2.3 (A:1-245) mRNA capping enzyme alpha subunit {Yeast (Candida albicans) [TaxId: 5476]} 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
>d1a0ia1 b.40.4.6 (A:241-349) ATP-dependent DNA ligase {Bacteriophage T7 [TaxId: 10760]} 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
>d1b04a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1ta8a_ d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} Back     information, alignment and structure
>d1xdna_ d.142.2.4 (A:) RNA editing ligase MP52 {Trypanosoma brucei [TaxId: 5691]} Back     information, alignment and structure
>d1dgsa3 d.142.2.2 (A:1-314) Adenylation domain of NAD+-dependent DNA ligase {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1x9na1 a.235.1.1 (A:262-533) DNA ligase I (LIG1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure