254781172

254781172

NAD-dependent DNA ligase LigA

GeneID in NCBI database:8210197Locus tag:CLIBASIA_05395
Protein GI in NCBI database:254781172Protein Accession:YP_003065585.1
Gene range:-(1169109, 1171304)Protein Length:731aa
Gene description:NAD-dependent DNA ligase LigA
COG prediction:[L] NAD-dependent DNA ligase (contains BRCT domain type II)
KEGG prediction:ligA; NAD-dependent DNA ligase LigA (EC:6.5.1.2); K01972 DNA ligase (NAD+) [EC:6.5.1.2]
SEED prediction:DNA ligase (EC 6.5.1.2)
Pathway involved in KEGG:DNA replication [PATH:las03030]
Base excision repair [PATH:las03410]
Nucleotide excision repair [PATH:las03420]
Mismatch repair [PATH:las03430]
Subsystem involved in SEED:DNA Repair Base Excision;
NAD and NADP cofactor biosynthesis global
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-
MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
ccccccccHHHccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHccccEEEccccccccHHcccHHHHHHHHHHHHHHHccccccccEEEEEEcccEEEEEEEEcccEEEEEEEcccccccccccccccHHHHccHHccccccccEEEEEEEEEEHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcHHHHHccccEEEEEcccccccccccHHHHHHHHHHcccccccccEEEccHHHHHHHHHHHHHHHHcccccccEEEEEEccHHHHHHccccccccccHHHccccHHHEEEEEEEEEEEEcccEEEEEEEEEEEEEEccEEEEEEEEccHHHHHHccccccccccccccccccEEEEEEccccccEEcccHHHHcccccccccccccccccccEEEEccccccccccEEEEcccccccHHHHHHHHHEEEEccccccccccHHHHHHHHHccccccccccHHHHEEccHHHcccHHHHHcccccccHHHHHHHHHHHHHHcccHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHccccHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHcccEEEEcccccccEEEEccccccHHHHHHHcccEEEcHHHHHHHHHHcccEEEEEccc
cccccccccccccHHHHHHHHHHHHHHHHHcccEEEEccccccccHHHHHHHHHHHHHHHHccHHHccccccccccccccccHHHHcccccccccccccccccHHHHHHHHHHHHHHHcccccccEEEEEcccEccEEEEEEEEccEEEEEEEcccccccccHHHccccHHHcccccccccccEEEEEEEEEccHHHHHHHHHHHHHccccEcEccHHHHHHHHHHccHHHcccccEEEEEEEEEEccccccHHHHHHHHHHHccccccccEEEcccHHHHHHHHHHHHHHHccccccccEEEEEEccHHHHHHHccccccccEEEEEEccHHHHHEEEEcEEEEEcccccEcccEEEcEEEEEEEEEEccccccHHHHHHccccccccccccccEEccEEEEEEcccccHHHHHHHHHHcccccccEEccccccccccEEEEEcccccccccEEEEcccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccHHHHHHccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccHHHHHHHHHcHHHHHHHHHHHHHHHHccHHHHHHHHHHHcccccccHHHHHcccccHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccccEEEEEcccHHccHHHHHHHHHHcccEEEEEEcccccEEEEcccccHHHHHHHHcccEEEcHHHHHHHHHHHccHEEEcccc
mkkrqlipiEALSIEQARKELSSLEQEIsyhddcyyqyskpiilDSEYDALKRRCDAIAHafpdlarsedpngplnkiggemnlslfkvthsiptlslekiWNIEDLRKFITRIYRFWqkkddnsifftlepkidgtmITIRYEKGKFVYAAlrgdghsgedVSACIraiptiprvlslnipeiIEVRgevyiskndfLALNDEMIavgrkpyanprnaasgilrrlnptdiTRYLNFFVHglgktseiFAKGQYEMLQKMRclgfpvnngvrqaNTFHGIVSYYNEMKSirstlpydidglvykVDEFSLQkqlgerarsprwmisHKFAEKQASTrlldidiqigrtgiltpvarlepvniggalitnatlhnedyikgldasgkvmrggrdirvgDRVLVKRAGEVIPKVVDIIVnerhpdaqpfsfpsfcpicqsrvvrdlnpktgklVAAHRCTGGLACSAQQLERLKHFVsrdafnieglgkqqldfffksedpafsiripadiFTLQRRQQTSTTKIenilgfgdvsvTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIahnnddwlsLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEvspsigrheknvsseienkkLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSrktdiiivgdnpgsklEKAQQLGVKIMNEEQFLFLLQQYNTtlrihddd
mkkrqlipieaLSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHafpdlarsedpNGPLNKIGGEMNLSLFKVTHSiptlslekiwniEDLRKFITRIYRfwqkkddnsifftlepkidgtMITIRYEKGKFVYAALRGDGHSGEDVSACIRAiptiprvlslniPEIIEVRGEVYISKNDFLALNDEMIAVGRkpyanprnaasgilRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQlgerarsprwmiSHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALItnatlhnedYIKGLdasgkvmrggrdirvgdrvlvkragevipkvvDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTsttkienilgfgdvsVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVspsigrheknvsseienkkLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDiiivgdnpgskLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKvmrggrdirvgdrvlvKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
*****************RKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSP************IENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQ************
MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
********IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRI****
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MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD
MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTDITRYLNFFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQYNTTLRIHDDD

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
254781196119 DNA ligase, NAD-dependent [Candidatus Liberibacter 9e-05
254780131119 DNA ligase, NAD-dependent [Candidatus Liberibacter 1e-04
>gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] Length = 119 Back     alignment
 Score = 40.4 bits (93), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 9   IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARS 68
           + +LS  +A  E+  L +   +H   YY+   P+  D  YD +  R DA+   FP+L   
Sbjct: 51  VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELF-- 108

Query: 69  EDPNGPLNKIG 79
            D + P N +G
Sbjct: 109 -DEDHPWNTVG 118

>gi|254780131|ref|YP_003064544.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] Length = 119 Back     alignment
 Score = 40.4 bits (93), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 9   IEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARS 68
           + +LS  +A  E+  L +   +H   YY+   P+  D  YD +  R DA+   FP+L   
Sbjct: 51  VTSLSKGEAMIEVEYLVKIALHHQKWYYRLDDPLFTDGLYDRVSERLDALQEQFPELF-- 108

Query: 69  EDPNGPLNKIG 79
            D + P N +G
Sbjct: 109 -DEDHPWNTVG 118

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
315122567739 NAD-dependent DNA ligase LigA [Candidatus Liberibacter 1 0.0
227822641717 NAD-dependent DNA ligase LigA [Sinorhizobium fredii NGR 1 0.0
86358438718 NAD-dependent DNA ligase LigA [Rhizobium etli CFN 42] L 1 0.0
209550159718 NAD-dependent DNA ligase LigA [Rhizobium leguminosarum 1 0.0
327194610718 DNA ligase (NAD+) protein [Rhizobium etli CNPAF512] Len 1 0.0
190892570718 DNA ligase (NAD+) protein [Rhizobium etli CIAT 652] Len 1 0.0
241205543718 NAD-dependent DNA ligase LigA [Rhizobium leguminosarum 1 0.0
222086432717 DNA ligase, NAD-dependent [Agrobacterium radiobacter K8 1 0.0
116253034718 NAD-dependent DNA ligase LigA [Rhizobium leguminosarum 1 0.0
150397271717 NAD-dependent DNA ligase LigA [Sinorhizobium medicae WS 1 0.0
>gi|315122567|ref|YP_004063056.1| NAD-dependent DNA ligase LigA [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 739 Back     alignment and organism information
 Score =  999 bits (2583), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 486/725 (67%), Positives = 582/725 (80%), Gaps = 5/725 (0%)

Query: 1   MKKRQLIPIEALSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAH 60
           M  R+ IPIE LS EQA+KELS L+ EISYHDD YYQ+S+P ILD EYD LK RCDAIA 
Sbjct: 1   MANRKFIPIEELSPEQAKKELSFLQHEISYHDDLYYQHSQPKILDFEYDQLKERCDAIAR 60

Query: 61  AFPDLARSEDPNGPLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQK 120
           AFP+ A   D NGPLNKIGGE N SLFK+THS P  SLEK   IED+  F+T+IYR  +K
Sbjct: 61  AFPEFASLADSNGPLNKIGGEKNFSLFKITHSPPMRSLEKSHQIEDINYFMTKIYRDLKK 120

Query: 121 KDDNSIFFTLEPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLN 180
              NSI FTLEPKIDG  ++IRYE+GKFV+A LRGDG+ GEDVSA I  +  IP+VLS  
Sbjct: 121 DCYNSIVFTLEPKIDGASLSIRYEQGKFVHAGLRGDGYIGEDVSANISMMSIIPQVLSFK 180

Query: 181 IPEIIEVRGEVYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTD---ITRYLN 237
           +PEI EVRGE+YISK DF  LN+EM    +K Y+NPRN  +G+LR  N T    I+RYL 
Sbjct: 181 VPEIFEVRGEIYISKKDFFVLNEEMRTTKKKLYSNPRNTVAGLLRSRNQTSKSRISRYLK 240

Query: 238 FFVHGLGKTSEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPY 297
           FFVHG+G  SE FA GQYEMLQKMR LGFPVN  ++QA+T  GIVSYY+E   IRS+LPY
Sbjct: 241 FFVHGIGTISEKFADGQYEMLQKMRALGFPVNERIQQAHTLEGIVSYYDETALIRSSLPY 300

Query: 298 DIDGLVYKVDEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVAR 357
           DIDG+VYKVD F+LQ+QLGER+RSP W ISHKF++++ ST LL IDIQIGRTG+LTP+AR
Sbjct: 301 DIDGIVYKVDSFTLQQQLGERSRSPIWAISHKFSDEEFSTPLLGIDIQIGRTGMLTPIAR 360

Query: 358 LEPVNIGGALITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDII 417
            E +N+GG  ++NATLHNE+YIKGLD+SGK++RGGRDIR+GD +LVKRAG+VIPKV D+I
Sbjct: 361 FESINMGGVFVSNATLHNENYIKGLDSSGKIIRGGRDIRIGDMILVKRAGDVIPKVTDVI 420

Query: 418 VNERHPDAQPFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVS 477
           + ER  D+Q FSFPS CP+CQS+VVR +NPKTGKL ++H CTGGL C AQQLE LK+FVS
Sbjct: 421 MEERPIDSQMFSFPSSCPVCQSKVVRAVNPKTGKLGSSHYCTGGLMCPAQQLEYLKYFVS 480

Query: 478 RDAFNIEGLGKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTN 537
           RDAFNIEGLG++QLDFFFKSEDP+FSIRIPADIFTLQ RQQTS  K+ENI GF  VSVTN
Sbjct: 481 RDAFNIEGLGEKQLDFFFKSEDPSFSIRIPADIFTLQHRQQTSFKKLENIPGFAHVSVTN 540

Query: 538 LYDSINKRRNISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLS 597
           LYDSINKRRNISL+RFIFSLGI HVG EIARSLA++Y SYQNF  EI NI+   ND  +S
Sbjct: 541 LYDSINKRRNISLQRFIFSLGIHHVGIEIARSLAQFYRSYQNFETEIKNILDKKNDADVS 600

Query: 598 LIRVPLVGDIIAQAIVEFYQNPRNICAVEALLKEVSPSIGRHEKNVS--SEIENKKLVFT 655
           L +V LVGD++AQ+I+ FYQNP N  A+ ALL E+S S+   +++ S  S + NK+LVFT
Sbjct: 601 LKKVALVGDMVAQSIIAFYQNPENNRAIAALLNEISLSVWDSQEDNSRNSILANKRLVFT 660

Query: 656 GTLQKIQRHKAQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFL 715
           GTLQKI RH+AQE V QLGA+VS+ +S KT I++VGDN GSKL KA+QLG++I+NEEQFL
Sbjct: 661 GTLQKITRHQAQEAVKQLGAIVSSTISHKTHIVVVGDNAGSKLNKARQLGIEIVNEEQFL 720

Query: 716 FLLQQ 720
            L+ +
Sbjct: 721 SLISE 725


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227822641|ref|YP_002826613.1| NAD-dependent DNA ligase LigA [Sinorhizobium fredii NGR234] Length = 717 Back     alignment and organism information
>gi|86358438|ref|YP_470330.1| NAD-dependent DNA ligase LigA [Rhizobium etli CFN 42] Length = 718 Back     alignment and organism information
>gi|209550159|ref|YP_002282076.1| NAD-dependent DNA ligase LigA [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 718 Back     alignment and organism information
>gi|327194610|gb|EGE61460.1| DNA ligase (NAD+) protein [Rhizobium etli CNPAF512] Length = 718 Back     alignment and organism information
>gi|190892570|ref|YP_001979112.1| DNA ligase (NAD+) protein [Rhizobium etli CIAT 652] Length = 718 Back     alignment and organism information
>gi|241205543|ref|YP_002976639.1| NAD-dependent DNA ligase LigA [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 718 Back     alignment and organism information
>gi|222086432|ref|YP_002544966.1| DNA ligase, NAD-dependent [Agrobacterium radiobacter K84] Length = 717 Back     alignment and organism information
>gi|116253034|ref|YP_768872.1| NAD-dependent DNA ligase LigA [Rhizobium leguminosarum bv. viciae 3841] Length = 718 Back     alignment and organism information
>gi|150397271|ref|YP_001327738.1| NAD-dependent DNA ligase LigA [Sinorhizobium medicae WSM419] Length = 717 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
PRK07956665 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validate 0.0
TIGR00575652 TIGR00575, dnlj, DNA ligase, NAD-dependent 0.0
PRK14351689 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisio 1e-133
PRK14350669 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisio 6e-90
COG0272667 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT d 0.0
smart00532441 smart00532, LIGANc, Ligase N family 1e-139
cd00114307 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation 2e-86
pfam01653315 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase ad 3e-83
PRK08097562 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed 4e-36
pfam0312082 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-f 7e-27
COG5275276 COG5275, COG5275, BRCT domain type II [General function 4e-12
PRK06195309 PRK06195, PRK06195, DNA polymerase III subunit epsilon; 1e-09
smart0029280 smart00292, BRCT, breast cancer carboxy-terminal domain 7e-08
cd0002772 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1) 1e-07
pfam0053377 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain 4e-07
KOG1968 871 KOG1968, KOG1968, KOG1968, Replication factor C, subuni 6e-04
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent Back     alignment and domain information
>gnl|CDD|184640 PRK14351, ligA, NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|128805 smart00532, LIGANc, Ligase N family Back     alignment and domain information
>gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain Back     alignment and domain information
>gnl|CDD|145016 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation domain Back     alignment and domain information
>gnl|CDD|181228 PRK08097, ligB, NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>gnl|CDD|145978 pfam03120, DNA_ligase_OB, NAD-dependent DNA ligase OB-fold domain Back     alignment and domain information
>gnl|CDD|34872 COG5275, COG5275, BRCT domain type II [General function prediction only] Back     alignment and domain information
>gnl|CDD|180459 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>gnl|CDD|128588 smart00292, BRCT, breast cancer carboxy-terminal domain Back     alignment and domain information
>gnl|CDD|28909 cd00027, BRCT, Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain Back     alignment and domain information
>gnl|CDD|144208 pfam00533, BRCT, BRCA1 C Terminus (BRCT) domain Back     alignment and domain information
>gnl|CDD|37179 KOG1968, KOG1968, KOG1968, Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 100.0
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 100.0
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 100.0
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 100.0
smart00532441 LIGANc Ligase N family. 100.0
pfam01653315 DNA_ligase_aden NAD-dependent DNA ligase adenylation do 100.0
cd00114307 LIGANc NAD+ dependent DNA ligase adenylation domain. DN 100.0
pfam0312082 DNA_ligase_OB NAD-dependent DNA ligase OB-fold domain. 99.91
PRK06195309 DNA polymerase III subunit epsilon; Validated 99.77
PRK06063313 DNA polymerase III subunit epsilon; Provisional 99.37
PRK05601377 DNA polymerase III subunit epsilon; Validated 98.71
pfam0053377 BRCT BRCA1 C Terminus (BRCT) domain. The BRCT domain is 98.67
smart0029280 BRCT breast cancer carboxy-terminal domain. 98.46
cd0002772 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy- 98.18
KOG1929 811 consensus 95.5
KOG3226 508 consensus 92.48
pfam00763117 THF_DHG_CYH Tetrahydrofolate dehydrogenase/cyclohydrola 92.28
COG5275276 BRCT domain type II [General function prediction only] 99.53
PHA00454312 ATP-dependent DNA ligase 98.8
PRK09125277 DNA ligase; Provisional 98.56
COG1793444 CDC9 ATP-dependent DNA ligase [DNA replication, recombi 98.38
PRK09247537 ATP-dependent DNA ligase; Validated 97.89
PRK08224345 ligC ATP-dependent DNA ligase; Reviewed 97.68
LOAD_ligase184 consensus 98.69
cd07898201 Adenylation_DNA_ligase The Adenylation domain of ATP-de 98.55
cd07906186 Adenylation_DNA_ligase_LigD The Adenylation domain of M 98.37
cd07903227 Adenylation_DNA_ligase_IV The Adenylation domain of DNA 98.3
pfam01068190 DNA_ligase_A_M ATP dependent DNA ligase domain. This do 98.25
cd07907213 Adenylation_DNA_ligase_Bac2 The Adenylation domain of p 98.23
PRK07636269 ligB ATP-dependent DNA ligase; Reviewed 98.21
cd07896174 Adenylation_kDNA_ligase_like The Adenylation domain of 98.2
cd06846187 Adenylation_DNA_ligase_family The Adenylation domain of 98.09
cd07897208 Adenylation_DNA_ligase_Bac1 The Adenylation domain of p 98.07
cd07905194 Adenylation_DNA_ligase_LigC The Adenylation domain of M 97.9
TIGR02776645 NHEJ_ligase_prk DNA ligase D; InterPro: IPR014143 Membe 97.59
PHA02142366 putative RNA ligase 97.37
TIGR02779328 NHEJ_ligase_lig DNA polymerase LigD, ligase domain; Int 97.36
PRK05972832 ligD ATP-dependent DNA ligase; Reviewed 97.33
cd08039235 Adenylation_DNA_ligase_Fungal The Adenylation domain of 97.28
pfam09414183 RNA_ligase RNA ligase. This is a family of RNA ligases. 97.24
pfam09513356 consensus 95.54
cd07901207 Adenylation_DNA_ligase_Arch_LigB The Adenylation domain 98.46
cd07900219 Adenylation_DNA_ligase_I_Euk The Adenylation domain of 98.24
cd07902213 Adenylation_DNA_ligase_III The Adenylation domain of DN 97.83
cd07894340 Adenylation_RNA_ligase The Adenylation domain of RNA ci 97.59
COG1423382 ATP-dependent DNA ligase, homolog of eukaryotic ligase 97.24
KOG0967714 consensus 92.17
PRK03180509 ligB ATP-dependent DNA ligase; Reviewed 98.23
PRK01109589 ATP-dependent DNA ligase; Provisional 98.19
PRK09633604 ligD ATP-dependent DNA ligase; Reviewed 97.99
KOG0966881 consensus 92.23
KOG1968871 consensus 97.85
PRK13766764 Hef nuclease; Provisional 97.78
PRK00558609 uvrC excinuclease ABC subunit C; Validated 97.7
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recombinati 96.69
COG0322581 UvrC Nuclease subunit of the excinuclease complex [DNA 96.68
PRK01172674 ski2-like helicase; Provisional 96.45
COG0632201 RuvA Holliday junction resolvasome, DNA-binding subunit 96.21
smart00483 334 POLXc DNA polymerase X family. includes vertebrate poly 95.94
PRK13482352 DNA integrity scanning protein DisA; Provisional 95.63
PRK00254717 ski2-like helicase; Provisional 95.36
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 94.89
pfam01367100 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold. 94.84
PRK09482256 xni exonuclease IX; Provisional 94.82
COG1796326 POL4 DNA polymerase IV (family X) [DNA replication, rec 94.23
smart00475259 53EXOc 5'-3' exonuclease. 93.54
COG2231215 Uncharacterized protein related to Endonuclease III [DN 93.54
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 93.52
COG1623349 Predicted nucleic-acid-binding protein (contains the HH 91.09
KOG2841254 consensus 97.62
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 97.26
smart00483334 POLXc DNA polymerase X family. includes vertebrate poly 97.19
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 96.74
PRK13901196 ruvA Holliday junction DNA helicase motor protein; Prov 96.08
PRK08609570 hypothetical protein; Provisional 97.57
PRK09632753 ATP-dependent DNA ligase; Reviewed 97.44
TIGR00574705 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR0 96.83
pfam0311927 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger 96.62
TIGR00084217 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR 96.62
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 95.04
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 96.46
PRK00024224 radC DNA repair protein RadC; Reviewed 90.23
PRK07997 928 consensus 96.41
PRK07456 975 consensus 94.71
PRK07300 880 consensus 94.65
PRK08835 931 consensus 94.18
PRK08434 887 consensus 93.93
PRK02362736 ski2-like helicase; Provisional 93.44
PRK08609570 hypothetical protein; Provisional 96.15
PRK07898 902 consensus 95.96
PRK08928 861 consensus 95.61
PRK05797 869 consensus 95.23
PRK08076 877 consensus 94.93
PRK05929 870 consensus 94.8
PRK05755 889 DNA polymerase I; Provisional 94.63
PRK06887 954 consensus 94.52
PRK07556 977 consensus 94.37
PRK07625 922 consensus 94.24
PRK08786 927 consensus 94.15
TIGR00593 1005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 92.92
PRK00558609 uvrC excinuclease ABC subunit C; Validated 92.06
TIGR01448 769 recD_rel helicase, RecD/TraA family; InterPro: IPR00634 95.61
TIGR01083192 nth endonuclease III; InterPro: IPR005759 The spectrum 90.5
COG1796326 POL4 DNA polymerase IV (family X) [DNA replication, rec 95.56
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 91.08
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA replica 91.01
PRK00254717 ski2-like helicase; Provisional 94.57
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 94.56
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 90.75
TIGR01448 769 recD_rel helicase, RecD/TraA family; InterPro: IPR00634 94.1
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease dom 93.41
PRK01172674 ski2-like helicase; Provisional 93.39
PRK13913218 3-methyladenine DNA glycosylase; Provisional 92.38
smart00478149 ENDO3c endonuclease III. includes endonuclease III (DNA 91.06
PRK10702211 endonuclease III; Provisional 90.55
cd00056158 ENDO3c endonuclease III; includes endonuclease III (DNA 90.51
KOG2534353 consensus 93.1
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 90.26
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 92.63
PRK07220740 DNA topoisomerase I; Validated 92.07
COG0190283 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Meth 91.35
TIGR01239502 galT_2 galactose-1-phosphate uridylyltransferase; Inter 90.01
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 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
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated 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
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>smart00532 LIGANc Ligase N family Back     alignment and domain information
>pfam01653 DNA_ligase_aden NAD-dependent DNA ligase adenylation domain Back     alignment and domain information
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain Back     alignment and domain information
>pfam03120 DNA_ligase_OB NAD-dependent DNA ligase OB-fold domain Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>pfam00533 BRCT BRCA1 C Terminus (BRCT) domain Back     alignment and domain information
>smart00292 BRCT breast cancer carboxy-terminal domain Back     alignment and domain information
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain Back     alignment and domain information
>KOG1929 consensus Back     alignment and domain information
>KOG3226 consensus Back     alignment and domain information
>pfam00763 THF_DHG_CYH Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain Back     alignment and domain information
>COG5275 BRCT domain type II [General function prediction only] Back     alignment and domain information
>PHA00454 ATP-dependent DNA ligase Back     alignment and domain information
>PRK09125 DNA ligase; Provisional Back     alignment and domain information
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09247 ATP-dependent DNA ligase; Validated Back     alignment and domain information
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>LOAD_ligase consensus Back     alignment and domain information
>cd07898 Adenylation_DNA_ligase The Adenylation domain of ATP-dependent DNA Ligases is a component of the catalytic core unit Back     alignment and domain information
>cd07906 Adenylation_DNA_ligase_LigD The Adenylation domain of Mycobacterium tuberculosis LigD-like ATP-dependent DNA ligases is a component of the catalytic core unit Back     alignment and domain information
>cd07903 Adenylation_DNA_ligase_IV The Adenylation domain of DNA Ligase IV is a component of the catalytic core unit Back     alignment and domain information
>pfam01068 DNA_ligase_A_M ATP dependent DNA ligase domain Back     alignment and domain information
>cd07907 Adenylation_DNA_ligase_Bac2 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit Back     alignment and domain information
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd07896 Adenylation_kDNA_ligase_like The Adenylation domain of kDNA ligase and similar proteins, which is involved in kDNA replication or repair, is a component of the catalytic core unit Back     alignment and domain information
>cd06846 Adenylation_DNA_ligase_family The Adenylation domain of proteins from the ATP-dependent polynucleotide ligase family is the minimal catalytic unit that is common to all family members Back     alignment and domain information
>cd07897 Adenylation_DNA_ligase_Bac1 The Adenylation domain of putative bacterial ATP-dependent DNA ligases is inferred by similarity to be a component of the catalytic core unit Back     alignment and domain information
>cd07905 Adenylation_DNA_ligase_LigC The Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases is a component of the catalytic core unit Back     alignment and domain information
>TIGR02776 NHEJ_ligase_prk DNA ligase D; InterPro: IPR014143 Members of this entry are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NheJ) Back     alignment and domain information
>PHA02142 putative RNA ligase Back     alignment and domain information
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain; InterPro: IPR014146 DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes Back     alignment and domain information
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>cd08039 Adenylation_DNA_ligase_Fungal The Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins is inferred by similarity to be a component of the catalytic core unit Back     alignment and domain information
>pfam09414 RNA_ligase RNA ligase Back     alignment and domain information
>pfam09513 consensus Back     alignment and domain information
>cd07901 Adenylation_DNA_ligase_Arch_LigB The Adenylation domain of archaeal and bacterial LigB-like DNA ligases is a component of the catalytic core unit Back     alignment and domain information
>cd07900 Adenylation_DNA_ligase_I_Euk The Adenylation domain of eukaryotic DNA Ligase I is a component of the catalytic core unit Back     alignment and domain information
>cd07902 Adenylation_DNA_ligase_III The Adenylation domain of DNA Ligase III is a component of the catalytic core unit Back     alignment and domain information
>cd07894 Adenylation_RNA_ligase The Adenylation domain of RNA circularization protein, which catalyzes the circularization of RNA molecules in an ATP-dependent reaction, comprises the enzyme's catalytic 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
>KOG0967 consensus Back     alignment and domain information
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>PRK01109 ATP-dependent DNA ligase; Provisional Back     alignment and domain information
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>KOG0966 consensus Back     alignment and domain information
>KOG1968 consensus Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA Back     alignment and domain information
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold Back     alignment and domain information
>PRK09482 xni exonuclease IX; Provisional Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only] Back     alignment and domain information
>KOG2841 consensus Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>PRK09632 ATP-dependent DNA ligase; Reviewed Back     alignment and domain information
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1); InterPro: IPR000977 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
>pfam03119 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger domain Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 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
>PRK00024 radC DNA repair protein RadC; Reviewed Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO Back     alignment and domain information
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated 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
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO Back     alignment and domain information
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>PRK13913 3-methyladenine DNA glycosylase; Provisional Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>KOG2534 consensus Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism] Back     alignment and domain information
>TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase; InterPro: IPR000766 Galactose-1-phosphate uridyl transferase 2 Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
2owo_A671 Last Stop On The Road To Repair: Structure Of E.Col 1e-167
1dgs_A667 Crystal Structure Of Nad+-Dependent Dna Ligase From 1e-128
1v9p_A584 Crystal Structure Of Nad+-Dependent Dna Ligase Leng 2e-99
1ta8_A332 Structural Rearrangement Accompanying Nad+ Synthesi 3e-75
1tae_A332 Structural Rearrangement Accompanying Nad+ Synthesi 3e-75
1b04_A318 Structure Of The Adenylation Domain Of An Nad+ Depe 1e-74
3pn1_A318 Novel Bacterial Nad+-Dependent Dna Ligase Inhibitor 3e-73
1zau_A328 Adenylation Domain Of Nad+ Dependent Dna Ligase Fro 1e-68
3jsl_A318 Crystal Structure Of The Adenylation Domain Of Nad+ 7e-66
3bac_A270 Structural Basis For The Inhibition Of Bacterial Na 1e-47
1l7b_A92 Solution Nmr Structure Of Brct Domain Of T. Thermop 2e-28
2k7f_A109 Haddock Calculated Model Of The Complex Between The 2e-24
2ebu_A112 Solution Structure Of The Brct Domain From Human Re 2e-24
gi|149242732|pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna Ligase Bound To Nicked Dna-Adenylate Length = 671 Back     alignment and structure
 Score =  594 bits (1531), Expect = e-167,   Method: Composition-based stats.
 Identities = 244/711 (34%), Positives = 394/711 (55%), Gaps = 48/711 (6%)

Query: 14  IEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDPNG 73
           +E   ++L+ L   + +H+  Y+    P I D+EYD L R    +    P+L     P+ 
Sbjct: 1   MESIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELI---TPDS 57

Query: 74  PLNKIGGEMNLSLFKVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTLEPK 133
           P  ++G     +  ++ H +P LSL+ +++ E    F  R+      K++  + +  E K
Sbjct: 58  PTQRVGAAPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRL--KNNEKVTWCCELK 115

Query: 134 IDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNI-PEIIEVRGEVY 192
           +DG  ++I YE G  V AA RGDG +GED+++ +R I  IP  L     P  +EVRGEV+
Sbjct: 116 LDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVF 175

Query: 193 ISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPT-DITRYLNFFVHGLGK-TSEIF 250
           + +  F  +N++    G K +ANPRNAA+G LR+L+P     R L FF +G+G       
Sbjct: 176 LPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGEL 235

Query: 251 AKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKVDEFS 310
                  L + +  G PV++ V    +   ++++Y++++  R TL +DIDG+V KV+  +
Sbjct: 236 PDTHLGRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLA 295

Query: 311 LQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGALITN 370
            Q+QLG  AR+PRW ++ KF  ++  T + D++ Q+GRTG +TPVARLEPV++ G L++N
Sbjct: 296 QQEQLGFVARAPRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSN 355

Query: 371 ATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQPFSF 430
           ATLHN D I+ L            +R+GD+V+++RAG+VIP+VV+++++ER  D +   F
Sbjct: 356 ATLHNADEIERL-----------GLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVF 404

Query: 431 PSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGLGKQQ 490
           P+ CP+C S V R          A  RCTGGL C AQ+ E LKHFVSR A +++G+G + 
Sbjct: 405 PTHCPVCGSDVERVEGE------AVARCTGGLICGAQRKESLKHFVSRRAMDVDGMGDKI 458

Query: 491 LDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRRNISL 550
           +D   + E     +  PAD+F L         K+  +   G  S  N+ +++ K +  + 
Sbjct: 459 IDQLVEKE----YVHTPADLFKLTA------GKLTGLERMGPKSAQNVVNALEKAKETTF 508

Query: 551 ERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGDIIAQ 610
            RF+++LGIR VG   A  LA Y+ + +                   L +VP VG ++A 
Sbjct: 509 ARFLYALGIREVGEATAAGLAAYFGTLEALEAA----------SIEELQKVPDVGIVVAS 558

Query: 611 AIVEFYQNPRNICAVEALLKEVS---PSIGRHEKNVSSEIENKKLVFTGTLQKIQRHKAQ 667
            +  F+    N   +  LL E       I  + + + S    K +V TG+L ++ R  A+
Sbjct: 559 HVHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVLTGSLSQMSRDDAK 618

Query: 668 EYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLL 718
             + +LGA V+  +S+KTD++I G+  GSKL KAQ+LG+++++E + L LL
Sbjct: 619 ARLVELGAKVAGSVSKKTDLVIAGEAAGSKLAKAQELGIEVIDEAEMLRLL 669


>gi|11513386|pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T. Filiformis Length = 667 Back     alignment and structure
>gi|47169437|pdb|1V9P|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase Length = 584 Back     alignment and structure
>gi|56966057|pdb|1TA8|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332 Back     alignment and structure
>gi|56966058|pdb|1TAE|A Chain A, Structural Rearrangement Accompanying Nad+ Synthesis Within A Bacterial Dna Ligase Crystal Length = 332 Back     alignment and structure
>gi|6573451|pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent Ligase Length = 318 Back     alignment and structure
>gi|317455470|pdb|3PN1|A Chain A, Novel Bacterial Nad+-Dependent Dna Ligase Inhibitors With Broad Spectrum Potency And Antibacterial Efficacy In Vivo Length = 318 Back     alignment and structure
>gi|71042246|pdb|1ZAU|A Chain A, Adenylation Domain Of Nad+ Dependent Dna Ligase From M.Tuberculosis Length = 328 Back     alignment and structure
>gi|281307118|pdb|3JSL|A Chain A, Crystal Structure Of The Adenylation Domain Of Nad+- Dependent Dna Ligase From Staphylococcus Aureus Length = 318 Back     alignment and structure
>gi|212374934|pdb|3BAC|A Chain A, Structural Basis For The Inhibition Of Bacterial Nad+ Dependent Dna Ligase Length = 270 Back     alignment and structure
>gi|37926542|pdb|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus: Northeast Structural Genomics Consortium Target Wr64tt Length = 92 Back     alignment and structure
>gi|257471690|pdb|2K7F|A Chain A, Haddock Calculated Model Of The Complex Between The Brct Region Of Rfc P140 And Dsdna Length = 109 Back     alignment and structure
>gi|159164362|pdb|2EBU|A Chain A, Solution Structure Of The Brct Domain From Human Replication Factor C Large Subunit 1 Length = 112 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 0.0
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 1e-120
3jsl_A318 DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA 1e-70
1ta8_A332 DNA ligase, NAD-dependent; nucleotidyl transferase fold 1e-59
1b04_A318 Protein (DNA ligase); DNA replication; 2.80A {Bacillus 6e-57
1zau_A328 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tub 1e-56
3bac_A270 DNA ligase; adenylation domain, DNA damage, DNA repair, 1e-51
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 1e-17
1l7b_A92 DNA ligase; BRCT, autostructure, structural genomics, N 2e-17
2ebu_A112 Replication factor C subunit 1; A/B/A 3 layers, paralle 1e-16
2k6g_A109 Replication factor C subunit 1; protein, BRCT, DNA bind 2e-16
2cok_A113 Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair 4e-10
3ef0_A372 RNA polymerase II subunit A C-terminal domain phosphata 5e-06
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleotide 2e-04
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 3e-07
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 4e-06
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 9e-06
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 0.003
3ef1_A442 RNA polymerase II subunit A C-terminal domain phosphata 7e-07
>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* Length = 667 Back     alignment and structure
 Score =  693 bits (1789), Expect = 0.0
 Identities = 243/715 (33%), Positives = 385/715 (53%), Gaps = 61/715 (8%)

Query: 12  LSIEQARKELSSLEQEISYHDDCYYQYSKPIILDSEYDALKRRCDAIAHAFPDLARSEDP 71
           ++ E+AR+ ++ L   I YH+  YY  + P I D+EYD L R    +   FP+      P
Sbjct: 1   MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKS---P 57

Query: 72  NGPLNKIGGEMNLSLF-KVTHSIPTLSLEKIWNIEDLRKFITRIYRFWQKKDDNSIFFTL 130
           + P  ++G       F  V H     SL+  +  E++  F  R+    +++ +    +T+
Sbjct: 58  DSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERL----EREAEAPSLYTV 113

Query: 131 EPKIDGTMITIRYEKGKFVYAALRGDGHSGEDVSACIRAIPTIPRVLSLNIPEIIEVRGE 190
           E K+DG  + + YE+G  V++   GDG  GE+V+  +  IPTIPR L   +P+ +EVRGE
Sbjct: 114 EHKVDGLSV-LYYEEG--VWSTGSGDGEVGEEVTQNLLTIPTIPRRLK-GVPDRLEVRGE 169

Query: 191 VYISKNDFLALNDEMIAVGRKPYANPRNAASGILRRLNPTD-ITRYLNFFVHGLGKT--- 246
           VY+    FL LN+E+   G K + NPRNAA+G LR+ +P     R L    + LG     
Sbjct: 170 VYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGL 229

Query: 247 SEIFAKGQYEMLQKMRCLGFPVNNGVRQANTFHGIVSYYNEMKSIRSTLPYDIDGLVYKV 306
            E   K QYE+L  ++  GFPV +   +A    G+   Y    + R  LP++ DG+V K+
Sbjct: 230 EESGLKSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKL 289

Query: 307 DEFSLQKQLGERARSPRWMISHKFAEKQASTRLLDIDIQIGRTGILTPVARLEPVNIGGA 366
           D+ +L  +LG  AR+PR+ +++KF  ++  TRLLD+  Q+GRTG +TPV  LEPV I G+
Sbjct: 290 DDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGS 349

Query: 367 LITNATLHNEDYIKGLDASGKVMRGGRDIRVGDRVLVKRAGEVIPKVVDIIVNERHPDAQ 426
            ++  TLHNE YI+ L           DIR+GD VLV +AG VIP+V+ ++   R    +
Sbjct: 350 EVSRVTLHNESYIEEL-----------DIRIGDWVLVHKAGGVIPEVLRVLKERRTGKER 398

Query: 427 PFSFPSFCPICQSRVVRDLNPKTGKLVAAHRCTGGLACSAQQLERLKHFVSRDAFNIEGL 486
           P  +P  CP C  R+V++           HRC   L C A++ E ++H+ SR A +IEGL
Sbjct: 399 PIRWPEACPECGHRLVKE--------GKVHRCPNPL-CPAKRFEAIRHYASRKAMDIEGL 449

Query: 487 GKQQLDFFFKSEDPAFSIRIPADIFTLQRRQQTSTTKIENILGFGDVSVTNLYDSINKRR 546
           G++ ++   +       +R  AD++ L++        +  +   G+ S  NL   I + +
Sbjct: 450 GEKLIERLLEKG----LVRDVADLYHLRKED------LLGLERMGEKSAQNLLRQIEESK 499

Query: 547 NISLERFIFSLGIRHVGAEIARSLAKYYLSYQNFAQEINNIIAHNNDDWLSLIRVPLVGD 606
           +  LER +++LG+  VG  +AR+LA+ + +     +               LI V  VG+
Sbjct: 500 HRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEA----------SLEELIEVEEVGE 549

Query: 607 IIAQAIVEFYQNPRNICAVEALLKE-VSPSIGRHEKNVSSEIENKKLVFTGTLQKIQRHK 665
           + A+AI+E  ++P     V  L +  VS      ++ VS  +     V TG L +  R +
Sbjct: 550 LTARAILETLKDPAFRDLVRRLKEAGVSMES---KEEVSDLLSGLTFVLTGELSR-PREE 605

Query: 666 AQEYVTQLGAVVSAILSRKTDIIIVGDNPGSKLEKAQQLGVKIMNEEQFLFLLQQ 720
            +  + +LGA V+  +SRKT  ++VG+NPGSKLEKA+ LGV ++ EE+F   L++
Sbjct: 606 VKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFWRFLKE 660


>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Length = 671 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} PDB: 3jsn_A* Length = 318 Back     alignment and structure
>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis V583} SCOP: d.142.2.2 PDB: 3ba8_A* 1tae_A* 3ba9_A* 3baa_A* 3bab_A* Length = 332 Back     alignment and structure
>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus stearothermophilus} SCOP: d.142.2.2 Length = 318 Back     alignment and structure
>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} Length = 328 Back     alignment and structure
>3bac_A DNA ligase; adenylation domain, DNA damage, DNA repair, DNA replication, NAD; HET: DNA 3B9; 3.00A {Haemophilus influenzae} Length = 270 Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Length = 241 Back     alignment and structure
>1l7b_A DNA ligase; BRCT, autostructure, structural genomics, NESG, PSI, protein structure initiative, northeast structural genomics consortium; HET: DNA; NMR {Thermus thermophilus} SCOP: c.15.1.2 Length = 92 Back     alignment and structure
>2ebu_A Replication factor C subunit 1; A/B/A 3 layers, parallel beta-sheet, DNA replication, clamp loader, RFC1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 112 Back     alignment and structure
>2k6g_A Replication factor C subunit 1; protein, BRCT, DNA binding, activator, alternative splicing, ATP-binding, DNA replication, DNA- binding; NMR {Homo sapiens} PDB: 2k7f_A Length = 109 Back     alignment and structure
>2cok_A Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 113 Back     alignment and structure
>3ef0_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, ALF4, transition state analog, cobalt, magnesium; 2.10A {Schizosaccharomyces pombe} Length = 372 Back     alignment and structure
>3l46_A Protein ECT2; alternative splicing, guanine-nucleotide releasing factor, phosphoprotein, polymorphism, proto-oncogene, structural genomics; 1.48A {Homo sapiens} Length = 112 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Length = 89 Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 91 Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Length = 75 Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Length = 78 Back     alignment and structure
>3ef1_A RNA polymerase II subunit A C-terminal domain phosphatase; CTD, FCPH, BRCT, hydrolase, BEF3, acylphosphate analog, cobalt, magnesium; HET: BFD; 2.15A {Schizosaccharomyces pombe} Length = 442 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target731 NAD-dependent DNA ligase LigA [Candidatus Liberibacter
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 100.0
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 100.0
1ta8_A332 DNA ligase, NAD-dependent; nucleotidyl transferase fold 100.0
1b04_A318 Protein (DNA ligase); DNA replication; 2.80A {Geobacill 100.0
1zau_A328 DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tub 100.0
3jsl_A318 DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA 100.0
3bac_A270 DNA ligase; adenylation domain, DNA damage, DNA repair, 100.0
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 99.89
2k6g_A109 Replication factor C subunit 1; protein, BRCT, DNA bind 99.81
2ebu_A112 Replication factor C subunit 1; A/B/A 3 layers, paralle 99.8
1l7b_A92 DNA ligase; BRCT, autostructure, structural genomics, N 99.73
2cok_A113 Poly [ADP-ribose] polymerase-1; BRCT domain, DNA repair 99.38
2xnk_A292 DNA topoisomerase 2-binding protein 1; phosphorylation, 98.73
3ef1_A442 RNA polymerase II subunit A C-terminal domain phosphata 98.71
2d8m_A129 DNA-repair protein XRCC1; parallel beta-sheet, DNA liga 98.61
3ef0_A372 RNA polymerase II subunit A C-terminal domain phosphata 98.55
3l3e_A107 DNA topoisomerase 2-binding protein 1; BRCT domain, DNA 98.43
3l46_A112 Protein ECT2; alternative splicing, guanine-nucleotide 98.41
2cou_A109 ECT2 protein; BRCT domain, RHO GTPase, structural genom 98.33
1wf6_A132 Similar to S.pombe -RAD4+/CUT5+product (A40727); BRCT, 98.3
1cdz_A96 Protein (DNA-repair protein XRCC1); BRCT, BRCA1, protei 98.26
3ii6_X263 DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternativ 98.26
2ebw_A97 DNA repair protein REV1; A/B/A 3 layers, parallel beta- 98.16
2xnk_A 292 DNA topoisomerase 2-binding protein 1; phosphorylation, 98.13
2wt8_A97 Microcephalin; cell cycle, chromosome condensation, dwa 98.11
2vxb_A241 DNA repair protein RHP9; BRCT, nucleus, cell cycle, DNA 97.78
2dun_A133 POL MU, DNA polymerase MU; layers A/B/A, parallel beta- 97.53
2nte_A210 BARD-1, BRCA1-associated ring domain protein 1; BRCT, r 97.49
1t15_A214 Breast cancer type 1 susceptibility protein; protein-pe 97.45
2coe_A120 Deoxynucleotidyltransferase, terminal variant; BRCT dom 97.42
2etx_A209 Mediator of DNA damage checkpoint protein 1; tandem BRC 97.42
1l0b_A229 BRCA1; TANDEM-BRCT, three-helix bundle, unknown functio 97.42
1kzy_C259 Tumor suppressor P53-binding protein 1; tandem-BRCT and 97.32
2etx_A 209 Mediator of DNA damage checkpoint protein 1; tandem BRC 97.31
3l41_A220 BRCT-containing protein 1; BRC1, BRCT domain, tandem BR 96.8
2jw5_A106 DNA polymerase lambda; BRCT domain, family X polymerase 96.77
1z56_C264 DNA ligase IV; DNA repair, BRCT, NHEJ, XRCC4, DNA ligas 96.72
1t15_A 214 Breast cancer type 1 susceptibility protein; protein-pe 96.69
2nte_A 210 BARD-1, BRCA1-associated ring domain protein 1; BRCT, r 96.58
1imo_A88 DNA ligase III; parallel beta sheet; HET: DNA; NMR {Hom 94.31
1l0b_A 229 BRCA1; TANDEM-BRCT, three-helix bundle, unknown functio 94.29
3ii6_X 263 DNA ligase 4; XRCC4, NHEJ, DNA repair, BRCT, alternativ 92.79
3huf_A325 DNA repair and telomere maintenance protein NBS1; NBS1, 91.35
2vug_A389 PAB1020; RNA, ligase, AMPPNP, nucleotidyl- transferase; 99.01
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 98.94
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 98.88
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 98.72
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 98.23
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 97.86
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 97.65
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 97.58
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucleotide 97.21
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse H, h 97.13