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Conserved domains on  [gi|1308675744|gb|PKM47636|]
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ATP-dependent DNA ligase [Firmicutes bacterium HGW-Firmicutes-8]

Protein Classification

DNA ligase-like domain-containing protein( domain architecture ID 36883)

DNA ligase-like domain-containing protein similar to ATP-dependent polynucleotide ligases, such as DNA and RNA ligases, which catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism

CATH:  3.30.470.30
PubMed:  11983065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CDC9 super family cl43518
ATP-dependent DNA ligase [Replication, recombination and repair];
10-315 1.72e-84

ATP-dependent DNA ligase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1793:

Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 261.39  E-value: 1.72e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDG-G 86
Cdd:COG1793   114 VPPMLATLvDSPPDGGDWAYEPKWDGYRVQAHRdGGEVRLYSRNGEDITDRFPELVEALRALPADDAVLDGEIVALDEdG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKRGRSEKLgsIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGE-RILAPEGIYEWGV--E 163
Cdd:COG1793   194 RPPFQALQQRLGRKRD--VAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPpPLRLSPHVIDWGEgeA 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 164 FYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQ-TNKASERVDALLLGRLSDGG---PIfqgmv 239
Cdd:COG1793   272 LFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPgKGRRAGGFGSLLLGVYDPGGelvYV----- 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 240 gvglggvmgTRVY------------QVLEPLKRDMPLFKVPREIsRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLRE 307
Cdd:COG1793   347 ---------GKVGtgftdaelaeltERLRPLTRERSPFAVPSDG-RPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRE 416


                  ....*...
gi 1308675744 308 DLKPKECT 315
Cdd:COG1793   417 DKPPEEAT 424
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
10-315 1.72e-84

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 261.39  E-value: 1.72e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDG-G 86
Cdd:COG1793   114 VPPMLATLvDSPPDGGDWAYEPKWDGYRVQAHRdGGEVRLYSRNGEDITDRFPELVEALRALPADDAVLDGEIVALDEdG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKRGRSEKLgsIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGE-RILAPEGIYEWGV--E 163
Cdd:COG1793   194 RPPFQALQQRLGRKRD--VAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPpPLRLSPHVIDWGEgeA 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 164 FYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQ-TNKASERVDALLLGRLSDGG---PIfqgmv 239
Cdd:COG1793   272 LFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPgKGRRAGGFGSLLLGVYDPGGelvYV----- 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 240 gvglggvmgTRVY------------QVLEPLKRDMPLFKVPREIsRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLRE 307
Cdd:COG1793   347 ---------GKVGtgftdaelaeltERLRPLTRERSPFAVPSDG-RPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRE 416


                  ....*...
gi 1308675744 308 DLKPKECT 315
Cdd:COG1793   417 DKPPEEAT 424
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 13-316 6.30e-78

DNA ligase D, ligase domain; 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. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 239.90  E-value: 6.30e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  13 MLATSSAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILD-GGVPSF 90
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIeGGKVRLISRNGHDWTEKFPILAAALAALPILPAVLDGEIVVLDeSGRSDF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  91 YELQKRGRSEKlgsiaaaaaRKPATYVVFDILYASDDKLTSLPLSERREILGQLIEG----GERILAPEGIYEWGVEFYR 166
Cdd:TIGR02779  81 SALQNRLRAGR---------DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAikgpLAPDRYSVHFEGDGQALLE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 167 ACIERDLEGVVAKKLDSPYVPGkRSFNWKKFKKAREGDFVICGYKQTNKASERVDALLLGRLSDGGPIFQGMVGVGLGGV 246
Cdd:TIGR02779 152 AACRLGLEGVVAKRRDSPYRSG-RSADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGRVGTGFSEA 230

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 247 MGTRVYQVLEPLKRdmPLFKVPREISRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLREDLKPKECTG 316
Cdd:TIGR02779 231 ELATIKERLKPLES--KPDKPGAREKRGVHWVKPELVAEVEFAGWTRDGRLRQASFVGLREDKPASEVTR 298
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 10-198 3.17e-70

Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.


Pssm-ID: 185715 [Multi-domain]  Cd Length: 190  Bit Score: 216.63  E-value: 3.17e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILD-GG 86
Cdd:cd07906     1 IEPMLATLvDEPPDGEDWLYEIKWDGYRALARVdGGRVRLYSRNGLDWTARFPELAEALAALPVRDAVLDGEIVVLDeGG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKRGRSEKLGSiaaaaARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGG-ERILAPEGIYEWGVEFY 165
Cdd:cd07906    81 RPDFQALQNRLRLRRRLA-----RTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGsPRLRVSEHFEGGGAALF 155

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1308675744 166 RACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:cd07906   156 AAACELGLEGIVAKRADSPYRSGRRSRDWLKIK 188
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 5-313 9.30e-67

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 222.96  E-value: 9.30e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   5 ETFKKLKPMLATSS--APFDSKEFIFEVKWDGYRCLGYLGEST-HLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIV 81
Cdd:PRK09632  456 EEADDLAPMLATAGtvAGLKASQWAFEGKWDGYRLLAEADHGAlRLRSRSGRDVTAEYPELAALAEDLADHHVVLDGEIV 535

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  82 ILD-GGVPSFYELQKRGRSEklgsiaaaaarkPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERILAPEGIYEW 160
Cdd:PRK09632  536 ALDdSGVPSFGLLQNRGRDT------------RVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGGSLTVPPLLPGD 603

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 161 GVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQTNKA-SERVDALLLGRLSDGGPIFQGMV 239
Cdd:PRK09632  604 GAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVIGGWRPGEGGrSSGIGSLLLGIPDPGGLRYVGRV 683

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 240 GVGLGGVMGTRVYQVLEPLKRDMPLF--KVPREISRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLREDLKPKE 313
Cdd:PRK09632  684 GTGFTERELASLKETLAPLHRDTSPFdaDLPAADAKGATWVRPELVGEVRYSEWTPDGRLRQPSWRGLRPDKKPGD 759
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 12-198 7.08e-36

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 128.55  E-value: 7.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  12 PMLATSSAPFD------SKEFIFEVKWDGYR-CLGYLGESTHLQSRNGFDLSLKFPELAGINKHAKQ---RPLVVDGEIV 81
Cdd:pfam01068   1 PMLAKSFKSIEealkkfGGAFIAEYKYDGERaQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKpdeKSFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  82 ILDGGVPSFYELQK-RGRSEKLGSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLI-EGGERILAPEGI-- 157
Cdd:pfam01068  81 AVDPETGEILPFQVlADRKKKKVDVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFkEIPGRIQLAESIvt 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1308675744 158 --YEWGVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:pfam01068 161 kdVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGKNWLKIK 203
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
10-315 1.72e-84

ATP-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 261.39  E-value: 1.72e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDG-G 86
Cdd:COG1793   114 VPPMLATLvDSPPDGGDWAYEPKWDGYRVQAHRdGGEVRLYSRNGEDITDRFPELVEALRALPADDAVLDGEIVALDEdG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKRGRSEKLgsIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGE-RILAPEGIYEWGV--E 163
Cdd:COG1793   194 RPPFQALQQRLGRKRD--VAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPpPLRLSPHVIDWGEgeA 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 164 FYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQ-TNKASERVDALLLGRLSDGG---PIfqgmv 239
Cdd:COG1793   272 LFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPgKGRRAGGFGSLLLGVYDPGGelvYV----- 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 240 gvglggvmgTRVY------------QVLEPLKRDMPLFKVPREIsRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLRE 307
Cdd:COG1793   347 ---------GKVGtgftdaelaeltERLRPLTRERSPFAVPSDG-RPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRE 416


                  ....*...
gi 1308675744 308 DLKPKECT 315
Cdd:COG1793   417 DKPPEEAT 424
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 13-316 6.30e-78

DNA ligase D, ligase domain; 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. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 239.90  E-value: 6.30e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  13 MLATSSAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILD-GGVPSF 90
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIeGGKVRLISRNGHDWTEKFPILAAALAALPILPAVLDGEIVVLDeSGRSDF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  91 YELQKRGRSEKlgsiaaaaaRKPATYVVFDILYASDDKLTSLPLSERREILGQLIEG----GERILAPEGIYEWGVEFYR 166
Cdd:TIGR02779  81 SALQNRLRAGR---------DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAikgpLAPDRYSVHFEGDGQALLE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 167 ACIERDLEGVVAKKLDSPYVPGkRSFNWKKFKKAREGDFVICGYKQTNKASERVDALLLGRLSDGGPIFQGMVGVGLGGV 246
Cdd:TIGR02779 152 AACRLGLEGVVAKRRDSPYRSG-RSADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGRVGTGFSEA 230

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 247 MGTRVYQVLEPLKRdmPLFKVPREISRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLREDLKPKECTG 316
Cdd:TIGR02779 231 ELATIKERLKPLES--KPDKPGAREKRGVHWVKPELVAEVEFAGWTRDGRLRQASFVGLREDKPASEVTR 298
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 10-198 3.17e-70

Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining.


Pssm-ID: 185715 [Multi-domain]  Cd Length: 190  Bit Score: 216.63  E-value: 3.17e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILD-GG 86
Cdd:cd07906     1 IEPMLATLvDEPPDGEDWLYEIKWDGYRALARVdGGRVRLYSRNGLDWTARFPELAEALAALPVRDAVLDGEIVVLDeGG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKRGRSEKLGSiaaaaARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGG-ERILAPEGIYEWGVEFY 165
Cdd:cd07906    81 RPDFQALQNRLRLRRRLA-----RTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGsPRLRVSEHFEGGGAALF 155

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1308675744 166 RACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:cd07906   156 AAACELGLEGIVAKRADSPYRSGRRSRDWLKIK 188
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 5-313 9.30e-67

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 222.96  E-value: 9.30e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   5 ETFKKLKPMLATSS--APFDSKEFIFEVKWDGYRCLGYLGEST-HLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIV 81
Cdd:PRK09632  456 EEADDLAPMLATAGtvAGLKASQWAFEGKWDGYRLLAEADHGAlRLRSRSGRDVTAEYPELAALAEDLADHHVVLDGEIV 535

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  82 ILD-GGVPSFYELQKRGRSEklgsiaaaaarkPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERILAPEGIYEW 160
Cdd:PRK09632  536 ALDdSGVPSFGLLQNRGRDT------------RVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGGSLTVPPLLPGD 603

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 161 GVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQTNKA-SERVDALLLGRLSDGGPIFQGMV 239
Cdd:PRK09632  604 GAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVIGGWRPGEGGrSSGIGSLLLGIPDPGGLRYVGRV 683

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 240 GVGLGGVMGTRVYQVLEPLKRDMPLF--KVPREISRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLREDLKPKE 313
Cdd:PRK09632  684 GTGFTERELASLKETLAPLHRDTSPFdaDLPAADAKGATWVRPELVGEVRYSEWTPDGRLRQPSWRGLRPDKKPGD 759
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 49-316 7.16e-55

DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; it only represents the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274293 [Multi-domain]  Cd Length: 552  Bit Score: 187.53  E-value: 7.16e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  49 SRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILD-GGVPSFYELQKrgrseklgsIAAAAARKPATYVVFDILYASDD 127
Cdd:TIGR02776   1 TRNGHDWTKRFPEIVKALALLKLLPAWIDGEIVVLDeRGRADFAALQN---------ALSAGASRPLTYYAFDLLFLSGE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 128 KLTSLPLSERREILGQLIEGGER--ILAPEGIYEWGVEFYRACIERDLEGVVAKKLDSPYVPGkRSFNWKKFKKAREGDF 205
Cdd:TIGR02776  72 DLRDLPLEERKKRLKQLLKAQDEpaIRYSDHFESDGDALLESACRLGLEGVVSKRLDSPYRSG-RSKDWLKLKCRRRQEF 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 206 VICGYKQTNkasERVDALLLGRLSDGGPIFQGMVGVGLGGVMGTRVYQVLEPLKR-DMPLFKVPREISRGLNWVNPAVCC 284
Cdd:TIGR02776 151 VITGYTPPN---RRFGALLVGVYEGGQLVYAGKVGTGFGADTLKTLLARLKALGAkASPFSGPAGAKTRGVHWVRPSLVA 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1308675744 285 AVEFLEPARDGGLRHPVFRGLREDLKPKECTG 316
Cdd:TIGR02776 228 EVEYAGITRDGILREASFKGLREDKPAEEVTL 259
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 9-311 1.02e-48

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 174.32  E-value: 1.02e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   9 KLKPMLATSS-APFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDG- 85
Cdd:PRK05972  233 FLAPQLATLVdRPPSGDGWIYEIKFDGYRILARIeGGEVRLFTRNGLDWTAKLPALAKAAAALGLPDAWLDGEIVVLDEd 312

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  86 GVPSFYELQ---KRGRSEKLgsiaaaaarkpaTYVVFDILYASDDKLTSLPLSERREILGQLIE--GGERILAPEgIYEW 160
Cdd:PRK05972  313 GVPDFQALQnafDEGRTEDL------------VYFAFDLPFLGGEDLRELPLEERRARLRALLEaaRSDRIRFSE-HFDA 379

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 161 GVE--FYRACiERDLEGVVAKKLDSPYVPGkRSFNWKKFK-KAREgDFVICGYKQTNKASERVDALLLGRLSDGGPIFQG 237
Cdd:PRK05972  380 GGDavLASAC-RLGLEGVIGKRADSPYVSG-RSEDWIKLKcRARQ-EFVIGGYTDPKGSRSGFGSLLLGVHDDDHLRYAG 456

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 238 MVGVGLGGVMGTRVYQVLEPLKRDMPLFKVPREIS--RGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLREDlKP 311
Cdd:PRK05972  457 RVGTGFGAATLKTLLPRLKALATDKSPFAGKPAPRkaRGVHWVKPELVAEVEFAGWTRDGIVRQAVFKGLRED-KP 531
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 10-201 5.12e-38

Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185714 [Multi-domain]  Cd Length: 194  Bit Score: 133.91  E-value: 5.12e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATS-SAPFDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDGGV 87
Cdd:cd07905     1 VEPMLARAvDALPEPGGWQYEPKWDGFRCLAFRdGDEVRLQSRSGKPLTRYFPELVAAARALLPPGCVLDGELVVWRGGR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  88 PSFYELQKRGRSEKLGsIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERILA-------PEGIYEW 160
Cdd:cd07905    81 LDFDALQQRIHPAASR-VRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHlspattdRAEAREW 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1308675744 161 GVEFYRAcierDLEGVVAKKLDSPYVPGKRSfnWKKFKKAR 201
Cdd:cd07905   160 LEEFEGA----GLEGVVAKRLDGPYRPGERA--MLKVKHRR 194
ligD PRK09633
DNA ligase D;
10-315 7.57e-38

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 142.10  E-value: 7.57e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPML--ATSSAPfDSKEFIFEVKWDGYRCLGYLGEST-HLQSRNGFDLSLKFPElagINKHAKQR--------PLVVDG 78
Cdd:PRK09633    1 MKPMQptLTTSIP-IGDEWRYEVKYDGFRCLLIIDETGiTLISRNGRELTNTFPE---IIEFCESNfehlkeelPLTLDG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  79 EIVILDGGVPS-FYELQKRGRSEKLGSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQL-----------IE 146
Cdd:PRK09633   77 ELVCLVNPYRSdFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLmkaaklpaspdPY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 147 GGERI-LAPEgiYEWGVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQTNkaservdALLL 225
Cdd:PRK09633  157 AKARIqYIPS--TTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWRYVHVIVTGYDPSN-------GYFT 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 226 GRLSDGGPIfqgmvgvglggvmgTRVYQVLEPLKRD-----MPLFKVPREISRGLNWV-NPAVCCAVEFLEpaRDGG-LR 298
Cdd:PRK09633  228 GSVYKDGQL--------------TEVGSVKHGMEDEerqtlRAIFKQNGTKTKSGEYTlEPSICVTVACIT--FDGGtLR 291

                         330
                  ....*....|....*..
gi 1308675744 299 HPVFRGLREDLKPKECT 315
Cdd:PRK09633  292 EPSFVSFLFDMDPTECT 308
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 10-232 1.35e-37

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 136.95  E-value: 1.35e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATSSA--PfDSKEFIFEVKWDGYRCLGYL-GESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVILDGG 86
Cdd:PRK08224    9 VEPMLAKSVDaiP-PGDGWSYEPKWDGFRCLVFRdGDEVELGSRNGKPLTRYFPELVAALRAELPERCVLDGEIVVARDG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  87 VPSFYELQKR-----GRSEKLGsiaaaaARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERI-LAP-----E 155
Cdd:PRK08224   88 GLDFEALQQRihpaaSRVRKLA------EETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGSGPVhLTPattdpA 161

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1308675744 156 GIYEWGVEFYRAcierDLEGVVAKKLDSPYVPGKRSFnwKKFKKAREGDFVICGYKqTNKASERVDALLLGRLSDGG 232
Cdd:PRK08224  162 TARRWFEEFEGA----GLDGVIAKPLDGPYQPGKRAM--FKVKHERTADCVVAGYR-YHKSGPVVGSLLLGLYDDDG 231
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 12-198 7.08e-36

ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653.


Pssm-ID: 426028 [Multi-domain]  Cd Length: 203  Bit Score: 128.55  E-value: 7.08e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  12 PMLATSSAPFD------SKEFIFEVKWDGYR-CLGYLGESTHLQSRNGFDLSLKFPELAGINKHAKQ---RPLVVDGEIV 81
Cdd:pfam01068   1 PMLAKSFKSIEealkkfGGAFIAEYKYDGERaQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKpdeKSFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  82 ILDGGVPSFYELQK-RGRSEKLGSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLI-EGGERILAPEGI-- 157
Cdd:pfam01068  81 AVDPETGEILPFQVlADRKKKKVDVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFkEIPGRIQLAESIvt 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1308675744 158 --YEWGVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:pfam01068 161 kdVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGKNWLKIK 203
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 12-306 1.38e-33

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 124.49  E-value: 1.38e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  12 PMLATSS-APFDSKEFIFEVKWDGYR-CLGYLGESTHLQSRNGFDLSLKFPELAGINKHAKqrpLVVDGEIVIL-DGGVP 88
Cdd:PRK07636    5 PMLLESAkEPFNSENYITEPKFDGIRlIASKNNGLIRLYTRHNNEVTAKFPELLNLDIPDG---TVLDGELIVLgSTGAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  89 SFYELQKRGRSEKlgsiaaAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERILAPEGIYEWGVEFYRAC 168
Cdd:PRK07636   82 DFEAVMERFQSKK------STKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHPNVKIIEGIEGHGTAYFELV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 169 IERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVICGYKQTNkaservDALLLGRLsDGGPIfqgMVGVGLGGVMG 248
Cdd:PRK07636  156 EERELEGIVIKKANSPYEINKRSDNWLKVINYQYTDVLITGYRKEE------FGLLLSYL-DGRSA---GIMEFMPYDAR 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1308675744 249 TRVYQVLEPLkrdmplfkVPREiSRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLR 306
Cdd:PRK07636  226 KKFYKRAKRL--------VVGE-DKKFVYIEPIIGCRVKHRFKTKNGMLRIPSFVEWR 274
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 10-200 4.26e-31

Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185709 [Multi-domain]  Cd Length: 201  Bit Score: 115.90  E-value: 4.26e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLAT--SSAP----FDSKEFIFEVKWDGYRCLGYLGES-THLQSRNGFDLSLKFPELAGINKHAKQrPLVVDGEIVI 82
Cdd:cd07898     1 IKPMLAHpeESAEaakaKKPAAAWVEDKYDGIRAQVHKDGGrVEIFSRSLEDITDQFPELAAAAKALPH-EFILDGEILA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  83 LD-GGVPSFYELQKR----GRSEKLGSiaaaaaRKPATYVVFDILYASDDKLTSLPLSERREILGQLI-EGGERILAPEG 156
Cdd:cd07898    80 WDdNRGLPFSELFKRlgrkFRDKFLDE------DVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFvEIPGRIRIAPA 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1308675744 157 IYEWGVE----FYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKA 200
Cdd:cd07898   154 LPVESAEeleaAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKKE 201
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 7-198 9.65e-31

Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185711 [Multi-domain]  Cd Length: 207  Bit Score: 114.94  E-value: 9.65e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   7 FKKLKPMLATSSAPFDS------KEFIFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKFPELA-GINKHAKQRPLVVDG 78
Cdd:cd07901     2 GRPVRPMLAQRAPSVEEalikegGEAAVEYKYDGIRVqIHKDGDEVRIFSRRLEDITNALPEVVeAVRELVKAEDAILDG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  79 EIVILD-GGVP-SFYELQKRGRseklgsiaaaaaRK----------PATYVVFDILYASDDKLTSLPLSERREILGQLIE 146
Cdd:cd07901    82 EAVAYDpDGRPlPFQETLRRFR------------RKydveeaaeeiPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVP 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 147 GGERILAPEGIY----EWGVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:cd07901   150 ETEAILLAPRIVtddpEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVK 205
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 7-198 4.96e-28

Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185713 [Multi-domain]  Cd Length: 225  Bit Score: 108.43  E-value: 4.96e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   7 FKKLKPMLAT-------SSAPFDSKEFIFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKF----------PELAGI-NK 67
Cdd:cd07903     9 FSPFRPMLAErlnigyvEIKLLKGKPFYIETKLDGERIqLHKDGNEFKYFSRNGNDYTYLYgasltpgsltPYIHLAfNP 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  68 HAKQrpLVVDGEIVILD---GGVPSFYELqkrgRSEKLGSIAAAAARKPaTYVVFDILYASDDKLTSLPLSERREILGQL 144
Cdd:cd07903    89 KVKS--CILDGEMVVWDketKRFLPFGTL----KDVAKLREVEDSDLQP-CFVVFDILYLNGKSLTNLPLHERKKLLEKI 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1308675744 145 IEGGERIL--APEGIYEWG---VEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:cd07903   162 ITPIPGRLevVKRTEASTKeeiEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIK 220
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 7-209 2.62e-24

DNA ligase I, ATP-dependent (dnl1); 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]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 102.78  E-value: 2.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   7 FKKLKPMLATSSAPFDSK------EFIFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKFPE-----LAGINKHAKQrpL 74
Cdd:TIGR00574 164 GIPFKPMLAERAKSIEEAlkkkgnGFYVEYKYDGERVqVHKDGDKFKIFSRRLENYTYQYPEiftefIKEAFPGIKS--C 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  75 VVDGEIVILD--GGVP-SFYELqkrGRSEKLGSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLI-EGGER 150
Cdd:TIGR00574 242 ILDGEMVAIDpeTGKPlPFGTL---LRRKRKYDIKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILkPIPNR 318

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308675744 151 ILAPEGIYEWGVE----FYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREG------DFVICG 209
Cdd:TIGR00574 319 IEIAEMKIVSNVEelekFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEgmgdtlDLVVIG 387
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 13-198 2.14e-22

Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.


Pssm-ID: 185708 [Multi-domain]  Cd Length: 207  Bit Score: 93.00  E-value: 2.14e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  13 MLATssaPFDSK--------EFIFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKFPELAGinkHAKQRPL--VVDGEIV 81
Cdd:cd07897     8 MLAH---PLEDDpedlgdpsDWQAEWKWDGIRGqLIRRGGEVFLWSRGEELITGSFPELLA---AAEALPDgtVLDGELL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  82 ILDGGVP-SFYELQKR-GR---SEKLgsiaaaAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEG--GERILAP 154
Cdd:cd07897    82 VWRDGRPlPFNDLQQRlGRktvGKKL------LAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARlpPPRLDLS 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1308675744 155 EGIYE--WGV--EFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:cd07897   156 PLIAFadWEElaALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWK 203
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 201-314 8.74e-22

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; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigD and similar bacterial proteins. LigD, or DNA ligase D, catalyzes the end-healing and end-sealing steps during nonhomologous end joining. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153440 [Multi-domain]  Cd Length: 115  Bit Score: 88.39  E-value: 8.74e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 201 REGDFVICGYKQTNKASERVDALLLGRLSDGGPIFQGMVGVGLGGVMGTRVYQVLEPLKRDMPLF-KVPREISRGLNWVN 279
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDGGRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFaDPPPADARGAVWVK 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1308675744 280 PAVCCAVEFLEPARDGGLRHPVFRGLREDLKPKEC 314
Cdd:cd07971    81 PELVAEVEFAEWTPDGRLRHPVFKGLREDKPAAEV 115
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 11-315 3.13e-21

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 94.27  E-value: 3.13e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  11 KPMLATSSApfDSKEF--------IFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKFPELA-GINKHAKQRPLVVDGEI 80
Cdd:PRK01109  229 RPMLAERLS--SPKEIlkkmggeaLVEYKYDGERAqIHKKGDKVKIFSRRLENITHQYPDVVeYAKEAIKAEEAIVEGEI 306

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  81 VILD---GGVPSFYELQKRGRSEklgSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERILAPEGI 157
Cdd:PRK01109  307 VAVDpetGEMRPFQELMHRKRKY---DIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKENDKVKLAERI 383

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 158 YEWGVE----FYRACIERDLEGVVAKKL--DSPYVPGKRSFNWKKFKKAREG------DFVICG-YKQTNKASERVDALL 224
Cdd:PRK01109  384 ITDDVEelekFFHRAIEEGCEGLMAKSLgkDSIYQAGARGWLWIKYKRDYQSemadtvDLVVVGaFYGRGRRGGKYGSLL 463

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 225 LGRLSDGGPIFQGMVGVGL--GGVMGTRVYQVLEPLKRDMplfKVPREISRGLN--WVNPAVC---------------CA 285
Cdd:PRK01109  464 MAAYDPKTDTFETVCKVGSgfTDEDLDELPKMLKPYKIDH---KHPRVVSKMEPdvWVEPKLVaeiigaeitlsplhtCC 540

                         330       340       350
                  ....*....|....*....|....*....|
gi 1308675744 286 VEFLEPARDGGLRHPVFRGLREDLKPKECT 315
Cdd:PRK01109  541 LGVVEKGAGLAIRFPRFIRWRDDKSPEDAT 570
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 10-199 6.74e-20

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 86.46  E-value: 6.74e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLA--TSSAP-----FDSKEFIFEVKWDGYRC---LGYLGEsTHLQSRNGFDLSLKFPELAG-----INKHAKQrpL 74
Cdd:cd07900    10 VKPMLAkpTKGVSevldrFEDKEFTCEYKYDGERAqihLLEDGK-VKIFSRNLENNTEKYPDIVAvlpksLKPSVKS--F 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  75 VVDGEIVILD---GGVPSFYELQKRGR-SEKLGSIAAaaarkPATYVVFDILYASDDKLTSLPLSERREIL--------G 142
Cdd:cd07900    87 ILDSEIVAYDretGKILPFQVLSTRKRkDVDANDIKV-----QVCVFAFDLLYLNGESLLKKPLRERRELLhslfkevpG 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 143 QL-------IEGGERILapegiyewgvEFYRACIERDLEGVVAKKLDSP--YVPGKRSFNWKKFKK 199
Cdd:cd07900   162 RFqfatskdSEDTEEIQ----------EFLEEAVKNNCEGLMVKTLDSDatYEPSKRSHNWLKLKK 217
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 25-198 6.37e-17

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 81.04  E-value: 6.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  25 EFIFEVKWDGYRclGYL---GESTHLQSRNGFDLSLKFPELAGINKHAKQrPLVVDGEIVIL---DGGVPSFYELQKR-G 97
Cdd:PRK09247  226 DWQAEWKWDGIR--VQLvrrGGEVRLWSRGEELITERFPELAEAAEALPD-GTVLDGELLVWrpeDGRPQPFADLQQRiG 302

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  98 R---SEKLgsiaaaAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIE--GGERILAPEGIY--EWGV--EFYRAC 168
Cdd:PRK09247  303 RktvGKKL------LADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIArlPDPRLDLSPLVPfsDWDElaALRAAA 376

                         170       180       190
                  ....*....|....*....|....*....|
gi 1308675744 169 IERDLEGVVAKKLDSPYVPGKRSFNWKKFK 198
Cdd:PRK09247  377 RERGVEGLMLKRRDSPYLVGRKKGPWWKWK 406
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 10-207 5.58e-15

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 75.39  E-value: 5.58e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATSSAPFDSK------EFIFEVKWDGYRC-LGYLGESTHLQSRNGFDLSLKFPELAGINKHAKQRPLVVDGEIVI 82
Cdd:PRK03180  184 VRPMLAQTATSVAEAlarlggPAAVEAKLDGARVqVHRDGDDVRVYTRTLDDITARLPEVVEAVRALPVRSLVLDGEAIA 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  83 LDG-GVP-SFYELQKR-GRSeklGSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERI---LAPEG 156
Cdd:PRK03180  264 LRPdGRPrPFQVTASRfGRR---VDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHRVprlVTADP 340

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1308675744 157 iyEWGVEFYRACIERDLEGVVAKKLDSPYVPGKRSFNWKKFKKAREGDFVI 207
Cdd:PRK03180  341 --AAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKPVHTLDLVV 389
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 11-199 8.05e-13

Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185712 [Multi-domain]  Cd Length: 213  Bit Score: 66.59  E-value: 8.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  11 KPMLATSSAPFD------SKEFIFEVKWDGYRC-LGYLGESTHLQSRngfdlSLKfPELAGINKHAKQ---------RPL 74
Cdd:cd07902    15 KPMLAEACKSVEdamkkcPNGMYAEIKYDGERVqVHKQGDNFKFFSR-----SLK-PVLPHKVAHFKDyipkafphgHSM 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  75 VVDGEIVILDggvpsfyelQKRGRSEKLGS--IAAAAARKPAT--YVVFDILYASDDKLTSLPLSERREILGQ-LIEGGE 149
Cdd:cd07902    89 ILDSEVLLVD---------TKTGKPLPFGTlgIHKKSAFKDANvcLFVFDCLYYNGESLMDKPLRERRKILEDnMVEIPN 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1308675744 150 RILAPEGIYEWGVEFYRACIER----DLEGVVAKKLDSPYVPGKRsfNWKKFKK 199
Cdd:cd07902   160 RIMLSEMKFVKKADDLSAMIARvikeGLEGLVLKDLKSVYEPGKR--HWLKVKK 211
30 PHA02587
DNA ligase; Provisional
 6-217 1.45e-12

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 67.81  E-value: 1.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744   6 TFKKLKP----MLATSSAPFDSKEFIF-----EVKWDGYRCLGYL-GESTHLQSRNGFD---LSLKFPELAGINKHAKQR 72
Cdd:PHA02587  125 VWKGLIPeqpqMLASSFSEKLIKKNIKfpayaQLKADGARCFADIdADGIEIRSRNGNEylgLDLLKEELKKMTAEARQR 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  73 P--LVVDGEIVI------LDGGVPSFYELQKR--------------GRSEKL--GSIAAAAaRKPATYVVFDIL----YA 124
Cdd:PHA02587  205 PggVVIDGELVYvevetkKPNGLSFLFDDSKAkefvgvvadratgnGIVNKSlkGTISKEE-AQEIVFQVWDIVplevYY 283

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 125 SDDKLTsLPLSERREILGQLIE--GGERILAPEGI----YEWGVEFYRACIERDLEGVVAKKLDSPYVPGkRSFNWKKFK 198
Cdd:PHA02587  284 GKEKSD-MPYDDRFSKLAQMFEdcGYDRVELIENQvvnnLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFK 361

                         250       260
                  ....*....|....*....|...
gi 1308675744 199 KAREGDFVICGY----KQTNKAS 217
Cdd:PHA02587  362 EVIDIDLEIVGVyehkKDPNKVG 384
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 249-308 1.09e-11

ATP dependent DNA ligase C terminal region; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase.


Pssm-ID: 398383 [Multi-domain]  Cd Length: 94  Bit Score: 60.30  E-value: 1.09e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 249 TRVYQVLEPLKRDMPLFKVPREISRGLNWVNPAVCCAVEFLEPARDGGLRHPVFRGLRED 308
Cdd:pfam04679  34 EELRERLKPLERKKPPFAEPPPEARGAVWVEPELVAEVEFAEWTRSGRLRFPRFKGLRED 93
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 24-199 9.20e-10

Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity.


Pssm-ID: 185704 [Multi-domain]  Cd Length: 182  Bit Score: 57.04  E-value: 9.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  24 KEFIFEVKWDGYRCLGY-LGESTHLQSRNGFDLSLKFP-ELAGINKHAKQrPLVVDGEIVILDGGVpsfyelqkrgrsek 101
Cdd:cd06846    19 DEYYVQEKYDGKRALIVaLNGGVFAISRTGLEVPLPSIlIPGRELLTLKP-GFILDGELVVENREV-------------- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 102 lgsiaaaaARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEGGERI-------LAPEGIYEwgvEFYRACIERDL- 173
Cdd:cd06846    84 --------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLdpvklvpLENAPSYD---ETLDDLLEKLKk 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 1308675744 174 ---EGVVAKKLDSPYVPG-KRSFNWKKFKK 199
Cdd:cd06846   153 kgkEGLVFKHPDAPYKGRpGSSGNQLKLKP 182
PLN03113 PLN03113
DNA ligase 1; Provisional
 12-199 4.15e-09

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 57.69  E-value: 4.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  12 PMLATSSA-------PFDSKEFIFEVKWDGYRCLGYLGE--STHLQSRNGFDLSLKFPELAGINKHAKQ---RPLVVDGE 79
Cdd:PLN03113  372 PMLAKPTKgvseivnKFQDMEFTCEYKYDGERAQIHFLEdgSVEIYSRNAERNTGKYPDVVVAISRLKKpsvKSFILDCE 451

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  80 IVILD---GGVPSFYELQKRGRSeklgSIAAAAARKPATYVVFDILYASDDKLTSLPLSERREILGQLIEggerilAPEG 156
Cdd:PLN03113  452 LVAYDrekKKILPFQILSTRARK----NVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFE------EDPG 521

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675744 157 IYEWGV-----------EFYRACIERDLEGVVAKKL--DSPYVPGKRSFNWKKFKK 199
Cdd:PLN03113  522 FFQFATaitsndleeiqKFLDAAVDASCEGLIIKTLnkDATYEPSKRSNNWLKLKK 577
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 75-199 6.81e-07

Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. This model characterizes the adenylation domain of this group of uncharacterized fungal proteins. It is not known whether these proteins also contain an OB-fold domain.


Pssm-ID: 185716 [Multi-domain]  Cd Length: 235  Bit Score: 49.32  E-value: 6.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  75 VVDGEIVILD---GGVPSFYELQKR-GRSEKLGSIAAAAARKPATY---VVFDILYASDDKLTSLPLSERREILGQLIE- 146
Cdd:cd08039    87 ILEGEMVVWSdrqGKIDPFHKIRKHvERSGSFIGTDNDSPPHEYEHlmiVFFDVLLLDDESLLSKPYSERRDLLESLVHv 166

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1308675744 147 -GGERILA---------PEGIYEWGVEFYRACIERDlEGVVAKKLDSPYVP-----GKRSFNWKKFKK 199
Cdd:cd08039   167 iPGYAGLSerfpidfsrSSGYERLRQIFARAIAERW-EGLVLKGDEEPYFDlfleqGSFSGCWIKLKK 233
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 10-199 1.33e-06

Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues.


Pssm-ID: 185707 [Multi-domain]  Cd Length: 174  Bit Score: 47.95  E-value: 1.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  10 LKPMLATssaPFDSKEFIFEV----KWDGYRCLgYLGEstHLQSRNGfdlsLKFPELAGINKHAKQRPLvvDGEIVIldg 85
Cdd:cd07896     1 PELLLAK---TYDEGEDISGYlvseKLDGVRAY-WDGK--QLLSRSG----KPIAAPAWFTAGLPPFPL--DGELWI--- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  86 gvpsfyelqKRGRSEKLGSI----AAAAARKPA-TYVVFDILYASddkltsLPLSERREILGQLIE--GGERILAPEGIY 158
Cdd:cd07896    66 ---------GRGQFEQTSSIvrskKPDDEDWRKvKFMVFDLPSAK------GPFEERLERLKNLLEkiPNPHIKIVPQIP 130

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1308675744 159 EWGVE----FYRACIERDLEGVVAKKLDSPYVPGkRSFNWKKFKK 199
Cdd:cd07896   131 VKSNEaldqYLDEVVAAGGEGLMLRRPDAPYETG-RSDNLLKLKP 174
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 216-315 8.74e-04

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; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar bacterial proteins. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153439 [Multi-domain]  Cd Length: 122  Bit Score: 38.45  E-value: 8.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 216 ASERVDALLLGRLSDGGPIFQGMVGVGLGGVMGTRVYQVLEPLKRDMP-LFKVPREISR-----GLNW--VNPAVCCAVE 287
Cdd:cd07970    13 HKDRPGSLLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPARAGHPwTGRAPGFPSRwgtrkSLEWvpVRPELVVEVS 92

                          90       100       110
                  ....*....|....*....|....*....|
gi 1308675744 288 FlEPARDGG-LRHPV-FRGLREDLKPKECT 315
Cdd:cd07970    93 A-DTAEGGGrFRHPLrFLRWRPDKSPEDCT 121
PHA00454 PHA00454
ATP-dependent DNA ligase
 27-306 3.06e-03

ATP-dependent DNA ligase


Pssm-ID: 222798 [Multi-domain]  Cd Length: 315  Bit Score: 38.86  E-value: 3.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  27 IFEVKWDGYRC-LGYLGESTHL-QSRNGfdlsLKFPELAGIN-------KHAKQ-RPLVVDGeiVILDG-----GVPsFY 91
Cdd:PHA00454   30 IADVKYDGVRGnIVVDNTADHGwLSREG----KTIPALEHLNgfdrrwaKLLNDdRCIFPDG--FMLDGelmvkGVD-FN 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744  92 ELQKRGRSEKLgsIAAAAARKPATYVVFDILY-------ASDDKLTSLPLSERREILGQLIE---GGERILAP------- 154
Cdd:PHA00454  103 TGSGLLRRKWK--VLFELHLKKLHVVVYDVTPldvlesgEDYDVMSLLMYEHVRAMVPLLMEyfpEIDWFLSEsyevydm 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 155 EGIYEWgVEFYRAcieRDLEGVVAKKLDSPYVPGKRSfNWKKFKKAREGDFVICGYK--QTNKASE------RVDaLLLG 226
Cdd:PHA00454  181 ESLQEL-YEKKRA---EGHEGLVVKDPSLIYRRGKKS-GWWKMKPECEADGTIVGVVwgTPGLANEgkvigfRVL-LEDG 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675744 227 RLSDGGPIFQgmvgvgLGGVMGTRVYQVLEPLKRDMPLfkvpreisrgLNWVnpavcCAVEFLEPARDGGLRHPVFRGLR 306
Cdd:PHA00454  255 RVVNATGISR------ALMEEFTANVKEHGEDYEAMPY----------NGRA-----CQVSYMERTPDGSLRHPSFDRFR 313
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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