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Conserved domains on  [gi|1125209170|gb|OLB60435|]
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ATP-dependent DNA ligase [Gemmatimonadetes bacterium 13_2_20CM_2_69_23]

Protein Classification

ATP-dependent DNA ligase( domain architecture ID 11483171)

ATP-dependent DNA ligase catalyzes the ATP-dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 1-346 0e+00

ATP-dependent DNA ligase; Reviewed


:

Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 542.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGLDF 80
Cdd:PRK08224   12 MLAKSVDAIPPGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRAELPERCVLDGEIVVARDGGLDF 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQMRLHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKlFAKLDPPLHLTPMTQDRGLAEQWLEQF 160
Cdd:PRK08224   92 EALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEA-AAAGSGPVHLTPATTDPATARRWFEEF 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 161 EGAGLDGVIAKPAALTYQPGKRAMIKVKHARTADCVVAGFRWHKTGkDAVGSLLLGLYDDRGALQHVGVTSSFTMAMRKQ 240
Cdd:PRK08224  171 EGAGLDGVIAKPLDGPYQPGKRAMFKVKHERTADCVVAGYRYHKSG-PVVGSLLLGLYDDDGQLHHVGVTSAFPMARRRE 249

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 241 LVKELAPLRKhALDKHPWrawaQADARSGRMPGGQSRWSAGKDLSWEPLRIERVCEVKYDHLQGDRFRHAATFLRWRPDK 320
Cdd:PRK08224  250 LTAELEPLRT-PFGDHPW----NWAAFTGRAPGGPSRWSAGKDLSWVPLRPERVVEVRYDHMEGGRFRHTAQFLRWRPDR 324

                         330       340
                  ....*....|....*....|....*.
gi 1125209170 321 RPAACRYDQLEVARPYQLAKVFSSGS 346
Cdd:PRK08224  325 DPRSCTYEQLEEPVRYDLADVLPGAR 350
 
Name Accession Description Interval E-value
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 1-346 0e+00

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 542.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGLDF 80
Cdd:PRK08224   12 MLAKSVDAIPPGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRAELPERCVLDGEIVVARDGGLDF 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQMRLHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKlFAKLDPPLHLTPMTQDRGLAEQWLEQF 160
Cdd:PRK08224   92 EALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEA-AAAGSGPVHLTPATTDPATARRWFEEF 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 161 EGAGLDGVIAKPAALTYQPGKRAMIKVKHARTADCVVAGFRWHKTGkDAVGSLLLGLYDDRGALQHVGVTSSFTMAMRKQ 240
Cdd:PRK08224  171 EGAGLDGVIAKPLDGPYQPGKRAMFKVKHERTADCVVAGYRYHKSG-PVVGSLLLGLYDDDGQLHHVGVTSAFPMARRRE 249

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 241 LVKELAPLRKhALDKHPWrawaQADARSGRMPGGQSRWSAGKDLSWEPLRIERVCEVKYDHLQGDRFRHAATFLRWRPDK 320
Cdd:PRK08224  250 LTAELEPLRT-PFGDHPW----NWAAFTGRAPGGPSRWSAGKDLSWVPLRPERVVEVRYDHMEGGRFRHTAQFLRWRPDR 324

                         330       340
                  ....*....|....*....|....*.
gi 1125209170 321 RPAACRYDQLEVARPYQLAKVFSSGS 346
Cdd:PRK08224  325 DPRSCTYEQLEEPVRYDLADVLPGAR 350
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
1-331 3.30e-112

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 333.43  E-value: 3.30e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHG-LD 79
Cdd:COG1793   117 MLATLVDSPPDGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDITDRFPELVEALRALPADDAVLDGEIVALDEDGrPP 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLHPAAsRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGLAEQWLEQ 159
Cdd:COG1793   197 FQALQQRLGRKR-DVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVIDWGEGEALFAA 275

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 160 FEGAGLDGVIAKPAALTYQPGKR--AMIKVKHARTADCVVAGFRWHKTG-KDAVGSLLLGLYDDRGALQHVGVTSS-FTM 235
Cdd:COG1793   276 AREAGLEGVMAKRLDSPYRPGRRsgDWLKVKCPRTQDLVVGGATPGKGRrAGGFGSLLLGVYDPGGELVYVGKVGTgFTD 355

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 236 AMRKQLVKELAPLRkhaLDKHPWRAWAqadarsgrmPGGQSRWsagkdlswepLRIERVCEVKYDHLQGD-RFRHAAtFL 314
Cdd:COG1793   356 AELAELTERLRPLT---RERSPFAVPS---------DGRPVRW----------VRPELVAEVAFDEITRSgALRFPR-FL 412

                         330
                  ....*....|....*..
gi 1125209170 315 RWRPDKRPAACRYDQLE 331
Cdd:COG1793   413 RLREDKPPEEATLEELE 429
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 1-191 2.74e-96

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: 283.75  E-value: 2.74e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGLDF 80
Cdd:cd07905     4 MLARAVDALPEPGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARALLPPGCVLDGELVVWRGGRLDF 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQMRLHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGLAEQWLEQF 160
Cdd:cd07905    84 DALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPATTDRAEAREWLEEF 163

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1125209170 161 EGAGLDGVIAKPAALTYQPGKRAMIKVKHAR 191
Cdd:cd07905   164 EGAGLEGVVAKRLDGPYRPGERAMLKVKHRR 194
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 1-188 6.65e-44

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: 150.13  E-value: 6.65e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDD-----GTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGS---VIDGEIVI 72
Cdd:pfam01068   2 MLAKSFKSIEEAlkkfgGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEksfILDGEIVA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  73 ---ATAHGLDFDALQMRLhPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQD 149
Cdd:pfam01068  82 vdpETGEILPFQVLADRK-KKKVDVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVT 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1125209170 150 RGL--AEQWLEQFEGAGLDGVIAKPAALTYQPGKRA--MIKVK 188
Cdd:pfam01068 161 KDVeeAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGknWLKIK 203
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 2-327 9.54e-42

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: 147.45  E-value: 9.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   2 LAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELhDSLLERLPKG-SVIDGEIVIATAHGL-D 79
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPIL-AAALAALPILpAVLDGEIVVLDESGRsD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLHpaasrvakLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTP-MTQDRGLAEQWLE 158
Cdd:TIGR02779  80 FSALQNRLR--------AGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRySVHFEGDGQALLE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 159 QFEGAGLDGVIAKPAALTYQPGK-RAMIKVKHARTADCVVAGFRWHKTGKDAVGSLLLGLYDDRGaLQHVG-VTSSFTMA 236
Cdd:TIGR02779 152 AACRLGLEGVVAKRRDSPYRSGRsADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGG-LRYVGrVGTGFSEA 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 237 MRKQLVKELAPLrKHALDKHPWRawaqadarsgrmpggqsrwsAGKDLSWepLRIERVCEVKYDHLQGD-RFRHAAtFLR 315
Cdd:TIGR02779 231 ELATIKERLKPL-ESKPDKPGAR--------------------EKRGVHW--VKPELVAEVEFAGWTRDgRLRQAS-FVG 286

                         330
                  ....*....|..
gi 1125209170 316 WRPDKRPAACRY 327
Cdd:TIGR02779 287 LREDKPASEVTR 298
 
Name Accession Description Interval E-value
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 1-346 0e+00

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 542.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGLDF 80
Cdd:PRK08224   12 MLAKSVDAIPPGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRAELPERCVLDGEIVVARDGGLDF 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQMRLHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKlFAKLDPPLHLTPMTQDRGLAEQWLEQF 160
Cdd:PRK08224   92 EALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEA-AAAGSGPVHLTPATTDPATARRWFEEF 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 161 EGAGLDGVIAKPAALTYQPGKRAMIKVKHARTADCVVAGFRWHKTGkDAVGSLLLGLYDDRGALQHVGVTSSFTMAMRKQ 240
Cdd:PRK08224  171 EGAGLDGVIAKPLDGPYQPGKRAMFKVKHERTADCVVAGYRYHKSG-PVVGSLLLGLYDDDGQLHHVGVTSAFPMARRRE 249

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 241 LVKELAPLRKhALDKHPWrawaQADARSGRMPGGQSRWSAGKDLSWEPLRIERVCEVKYDHLQGDRFRHAATFLRWRPDK 320
Cdd:PRK08224  250 LTAELEPLRT-PFGDHPW----NWAAFTGRAPGGPSRWSAGKDLSWVPLRPERVVEVRYDHMEGGRFRHTAQFLRWRPDR 324

                         330       340
                  ....*....|....*....|....*.
gi 1125209170 321 RPAACRYDQLEVARPYQLAKVFSSGS 346
Cdd:PRK08224  325 DPRSCTYEQLEEPVRYDLADVLPGAR 350
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
1-331 3.30e-112

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 333.43  E-value: 3.30e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHG-LD 79
Cdd:COG1793   117 MLATLVDSPPDGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDITDRFPELVEALRALPADDAVLDGEIVALDEDGrPP 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLHPAAsRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGLAEQWLEQ 159
Cdd:COG1793   197 FQALQQRLGRKR-DVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVIDWGEGEALFAA 275

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 160 FEGAGLDGVIAKPAALTYQPGKR--AMIKVKHARTADCVVAGFRWHKTG-KDAVGSLLLGLYDDRGALQHVGVTSS-FTM 235
Cdd:COG1793   276 AREAGLEGVMAKRLDSPYRPGRRsgDWLKVKCPRTQDLVVGGATPGKGRrAGGFGSLLLGVYDPGGELVYVGKVGTgFTD 355

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 236 AMRKQLVKELAPLRkhaLDKHPWRAWAqadarsgrmPGGQSRWsagkdlswepLRIERVCEVKYDHLQGD-RFRHAAtFL 314
Cdd:COG1793   356 AELAELTERLRPLT---RERSPFAVPS---------DGRPVRW----------VRPELVAEVAFDEITRSgALRFPR-FL 412

                         330
                  ....*....|....*..
gi 1125209170 315 RWRPDKRPAACRYDQLE 331
Cdd:COG1793   413 RLREDKPPEEATLEELE 429
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 1-191 2.74e-96

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: 283.75  E-value: 2.74e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGLDF 80
Cdd:cd07905     4 MLARAVDALPEPGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARALLPPGCVLDGELVVWRGGRLDF 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQMRLHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGLAEQWLEQF 160
Cdd:cd07905    84 DALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPATTDRAEAREWLEEF 163

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1125209170 161 EGAGLDGVIAKPAALTYQPGKRAMIKVKHAR 191
Cdd:cd07905   164 EGAGLEGVVAKRLDGPYRPGERAMLKVKHRR 194
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 1-189 3.48e-48

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: 160.78  E-value: 3.48e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIATAHGL-D 79
Cdd:cd07906     4 MLATLVDEPPDGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAALPVRDAVLDGEIVVLDEGGRpD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLHPAasrvAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGlaEQWLEQ 159
Cdd:cd07906    84 FQALQNRLRLR----RRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHFEGGG--AALFAA 157

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1125209170 160 FEGAGLDGVIAKPAALTYQPGKR--AMIKVKH 189
Cdd:cd07906   158 ACELGLEGIVAKRADSPYRSGRRsrDWLKIKC 189
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 191-327 1.90e-47

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: 156.32  E-value: 1.90e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 191 RTADCVVAGFRWHKtgkDAVGSLLLGLYDDRGALQHVGVTSSFTMAMRKQLVKELAPLRkhalDKHPWRAWAqadarsgr 270
Cdd:cd07970     1 RTADCVVGGVRGHK---DRPGSLLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPAR----AGHPWTGRA-------- 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1125209170 271 mPGGQSRWSAGKDLSWEPLRIERVCEVKYDHLQGD-RFRHAATFLRWRPDKRPAACRY 327
Cdd:cd07970    66 -PGFPSRWGTRKSLEWVPVRPELVVEVSADTAEGGgRFRHPLRFLRWRPDKSPEDCTL 122
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 17-323 3.66e-44

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 161.71  E-value: 3.66e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  17 FEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDsLLERLPKGSVI-DGEIVIATAHGL-DFDALQMRlhpaasrv 94
Cdd:PRK09632  481 FEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAA-LAEDLADHHVVlDGEIVALDDSGVpSFGLLQNR-------- 551

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  95 aklAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKlDPPLHLTPmtQDRGLAEQWLEQFEGAGLDGVIAKPAA 174
Cdd:PRK09632  552 ---GRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGSLTVPP--LLPGDGAEALAYSRELGWEGVVAKRRD 625

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 175 LTYQPGKR--AMIKVKHARTADCVVAGFRWHKTGK-DAVGSLLLGLYDDRGaLQHVG-VTSSFTMAMRKQLVKELAPLRK 250
Cdd:PRK09632  626 STYQPGRRssSWIKDKHWRTQEVVIGGWRPGEGGRsSGIGSLLLGIPDPGG-LRYVGrVGTGFTERELASLKETLAPLHR 704

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1125209170 251 halDKHPWRA-WAQADArsgrmpggqsrwsagKDLSWepLRIERVCEVKYDHLQGD-RFRHAAtFLRWRPDKRPA 323
Cdd:PRK09632  705 ---DTSPFDAdLPAADA---------------KGATW--VRPELVGEVRYSEWTPDgRLRQPS-WRGLRPDKKPG 758
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 1-188 6.65e-44

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: 150.13  E-value: 6.65e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDD-----GTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGS---VIDGEIVI 72
Cdd:pfam01068   2 MLAKSFKSIEEAlkkfgGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEksfILDGEIVA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  73 ---ATAHGLDFDALQMRLhPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQD 149
Cdd:pfam01068  82 vdpETGEILPFQVLADRK-KKKVDVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVT 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1125209170 150 RGL--AEQWLEQFEGAGLDGVIAKPAALTYQPGKRA--MIKVK 188
Cdd:pfam01068 161 KDVeeAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGknWLKIK 203
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 2-327 9.54e-42

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: 147.45  E-value: 9.54e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   2 LAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELhDSLLERLPKG-SVIDGEIVIATAHGL-D 79
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPIL-AAALAALPILpAVLDGEIVVLDESGRsD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLHpaasrvakLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTP-MTQDRGLAEQWLE 158
Cdd:TIGR02779  80 FSALQNRLR--------AGRDRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRySVHFEGDGQALLE 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 159 QFEGAGLDGVIAKPAALTYQPGK-RAMIKVKHARTADCVVAGFRWHKTGKDAVGSLLLGLYDDRGaLQHVG-VTSSFTMA 236
Cdd:TIGR02779 152 AACRLGLEGVVAKRRDSPYRSGRsADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGG-LRYVGrVGTGFSEA 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 237 MRKQLVKELAPLrKHALDKHPWRawaqadarsgrmpggqsrwsAGKDLSWepLRIERVCEVKYDHLQGD-RFRHAAtFLR 315
Cdd:TIGR02779 231 ELATIKERLKPL-ESKPDKPGAR--------------------EKRGVHW--VKPELVAEVEFAGWTRDgRLRQAS-FVG 286

                         330
                  ....*....|..
gi 1125209170 316 WRPDKRPAACRY 327
Cdd:TIGR02779 287 LREDKPASEVTR 298
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 1-190 1.38e-29

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: 112.43  E-value: 1.38e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAES-----LPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDsLLERLPKGSVIDGEIV-IAT 74
Cdd:cd07898     4 MLAHPEESaeaakAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAA-AAKALPHEFILDGEILaWDD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  75 AHGLDFDALQMRLHPAAsRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDRGlAE 154
Cdd:cd07898    83 NRGLPFSELFKRLGRKF-RDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPALPVES-AE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1125209170 155 QWLEQFEGA---GLDGVIAKPAALTYQPGKR--AMIKVKHA 190
Cdd:cd07898   161 ELEAAFARArarGNEGLMLKDPDSPYEPGRRglAWLKLKKE 201
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 1-188 1.61e-26

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: 104.54  E-value: 1.61e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPD-----DGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVI-DGEIVIAT 74
Cdd:cd07901     8 MLAQRAPSVEEalikeGGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVRELVKAEDAIlDGEAVAYD 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  75 AHGlDFDALQMRLHPAASR--VAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFaKLDPPLHLTPM--TQDR 150
Cdd:cd07901    88 PDG-RPLPFQETLRRFRRKydVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIV-PETEAILLAPRivTDDP 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1125209170 151 GLAEQWLEQFEGAGLDGVIAKPAALTYQPGKR--AMIKVK 188
Cdd:cd07901   166 EEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRgkNWLKVK 205
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 49-330 4.30e-26

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: 108.95  E-value: 4.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  49 FPELHDSL--LERLPkgSVIDGEIVIATAHGL-DFDALQMRLHPAASRvaklaketPSSFVAFDLLASGGRDRMATPQRE 125
Cdd:TIGR02776  11 FPEIVKALalLKLLP--AWIDGEIVVLDERGRaDFAALQNALSAGASR--------PLTYYAFDLLFLSGEDLRDLPLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 126 RRALLEKLFAKLDPPLhLTPMTQDRGLAEQWLEQFEGAGLDGVIAKPAALTYQPGKRA-MIKVKHARTADCVVAGFrwhK 204
Cdd:TIGR02776  81 RKKRLKQLLKAQDEPA-IRYSDHFESDGDALLESACRLGLEGVVSKRLDSPYRSGRSKdWLKLKCRRRQEFVITGY---T 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 205 TGKDAVGSLLLGLYDDrGALQHVG-VTSSFTMAMRKQLVKELAPLrkhaldkhpwrawaqadaRSGRMPGGQSRWSAGKD 283
Cdd:TIGR02776 157 PPNRRFGALLVGVYEG-GQLVYAGkVGTGFGADTLKTLLARLKAL------------------GAKASPFSGPAGAKTRG 217

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1125209170 284 LSWepLRIERVCEVKYDHLQGDR-FRHAAtFLRWRPDKRPAACRYDQL 330
Cdd:TIGR02776 218 VHW--VRPSLVAEVEYAGITRDGiLREAS-FKGLREDKPAEEVTLETP 262
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 1-182 1.68e-25

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: 101.86  E-value: 1.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGT----FLFEPKWDGFRAIVFRGAADVYIQSR--DLkpLDRYFPELHDsLLERLPKGSVIDGEIVIAT 74
Cdd:cd07897     8 MLAHPLEDDPEDLGdpsdWQAEWKWDGIRGQLIRRGGEVFLWSRgeEL--ITGSFPELLA-AAEALPDGTVLDGELLVWR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  75 AHG-LDFDALQMRLhpaaSR---VAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPP-LHLTPMTQ- 148
Cdd:cd07897    85 DGRpLPFNDLQQRL----GRktvGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPrLDLSPLIAf 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1125209170 149 -DRGLAEQWLEQFEGAGLDGVIAKPAALTYQPGKR 182
Cdd:cd07897   161 aDWEELAALRAQSRERGAEGLMLKRRDSPYLVGRK 195
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 10-196 2.14e-24

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 103.77  E-value: 2.14e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  10 PDDgtFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDsLLERLPKGSVIDGEIVIATAHG---LDFDALQMR 86
Cdd:PRK09247  224 PAD--WQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAE-AAEALPDGTVLDGELLVWRPEDgrpQPFADLQQR 300

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  87 LhpaaSR---VAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPP-LHLTPMTQdrglAEQW--LEQF 160
Cdd:PRK09247  301 I----GRktvGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPrLDLSPLVP----FSDWdeLAAL 372

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1125209170 161 EGA----GLDGVIAKPAALTYQPGKRAMIKVKHAR---TADCV 196
Cdd:PRK09247  373 RAAarerGVEGLMLKRRDSPYLVGRKKGPWWKWKRdplTIDAV 415
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 1-323 1.10e-23

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: 101.62  E-value: 1.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPD-----DGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPE-LHDSLLERLP--KGSVIDGEIV- 71
Cdd:TIGR00574 170 MLAERAKSIEEalkkkGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEiFTEFIKEAFPgiKSCILDGEMVa 249

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  72 IATAHG--LDFDALQMRLHpaASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQD 149
Cdd:TIGR00574 250 IDPETGkpLPFGTLLRRKR--KYDIKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILKPIPNRIEIAEMKIV 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 150 RGL--AEQWLEQFEGAGLDGVIAKPAALTYQPGKRA--MIKVKH------ARTADCVVAGFRWHKTGK-DAVGSLLLGLY 218
Cdd:TIGR00574 328 SNVeeLEKFLNEAISEGCEGLMLKDLKSIYEPGKRGwlWLKIKPeylegmGDTLDLVVIGAYYGKGSRgGMYGSFLCACY 407

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 219 D-DRGALQHVG-VTSSFTMAMRKQLVKELAPLRKHALDKHPwrawaqadarsgrmpggqSRWSAGKDLSWEPLRIerVCE 296
Cdd:TIGR00574 408 DpESEEFKTITkVGTGFTDADLQELGKKLPPLWIDPPGSRV------------------PSILPDEPDIWPDPAI--VWE 467

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 1125209170 297 VKYDHLQ----------GDRFRhaaTFLRWRPDKRPA 323
Cdd:TIGR00574 468 VTGAEITkspaykangiSLRFP---RFSRIRDDKGPE 501
ligD PRK09633
DNA ligase D;
1-240 2.12e-23

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 101.27  E-value: 2.12e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHD-------SLLERLPkgSVIDGEIVIA 73
Cdd:PRK09633    4 MQPTLTTSIPIGDEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEfcesnfeHLKEELP--LTLDGELVCL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  74 T-AHGLDFDALQMR-LHPAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQDR- 150
Cdd:PRK09633   82 VnPYRSDFEHVQQRgRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPASPDPYAKARi 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 151 GLAE---------QWLEQFEGaglDGVIAKPAALTYQPGKRAM--IKVKHARTADCVVAGFrwhktgkDAVGSLLLGLYD 219
Cdd:PRK09633  162 QYIPsttdfdalwEAVKRYDG---EGIVAKKKTSKWLENKRSKdwLKIKNWRYVHVIVTGY-------DPSNGYFTGSVY 231

                         250       260
                  ....*....|....*....|.
gi 1125209170 220 DRGALQHVGvtsSFTMAMRKQ 240
Cdd:PRK09633  232 KDGQLTEVG---SVKHGMEDE 249
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 2-324 4.66e-22

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 97.28  E-value: 4.66e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   2 LAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRdlKPLD--RYFPELHDSLlERLPKGS-VIDGEIVIATAHGL 78
Cdd:PRK05972  238 LATLVDRPPSGDGWIYEIKFDGYRILARIEGGEVRLFTR--NGLDwtAKLPALAKAA-AALGLPDaWLDGEIVVLDEDGV 314

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  79 -DFDALQMRLhpAASRVAKLAketpssFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLhltpmtqdrglaEQWL 157
Cdd:PRK05972  315 pDFQALQNAF--DEGRTEDLV------YFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDR------------IRFS 374

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 158 EQFEGAG-----------LDGVIAKPAALTYQPGKRA-MIKVKHARTADCVVAGFRWHKTGKDAVGSLLLGLYDDrGALQ 225
Cdd:PRK05972  375 EHFDAGGdavlasacrlgLEGVIGKRADSPYVSGRSEdWIKLKCRARQEFVIGGYTDPKGSRSGFGSLLLGVHDD-DHLR 453

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 226 HVG-VTSSFTMAMRKQLVKELAPLrkhALDKHPWrawaqadarSGRMPGGQSRwsagkDLSWepLRIERVCEVKYDHLQG 304
Cdd:PRK05972  454 YAGrVGTGFGAATLKTLLPRLKAL---ATDKSPF---------AGKPAPRKAR-----GVHW--VKPELVAEVEFAGWTR 514

                         330       340
                  ....*....|....*....|.
gi 1125209170 305 D-RFRHAAtFLRWRPDKrPAA 324
Cdd:PRK05972  515 DgIVRQAV-FKGLREDK-PAR 533
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 1-214 5.77e-21

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 90.97  E-value: 5.77e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLlerLPKGSVIDGEIVIATAHGL-D 79
Cdd:PRK07636    6 MLLESAKEPFNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLD---IPDGTVLDGELIVLGSTGApD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  80 FDALQMRLhpaasRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLfaKLDPP-LHLTPMTQDRGLAeqWLE 158
Cdd:PRK07636   83 FEAVMERF-----QSKKSTKIHPVVFCVFDVLYINGVSLTALPLSERKEILASL--LLPHPnVKIIEGIEGHGTA--YFE 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1125209170 159 QFEGAGLDGVIAKPAALTYQPGKRA--MIKVKHARTADCVVAGFRwhktgKDAVGSLL 214
Cdd:PRK07636  154 LVEERELEGIVIKKANSPYEINKRSdnWLKVINYQYTDVLITGYR-----KEEFGLLL 206
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 5-322 7.54e-21

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 93.50  E-value: 7.54e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   5 LAESLPD--------DGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVI-DGEIVIATA 75
Cdd:PRK01109  232 LAERLSSpkeilkkmGGEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEAIKAEEAIvEGEIVAVDP 311

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  76 HGLDFDALQMRLHpaasR-----VAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDpPLHLTP--MTQ 148
Cdd:PRK01109  312 ETGEMRPFQELMH----RkrkydIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-KVKLAEriITD 386

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 149 DRGLAEQWLEQFEGAGLDGVIAKPAALT--YQPGKRAM--IKVKH------ARTADCVVAGFRWHKtGKDA--VGSLLLG 216
Cdd:PRK01109  387 DVEELEKFFHRAIEEGCEGLMAKSLGKDsiYQAGARGWlwIKYKRdyqsemADTVDLVVVGAFYGR-GRRGgkYGSLLMA 465

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 217 LYD-DRGALQHVG-VTSSFTMAMRKQLVKELAPL-RKHaldKHPwRAWAQADArsgrmpggqSRW--------SAGKDLS 285
Cdd:PRK01109  466 AYDpKTDTFETVCkVGSGFTDEDLDELPKMLKPYkIDH---KHP-RVVSKMEP---------DVWvepklvaeIIGAEIT 532

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 1125209170 286 WEPLRIERVCEVKYDHLQGDRF-RhaatFLRWRPDKRP 322
Cdd:PRK01109  533 LSPLHTCCLGVVEKGAGLAIRFpR----FIRWRDDKSP 566
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 1-323 1.12e-19

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 89.64  E-value: 1.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPD-----DGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLeRLPKGSVI-DGEiVIAt 74
Cdd:PRK03180  187 MLAQTATSVAEalarlGGPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVR-ALPVRSLVlDGE-AIA- 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  75 ahgLDFDALQMRLHPAASR------VAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFakldPPLHLTP--M 146
Cdd:PRK03180  264 ---LRPDGRPRPFQVTASRfgrrvdVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALV----PAAHRVPrlV 336

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 147 TQDRGLAEQWLEQFEGAGLDGVIAKPAALTYQPGKR--AMIKVKHARTADCVVAGFRW---HKTGKdaVGSLLLGLYD-D 220
Cdd:PRK03180  337 TADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRgaGWLKVKPVHTLDLVVLAAEWgsgRRTGK--LSNLHLGARDpA 414

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 221 RGALQHVGVT-SSFTMAMrkqLVKELAPLRKHALDKHPWRAWaqadarsgrmpggqsrwsagkdlswepLRIERVCEVKY 299
Cdd:PRK03180  415 TGGFVMLGKTfKGMTDAM---LAWQTERFLELAVGRDGWTVY---------------------------VRPELVVEIAF 464

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1125209170 300 DHLQGD---------RFrhaATFLRWRPDKRPA 323
Cdd:PRK03180  465 DGVQRStrypggvalRF---ARVLRYRPDKTPA 494
OBF_DNA_ligase_family cd08040
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 191-317 5.41e-19

The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; 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 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: 153442  Cd Length: 108  Bit Score: 81.15  E-value: 5.41e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 191 RTADCVVAGFRWHKTGK-DAVGSLLLGLYDDRGALQHVGVTSSFTMAMRKQLVKELAPLRKhALDKHPWrawaqadarsg 269
Cdd:cd08040     1 KTAEAVIIGMRAGFGNRsDVMGSLLLGYYGEDGLQAVFSVGTGFSADERRDLWQNLEPLVT-SFDDHPV----------- 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1125209170 270 rmpggqsrWSAGKDLSWEPLRIERVCEVKYDHLQGDRFRHAATFLRWR 317
Cdd:cd08040    69 --------WNVGKDLSFVPLYPGKVVEVKYFEMGSKDCLRFPVFIGIR 108
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 191-325 9.30e-17

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: 75.29  E-value: 9.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 191 RTADCVVAGFRWHKTGKDAVGSLLLGLYDDrGALQHVG-VTSSFTMAMRKQLVKELAPLRKhalDKHPWRAWAQADARsg 269
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDG-GRLVYVGrVGTGFSAATLRELRERLAPLER---KTSPFADPPPADAR-- 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1125209170 270 rmpggQSRWsagkdlsWEPlriERVCEVKYDHLQGD-RFRHAAtFLRWRPDKRPAAC 325
Cdd:cd07971    75 -----GAVW-------VKP---ELVAEVEFAEWTPDgRLRHPV-FKGLREDKPAAEV 115
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 206-320 1.49e-15

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: 71.08  E-value: 1.49e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 206 GKDAVGSLLLGLYDDrGALQHVGVTSS-FTMAMRKQLVKELAPLRKhalDKHPWRAWAQadarsgrmPGGQSRWsagkdl 284
Cdd:pfam04679   1 RRGGFGSLLLGVYDD-GRLVYVGKVGTgFTDADLEELRERLKPLER---KKPPFAEPPP--------EARGAVW------ 62

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1125209170 285 swepLRIERVCEVKYDHLQGD-RFRHAAtFLRWRPDK 320
Cdd:pfam04679  63 ----VEPELVAEVEFAEWTRSgRLRFPR-FKGLREDK 94
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 1-189 2.76e-10

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: 59.49  E-value: 2.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLP------DDGTFLFEPKWDGFRA-IVFRGAADVYIQSRDLKPLDRYFPELHDSLLERL---PKGSVIDGEI 70
Cdd:cd07900    13 MLAKPTKGVSevldrfEDKEFTCEYKYDGERAqIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLkpsVKSFILDSEI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  71 V-IATAHG--LDFDALQMRlhpAASRVAKLAKETPSSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHL-TPM 146
Cdd:cd07900    93 VaYDRETGkiLPFQVLSTR---KRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFaTSK 169

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1125209170 147 TQDRGLA-EQWLEQFEGAGLDGVIAKpaAL----TYQPGKRAM--IKVKH 189
Cdd:cd07900   170 DSEDTEEiQEFLEEAVKNNCEGLMVK--TLdsdaTYEPSKRSHnwLKLKK 217
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 1-188 2.10e-09

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: 56.96  E-value: 2.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPD------DGtFLFEPKWDGFRAIVFRGAADVYIQSRDLKP-LDRYFPELHDSLLERLPKGS--VIDGEIV 71
Cdd:cd07902    17 MLAEACKSVEDamkkcpNG-MYAEIKYDGERVQVHKQGDNFKFFSRSLKPvLPHKVAHFKDYIPKAFPHGHsmILDSEVL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  72 IA---TAHGLDFDALqmrlhpAASRVAKLAKETPSSFVaFDLLASGGRDRMATPQRERRALLEKLFAKLDPPLHLTPMTQ 148
Cdd:cd07902    96 LVdtkTGKPLPFGTL------GIHKKSAFKDANVCLFV-FDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIMLSEMKF 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1125209170 149 DRGLAE--QWLEQFEGAGLDGVIAKPAALTYQPGKRAMIKVK 188
Cdd:cd07902   169 VKKADDlsAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVK 210
PHA00454 PHA00454
ATP-dependent DNA ligase
 13-211 1.35e-08

ATP-dependent DNA ligase


Pssm-ID: 222798 [Multi-domain]  Cd Length: 315  Bit Score: 55.43  E-value: 1.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  13 GTFLFEPKWDGFRAIVF-RGAADVYIQSRDLKPldryFPEL-----HDSLLERL--------PKGSVIDGEIVIAtahGL 78
Cdd:PHA00454   27 GYLIADVKYDGVRGNIVvDNTADHGWLSREGKT----IPALehlngFDRRWAKLlnddrcifPDGFMLDGELMVK---GV 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  79 DFDALQMRLHpaasRVAKLAKETPSSFVAFDLLASGGRDRMATP----------QRERRA---LLEKLFAKLDPPLHLTP 145
Cdd:PHA00454  100 DFNTGSGLLR----RKWKVLFELHLKKLHVVVYDVTPLDVLESGedydvmsllmYEHVRAmvpLLMEYFPEIDWFLSESY 175

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1125209170 146 MTQDRGLAEQWLEQFEGAGLDGVIAKPAALTYQPGKRA-MIKVKHARTADCVVAGFRWHKTGKDAVG 211
Cdd:PHA00454  176 EVYDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSgWWKMKPECEADGTIVGVVWGTPGLANEG 242
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 1-188 3.91e-08

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: 52.18  E-value: 3.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAKLAESLPDDGTFLFEPKWDGFRAIVFRGAadvyIQSRDLKPLdrYFPELhdsLLERLPKGsVIDGEIVIATAhglDF 80
Cdd:cd07896     4 LLAKTYDEGEDISGYLVSEKLDGVRAYWDGKQ----LLSRSGKPI--AAPAW---FTAGLPPF-PLDGELWIGRG---QF 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  81 DALQ---MRLHPAASRVAKLaketpsSFVAFDLLASGGrdrmatPQRERRALLEKLFAKLDPP-LHLTPMTQDRGLAE-- 154
Cdd:cd07896    71 EQTSsivRSKKPDDEDWRKV------KFMVFDLPSAKG------PFEERLERLKNLLEKIPNPhIKIVPQIPVKSNEAld 138

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1125209170 155 QWLEQFEGAGLDGVIAKPAALTYQPGK-RAMIKVK 188
Cdd:cd07896   139 QYLDEVVAAGGEGLMLRRPDAPYETGRsDNLLKLK 173
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 1-188 1.68e-06

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: 48.34  E-value: 1.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   1 MLAK------LAESLPDDGTFLFEPKWDGFRAIVFRGAADV-----------YIQSRDLKPlDRYFPELHDSLLERLPkg 63
Cdd:cd07903    15 MLAErlnigyVEIKLLKGKPFYIETKLDGERIQLHKDGNEFkyfsrngndytYLYGASLTP-GSLTPYIHLAFNPKVK-- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  64 SVI-DGEIVIatahgldFDALQMRLHPAASR--VAKLAKETPSS----FVAFDLLASGGRDRMATPQRERRALLEKLFAK 136
Cdd:cd07903    92 SCIlDGEMVV-------WDKETKRFLPFGTLkdVAKLREVEDSDlqpcFVVFDILYLNGKSLTNLPLHERKKLLEKIITP 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1125209170 137 LDPPLHLTPMTQDRGlAEQWLEQFEGA---GLDGVIAKPAALTYQPGKRA--MIKVK 188
Cdd:cd07903   165 IPGRLEVVKRTEAST-KEEIEEALNEAidnREEGIVVKDLDSKYKPGKRGggWIKIK 220
PRK09125 PRK09125
DNA ligase; Provisional
 66-214 3.18e-06

DNA ligase; Provisional


Pssm-ID: 181662 [Multi-domain]  Cd Length: 282  Bit Score: 47.94  E-value: 3.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  66 IDGEIVIAtaHGlDFDALQ---MRLHPAASRVAKLaketpsSFVAFDLLASGGrdrmatPQRERRALLEKLFAKLDPPlH 142
Cdd:PRK09125   86 LDGELWAG--RG-QFEAISsivRDKTPDDAAWRKV------RFMVFDLPDAPG------DFEERLAVLKKLLAKLPSP-Y 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 143 LTPMTQ----DRGLAEQWLEQFEGAGLDGVIAKPAALTYQPGK-RAMIKVKHARTADCVVAGfrwHKTGK----DAVGSL 213
Cdd:PRK09125  150 IKIIEQirvrSEAALQQFLDQIVAAGGEGLMLHRPDAPYEAGRsDDLLKLKPYYDAEATVIG---HLPGKgkfaGMLGAL 226


                  .
gi 1125209170 214 L 214
Cdd:PRK09125  227 L 227
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 4-171 5.57e-05

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: 43.18  E-value: 5.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170   4 KLAESLPDDGTFLFEPKWDGFRAIVFRGAADVYIQSRDLKPLDRYFPELHDSLLERLPKGSVIDGEIVIatahgldfdal 83
Cdd:cd06846    10 EALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGRELLTLKPGFILDGELVV----------- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  84 qmrlhpaasRVAKLAKETPsSFVAFDLLASGGRDRMATPQRERRALLEKLFAKLDPPL-----HLTPMTQDRGLAEQWLE 158
Cdd:cd06846    79 ---------ENREVANPKP-TYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDpvklvPLENAPSYDETLDDLLE 148

                         170
                  ....*....|...
gi 1125209170 159 QFEGAGLDGVIAK 171
Cdd:cd06846   149 KLKKKGKEGLVFK 161
30 PHA02587
DNA ligase; Provisional
 18-270 8.11e-05

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 44.31  E-value: 8.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  18 EPKWDGFRAIVFRGAADVYIQSRDLKP---LDRYFPEL--HDSLLERLPKGSVIDGEIVI-----ATAHGLDFdalQMRL 87
Cdd:PHA02587  157 QLKADGARCFADIDADGIEIRSRNGNEylgLDLLKEELkkMTAEARQRPGGVVIDGELVYvevetKKPNGLSF---LFDD 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  88 HPAASRVAKLAKETPSSFVAFDLLASG-----------------------GRDRMATPQRERRALLEKLFAKLDPPLhLT 144
Cdd:PHA02587  234 SKAKEFVGVVADRATGNGIVNKSLKGTiskeeaqeivfqvwdivplevyyGKEKSDMPYDDRFSKLAQMFEDCGYDR-VE 312

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 145 PMTQdrglaeQWLEQFEGA----------GLDGVIAKPAALTYQPGKRA-MIKVKHARTADCVVAGFRWHKTGKDAVGSL 213
Cdd:PHA02587  313 LIEN------QVVNNLEEAkeiykryvdqGLEGIILKNTDGLWEDGRSKdQIKFKEVIDIDLEIVGVYEHKKDPNKVGGF 386

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170 214 LlgLYDDRGALQhVGVTSSF--TMAMRKQLVKELAPL-RKHALDKHpwRAWAQADARSGR 270
Cdd:PHA02587  387 T--LESACGKIT-VNTGSGLtdTTHRKKDGKKVVIPLsERHELDRE--ELMANKGKYIGK 441
OBF_DNA_ligase cd07893
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 192-250 5.06e-04

The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; 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 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: 153435 [Multi-domain]  Cd Length: 129  Bit Score: 39.64  E-value: 5.06e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1125209170 192 TADCVVAGFRWHKtGKDA--VGSLLLGLYD-DRGALQHVG-VTSSFTMAMRKQLVKELAPLRK 250
Cdd:cd07893     2 TLDLVIVGAYYGK-GRRGggIGAFLCAVYDpERDEFQTICkVGSGFTDEELEELRELLKELKT 63
mRNA_cap_enzyme pfam01331
mRNA capping enzyme, catalytic domain; This family represents the ATP binding catalytic domain ...
 20-136 3.47e-03

mRNA capping enzyme, catalytic domain; This family represents the ATP binding catalytic domain of the mRNA capping enzyme.


Pssm-ID: 396068 [Multi-domain]  Cd Length: 194  Bit Score: 38.16  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125209170  20 KWDGFRAIVF--RGAADVYIQSRD-----LKPLDryFPELHDSLLERLPKGSVIDGEIVIatahgldfDALQMRLHPAAs 92
Cdd:pfam01331  23 KADGTRYMMLitRDPEGCYIIDRDnnvylVENLR--FPRENDEGLEKHLDGTLLDGELVI--------DTVPGQKQQPR- 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1125209170  93 rvaklaketpssFVAFDLLASGGRDRMATPQRERRALLEKLFAK 136
Cdd:pfam01331  92 ------------YLIYDIVAINGQTVMQRPFYSRLFIIKREIIK 123
 
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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