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Conserved domains on  [gi|1896675212|gb|QNK53719|]
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DNA ligase [Dermacoccus sp. PAMC28757]

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 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
1-309 1.27e-95

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


:

Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 289.51  E-value: 1.27e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVAL-VDG 78
Cdd:COG1793   114 VPPMLATLVDSPPDGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDITDRFPELVEALRAlPADDAVLDGEIVALdEDG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  79 APDFRTVMHRLAPGGGRSRMsatspedarrMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAY 158
Cdd:COG1793   194 RPPFQALQQRLGRKRDVAKL----------AREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHV 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 159 ---EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRPVAGSLAQ-VGAILVGEVTDDG-L 233
Cdd:COG1793   264 idwGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPGKGRRAGgFGSLLLGVYDPGGeL 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1896675212 234 RYRGRVGTGFSASSGRALLEWLTPM--PQCPFTAddlpPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:COG1793   344 VYVGKVGTGFTDAELAELTERLRPLtrERSPFAV----PSDGRPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRED 417
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
1-309 1.27e-95

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 289.51  E-value: 1.27e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVAL-VDG 78
Cdd:COG1793   114 VPPMLATLVDSPPDGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDITDRFPELVEALRAlPADDAVLDGEIVALdEDG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  79 APDFRTVMHRLAPGGGRSRMsatspedarrMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAY 158
Cdd:COG1793   194 RPPFQALQQRLGRKRDVAKL----------AREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHV 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 159 ---EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRPVAGSLAQ-VGAILVGEVTDDG-L 233
Cdd:COG1793   264 idwGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPGKGRRAGgFGSLLLGVYDPGGeL 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1896675212 234 RYRGRVGTGFSASSGRALLEWLTPM--PQCPFTAddlpPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:COG1793   344 VYVGKVGTGFTDAELAELTERLRPLtrERSPFAV----PSDGRPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRED 417
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 5-310 1.21e-82

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: 251.84  E-value: 1.21e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   5 LASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGS-HLADFDDIVLDGEIVALVD-GAPDF 82
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAAlAALPILPAVLDGEIVVLDEsGRSDF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  83 RTVMHRLAPGGGRsrmsatspedarrmartPVRFMAFDVLRAAGHDVVTMPWSARRALLEG-AGVADGVAVEVP---EAY 158
Cdd:TIGR02779  81 SALQNRLRAGRDR-----------------PATYYAFDLLYLDGEDLRDLPLSERKKLLEElLKAIKGPLAPDRysvHFE 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 159 EDGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEWLKSVHRQADSFVVGGWRPVAGSLAQVGAILVGEVTDDGLRYRGR 238
Cdd:TIGR02779 144 GDGQALLEAACRLGLEGVVAKRRDSPYRSG-RSADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGR 222

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1896675212 239 VGTGFSASSGRALLEWLTPMPQCPftaDDLPPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLDI 310
Cdd:TIGR02779 223 VGTGFSEAELATIKERLKPLESKP---DKPGAREKRGVHWVKPELVAEVEFAGWTRDGRLRQASFVGLREDK 291
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 2-309 3.54e-79

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 255.70  E-value: 3.54e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPA-AAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG--SHLADfDDIVLDGEIVALVD- 77
Cdd:PRK09632  462 APMLATAGtVAGLKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAAlaEDLAD-HHVVLDGEIVALDDs 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  78 GAPDFrtvmHRLApgggrsrmsatspedaRRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGvAVEVPEA 157
Cdd:PRK09632  541 GVPSF----GLLQ----------------NRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGG-SLTVPPL 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 158 YE-DGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRPVAGSLAQ-VGAILVGEVTDDGLRY 235
Cdd:PRK09632  600 LPgDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVIGGWRPGEGGRSSgIGSLLLGIPDPGGLRY 679

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1896675212 236 RGRVGTGFSASSGRALLEWLTPMP--QCPFTAdDLPPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:PRK09632  680 VGRVGTGFTERELASLKETLAPLHrdTSPFDA-DLPAADAKGATWVRPELVGEVRYSEWTPDGRLRQPSWRGLRPD 754
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 1-200 3.57e-65

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: 203.15  E-value: 3.57e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVALVD-G 78
Cdd:cd07906     1 IEPMLATLVDEPPDGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAAlPVRDAVLDGEIVVLDEgG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  79 APDFRTVMHRLAPGGgrsrmsatspedaRRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAY 158
Cdd:cd07906    81 RPDFQALQNRLRLRR-------------RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1896675212 159 ED-GAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHR 200
Cdd:cd07906   148 EGgGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKCR 190
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 3-196 1.30e-35

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: 127.40  E-value: 1.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   3 PMLASPAAAPPT-----GPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG--SHLADFDD--IVLDGEIV 73
Cdd:pfam01068   1 PMLAKSFKSIEEalkkfGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEalKEAFKPDEksFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  74 ALV--DGAP-DFRTVMHRLapgggrSRMSatspEDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGV 150
Cdd:pfam01068  81 AVDpeTGEIlPFQVLADRK------KKKV----DVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPG 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1896675212 151 AVEVPEAY-----EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:pfam01068 151 RIQLAESIvtkdvEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGKNWLK 201
 
Name Accession Description Interval E-value
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
1-309 1.27e-95

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 289.51  E-value: 1.27e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVAL-VDG 78
Cdd:COG1793   114 VPPMLATLVDSPPDGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDITDRFPELVEALRAlPADDAVLDGEIVALdEDG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  79 APDFRTVMHRLAPGGGRSRMsatspedarrMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAY 158
Cdd:COG1793   194 RPPFQALQQRLGRKRDVAKL----------AREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHV 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 159 ---EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRPVAGSLAQ-VGAILVGEVTDDG-L 233
Cdd:COG1793   264 idwGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRSGDWLKVKCPRTQDLVVGGATPGKGRRAGgFGSLLLGVYDPGGeL 343

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1896675212 234 RYRGRVGTGFSASSGRALLEWLTPM--PQCPFTAddlpPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:COG1793   344 VYVGKVGTGFTDAELAELTERLRPLtrERSPFAV----PSDGRPVRWVRPELVAEVAFDEITRSGALRFPRFLRLRED 417
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 5-310 1.21e-82

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: 251.84  E-value: 1.21e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   5 LASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGS-HLADFDDIVLDGEIVALVD-GAPDF 82
Cdd:TIGR02779   1 LATLVTTPPTGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAAlAALPILPAVLDGEIVVLDEsGRSDF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  83 RTVMHRLAPGGGRsrmsatspedarrmartPVRFMAFDVLRAAGHDVVTMPWSARRALLEG-AGVADGVAVEVP---EAY 158
Cdd:TIGR02779  81 SALQNRLRAGRDR-----------------PATYYAFDLLYLDGEDLRDLPLSERKKLLEElLKAIKGPLAPDRysvHFE 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 159 EDGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEWLKSVHRQADSFVVGGWRPVAGSLAQVGAILVGEVTDDGLRYRGR 238
Cdd:TIGR02779 144 GDGQALLEAACRLGLEGVVAKRRDSPYRSG-RSADWLKLKCRRRQEFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGR 222

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1896675212 239 VGTGFSASSGRALLEWLTPMPQCPftaDDLPPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLDI 310
Cdd:TIGR02779 223 VGTGFSEAELATIKERLKPLESKP---DKPGAREKRGVHWVKPELVAEVEFAGWTRDGRLRQASFVGLREDK 291
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 2-309 3.54e-79

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 255.70  E-value: 3.54e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPA-AAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG--SHLADfDDIVLDGEIVALVD- 77
Cdd:PRK09632  462 APMLATAGtVAGLKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAAlaEDLAD-HHVVLDGEIVALDDs 540

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  78 GAPDFrtvmHRLApgggrsrmsatspedaRRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGvAVEVPEA 157
Cdd:PRK09632  541 GVPSF----GLLQ----------------NRGRDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGG-SLTVPPL 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 158 YE-DGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRPVAGSLAQ-VGAILVGEVTDDGLRY 235
Cdd:PRK09632  600 LPgDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWRTQEVVIGGWRPGEGGRSSgIGSLLLGIPDPGGLRY 679

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1896675212 236 RGRVGTGFSASSGRALLEWLTPMP--QCPFTAdDLPPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:PRK09632  680 VGRVGTGFTERELASLKETLAPLHrdTSPFDA-DLPAADAKGATWVRPELVGEVRYSEWTPDGRLRQPSWRGLRPD 754
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 1-200 3.57e-65

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: 203.15  E-value: 3.57e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVALVD-G 78
Cdd:cd07906     1 IEPMLATLVDEPPDGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAAlPVRDAVLDGEIVVLDEgG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  79 APDFRTVMHRLAPGGgrsrmsatspedaRRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAY 158
Cdd:cd07906    81 RPDFQALQNRLRLRR-------------RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1896675212 159 ED-GAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHR 200
Cdd:cd07906   148 EGgGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKCR 190
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 3-309 7.52e-60

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 205.14  E-value: 7.52e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   3 PMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVAL-VDGAP 80
Cdd:PRK05972  236 PQLATLVDRPPSGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAAAlGLPDAWLDGEIVVLdEDGVP 315

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  81 DFRTVMHRLApgGGRSrmsatspEDarrmartpVRFMAFDVLRAAGHDVVTMPWSARRALLEGA-GVADGVAVEVPEAYE 159
Cdd:PRK05972  316 DFQALQNAFD--EGRT-------ED--------LVYFAFDLPFLGGEDLRELPLEERRARLRALlEAARSDRIRFSEHFD 378

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 160 -DGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEWLKSVHRQADSFVVGGWRPVAGSLAQVGAILVGEVTDDGLRYRGR 238
Cdd:PRK05972  379 aGGDAVLASACRLGLEGVIGKRADSPYVSG-RSEDWIKLKCRARQEFVIGGYTDPKGSRSGFGSLLLGVHDDDHLRYAGR 457

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1896675212 239 VGTGFSASSGRALLEWLTPM--PQCPFtADDLPPEDLEGTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:PRK05972  458 VGTGFGAATLKTLLPRLKALatDKSPF-AGKPAPRKARGVHWVKPELVAEVEFAGWTRDGIVRQAVFKGLRED 529
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 42-310 5.17e-52

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: 179.44  E-value: 5.17e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  42 TRSGADATARFPEITGS-HLADFDDIVLDGEIVALVD-GAPDFRTVMHRLAPGGGRsrmsatspedarrmartPVRFMAF 119
Cdd:TIGR02776   1 TRNGHDWTKRFPEIVKAlALLKLLPAWIDGEIVVLDErGRADFAALQNALSAGASR-----------------PLTYYAF 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 120 DVLRAAGHDVVTMPWSARR----ALLEGAGVADGVAVE-VPEayeDGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEW 194
Cdd:TIGR02776  64 DLLFLSGEDLRDLPLEERKkrlkQLLKAQDEPAIRYSDhFES---DGDALLESACRLGLEGVVSKRLDSPYRSG-RSKDW 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 195 LKSVHRQADSFVVGGWRPVAGSLaqvGAILVGEVTDDGLRYRGRVGTGFSASSGRALLEWLTPMPQCPFTADDLPPEDLE 274
Cdd:TIGR02776 140 LKLKCRRRQEFVITGYTPPNRRF---GALLVGVYEGGQLVYAGKVGTGFGADTLKTLLARLKALGAKASPFSGPAGAKTR 216

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1896675212 275 GTHWVRPEITVDVTHLGRSAGGRLRQPSYKGLRLDI 310
Cdd:TIGR02776 217 GVHWVRPSLVAEVEYAGITRDGILREASFKGLREDK 252
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 1-200 3.52e-42

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: 144.31  E-value: 3.52e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADF-DDIVLDGEIVALVDGA 79
Cdd:cd07905     1 VEPMLARAVDALPEPGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARALLpPGCVLDGELVVWRGGR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  80 PDFRTVMHRLAPGGGRSRMSAtspedarrmARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEG--AGVADGVAVEVPEA 157
Cdd:cd07905    81 LDFDALQQRIHPAASRVRRLA---------EETPASFVAFDLLALGGRDLRGRPLRERRAALEAllAGWGPPLHLSPATT 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1896675212 158 YEDGAALFAATLE-QGVEGIVSKRVDAPYRPGVRSeeWLKSVHR 200
Cdd:cd07905   152 DRAEAREWLEEFEgAGLEGVVAKRLDGPYRPGERA--MLKVKHR 193
ligD PRK09633
DNA ligase D;
1-310 6.31e-37

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 139.02  E-value: 6.31e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG------SHLADFDDIVLDGEIVA 74
Cdd:PRK09633    1 MKPMQPTLTTSIPIGDEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEfcesnfEHLKEELPLTLDGELVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  75 LVDG-APDFRTVMHRlapggGRSRmsatSPED-ARRMARTPVRFMAFDVLRAAGHDVVTMPWSARR----ALLEGAGVA- 147
Cdd:PRK09633   81 LVNPyRSDFEHVQQR-----GRLK----NTEViAKSANARPCQLLAFDLLELKGESLTSLPYLERKkqldKLMKAAKLPa 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 148 ----DGVAV-EVPEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVH-RQADSFVVgGWRPVAGslaqvg 221
Cdd:PRK09633  152 spdpYAKARiQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNwRYVHVIVT-GYDPSNG------ 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 222 aILVGEVTDDG-LRYRGRVGTGFSASSGRALLEWLTPMPQcpftaddlppEDLEGTHWVRPEITVDVTHLGRSaGGRLRQ 300
Cdd:PRK09633  225 -YFTGSVYKDGqLTEVGSVKHGMEDEERQTLRAIFKQNGT----------KTKSGEYTLEPSICVTVACITFD-GGTLRE 292

                         330
                  ....*....|
gi 1896675212 301 PSYKGLRLDI 310
Cdd:PRK09633  293 PSFVSFLFDM 302
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 1-257 1.76e-36

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 133.87  E-value: 1.76e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADF-DDIVLDGEIVALVDGA 79
Cdd:PRK08224    9 VEPMLAKSVDAIPPGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRAELpERCVLDGEIVVARDGG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  80 PDFRTVMHRLAPGGGRSRMSAtspedarrmARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAgVADGVAVEVPEAYE 159
Cdd:PRK08224   89 LDFEALQQRIHPAASRVRKLA---------EETPASFVAFDLLALGDRDLTGRPFAERRAALEAA-AAGSGPVHLTPATT 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 160 DgAALFAATLEQ----GVEGIVSKRVDAPYRPGVRseEWLKSVH-RQADSfVVGGWRPVAGSlAQVGAILVGEVTDDG-L 233
Cdd:PRK08224  159 D-PATARRWFEEfegaGLDGVIAKPLDGPYQPGKR--AMFKVKHeRTADC-VVAGYRYHKSG-PVVGSLLLGLYDDDGqL 233

                         250       260
                  ....*....|....*....|....
gi 1896675212 234 RYRGRVGTgFSASSGRALLEWLTP 257
Cdd:PRK08224  234 HHVGVTSA-FPMARRRELTAELEP 256
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 1-196 1.14e-35

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: 127.84  E-value: 1.14e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPA-----AAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADFDDIVLDGEIVAL 75
Cdd:cd07898     1 IKPMLAHPEesaeaAKAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAKALPHEFILDGEILAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  76 VDGAPdfrtvMHRLAPGGGRSRMSatspEDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVP 155
Cdd:cd07898    81 DDNRG-----LPFSELFKRLGRKF----RDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIA 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1896675212 156 EAY-----EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:cd07898   152 PALpvesaEELEAAFARARARGNEGLMLKDPDSPYEPGRRGLAWLK 197
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 3-196 1.30e-35

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: 127.40  E-value: 1.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   3 PMLASPAAAPPT-----GPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG--SHLADFDD--IVLDGEIV 73
Cdd:pfam01068   1 PMLAKSFKSIEEalkkfGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEalKEAFKPDEksFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  74 ALV--DGAP-DFRTVMHRLapgggrSRMSatspEDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGV 150
Cdd:pfam01068  81 AVDpeTGEIlPFQVLADRK------KKKV----DVEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPG 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1896675212 151 AVEVPEAY-----EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:pfam01068 151 RIQLAESIvtkdvEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRGKNWLK 201
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 3-307 1.31e-35

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 129.49  E-value: 1.31e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   3 PMLASPAAAPPTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADfdDIVLDGEIVAL-VDGAPD 81
Cdd:PRK07636    5 PMLLESAKEPFNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLDIPD--GTVLDGELIVLgSTGAPD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  82 FRTVMHRLapgggRSRMSATSpedarrmarTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVADGVAVEVPEAYEDG 161
Cdd:PRK07636   83 FEAVMERF-----QSKKSTKI---------HPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHPNVKIIEGIEGHG 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 162 AALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGGWRpvagslaqvgailvgevtddglryRGRVGT 241
Cdd:PRK07636  149 TAYFELVEERELEGIVIKKANSPYEINKRSDNWLKVINYQYTDVLITGYR------------------------KEEFGL 204

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 242 GFSASSGR--ALLEWLTPMPQCPFTADDLPPEDLEGTHWV--RPEITVDVTHLGRSAGGRLRQPSYKGLR 307
Cdd:PRK07636  205 LLSYLDGRsaGIMEFMPYDARKKFYKRAKRLVVGEDKKFVyiEPIIGCRVKHRFKTKNGMLRIPSFVEWR 274
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 201-309 7.49e-35

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: 122.67  E-value: 7.49e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 201 QADSFVVGGWRPVAGSLAQVGAILVGEVTDDGLRYRGRVGTGFSASSGRALLEWLTPMPQCPFTADDLPPEDLEGTHWVR 280
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDGGRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFADPPPADARGAVWVK 80

                          90       100
                  ....*....|....*....|....*....
gi 1896675212 281 PEITVDVTHLGRSAGGRLRQPSYKGLRLD 309
Cdd:cd07971    81 PELVAEVEFAEWTPDGRLRHPVFKGLRED 109
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 2-196 2.87e-32

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: 118.80  E-value: 2.87e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPAAAPPT-----GPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITG--SHLADFDDIVLDGEIVA 74
Cdd:cd07901     6 RPMLAQRAPSVEEalikeGGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEavRELVKAEDAILDGEAVA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  75 L-VDGAP-DFRTVMHRLapggGRSRmsatspEDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEG-------AG 145
Cdd:cd07901    86 YdPDGRPlPFQETLRRF----RRKY------DVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEivpeteaIL 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1896675212 146 VADGVAVEVPEayeDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:cd07901   156 LAPRIVTDDPE---EAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLK 203
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 2-196 2.40e-30

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: 113.80  E-value: 2.40e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RP-MLASP---AAAPPTGPS-WRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADFDDIVLDGEIVALV 76
Cdd:cd07897     5 YPfMLAHPledDPEDLGDPSdWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAEALPDGTVLDGELLVWR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  77 DGAP-DFRTVMHRLapggGRSRMSATSPEDArrmartPVRFMAFDVLRAAGHDVVTMPWSARRALLE------GAGVADG 149
Cdd:cd07897    85 DGRPlPFNDLQQRL----GRKTVGKKLLAEA------PAAFRAYDLLELNGEDLRALPLRERRARLEallarlPPPRLDL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1896675212 150 VAVEVPEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:cd07897   155 SPLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWK 201
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 2-196 2.08e-24

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 103.00  E-value: 2.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RP-MLASPAAAPP---TGPS-WRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLADFDDIVLDGEIVAL- 75
Cdd:PRK09247  206 YPfFLAHPLEDEDltlGDPAdWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAEALPDGTVLDGELLVWr 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  76 -VDGAP-DFRTVMHRLapggGRSRMSatspedARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEG--AGVADGV- 150
Cdd:PRK09247  286 pEDGRPqPFADLQQRI----GRKTVG------KKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEAliARLPDPRl 355

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1896675212 151 ---AVEVPEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:PRK09247  356 dlsPLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKGPWWK 404
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 2-196 8.27e-22

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 95.42  E-value: 8.27e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPAAAPPT-----GPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA-DFDDIVLDGEIVAL 75
Cdd:PRK03180  185 RPMLAQTATSVAEalarlGGPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVRAlPVRSLVLDGEAIAL 264

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  76 -VDGAPD-FRTVMHRLAPGGGRSRMSATspedarrmarTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAG----VADG 149
Cdd:PRK03180  265 rPDGRPRpFQVTASRFGRRVDVAAARAT----------QPLSPFFFDALHLDGRDLLDAPLSERLAALDALVpaahRVPR 334

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1896675212 150 VAVEVPEAyedGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:PRK03180  335 LVTADPAA---AAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLK 378
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 220-309 9.16e-21

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: 84.95  E-value: 9.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 220 VGAILVGEVTDDGLRYRGRVGTGFSASSGRALLEWLTP--MPQCPFTAddlPPEDLEGTHWVRPEITVDVTHLGRSAGGR 297
Cdd:pfam04679   5 FGSLLLGVYDDGRLVYVGKVGTGFTDADLEELRERLKPleRKKPPFAE---PPPEARGAVWVEPELVAEVEFAEWTRSGR 81

                          90
                  ....*....|..
gi 1896675212 298 LRQPSYKGLRLD 309
Cdd:pfam04679  82 LRFPRFKGLRED 93
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 2-309 4.07e-20

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: 90.45  E-value: 4.07e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPAAAP-----PTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLAD-FDDI---VLDGEI 72
Cdd:TIGR00574 168 KPMLAERAKSIeealkKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKEaFPGIkscILDGEM 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  73 VAlVD---GAP-DFRTVMHRLAPgggRSRMSAtspedarrMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGAGVAD 148
Cdd:TIGR00574 248 VA-IDpetGKPlPFGTLLRRKRK---YDIKAM--------DQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILKPI 315

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 149 GVAVEVPEAY-----EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK-------SVHRQADSFVVGGWRPVAGS 216
Cdd:TIGR00574 316 PNRIEIAEMKivsnvEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKikpeyleGMGDTLDLVVIGAYYGKGSR 395

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 217 LAQVGAILVGeVTD---DGLRYRGRVGTGFSASSGRALLEWLTPMPQCPftADDLPPEDL--EGTHWVRPEITVDVTH-- 289
Cdd:TIGR00574 396 GGMYGSFLCA-CYDpesEEFKTITKVGTGFTDADLQELGKKLPPLWIDP--PGSRVPSILpdEPDIWPDPAIVWEVTGae 472

                         330       340
                  ....*....|....*....|....*
gi 1896675212 290 -----LGRSAGGRLRQPSYKGLRLD 309
Cdd:TIGR00574 473 itkspAYKANGISLRFPRFSRIRDD 497
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 2-309 5.69e-18

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 84.25  E-value: 5.69e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPAAAP-----PTGPSWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSHLA--DFDDIVLDGEIVA 74
Cdd:PRK01109  229 RPMLAERLSSPkeilkKMGGEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEaiKAEEAIVEGEIVA 308

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  75 lVDgaPD------FRTVMHRlapggGRSRmsatspEDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLEGA---- 144
Cdd:PRK01109  309 -VD--PEtgemrpFQELMHR-----KRKY------DIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIvken 374

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 145 ---GVADGVAVEVPEAYEdgaALFAATLEQGVEGIVSKRV--DAPYRPGVRSEEWLK-----------SVhrqaDSFVVG 208
Cdd:PRK01109  375 dkvKLAERIITDDVEELE---KFFHRAIEEGCEGLMAKSLgkDSIYQAGARGWLWIKykrdyqsemadTV----DLVVVG 447

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 209 -----GWRpvAGSLaqvGAILVG---EVTDDGLRYrGRVGTGFSassgRALLEWLTPMPQcPFTADDLPPE---DLEGTH 277
Cdd:PRK01109  448 afygrGRR--GGKY---GSLLMAaydPKTDTFETV-CKVGSGFT----DEDLDELPKMLK-PYKIDHKHPRvvsKMEPDV 516

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 1896675212 278 WVRP---------EITVDVTH------LGRSAGGRLRQPSYKGLRLD 309
Cdd:PRK01109  517 WVEPklvaeiigaEITLSPLHtcclgvVEKGAGLAIRFPRFIRWRDD 563
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 2-196 1.71e-17

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: 79.54  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLAspAAAPPTGPSWRH--------EVKWDGIRAIVTVSGGEMSIATRSGADATARF-----PEITGSHLADF----- 63
Cdd:cd07903    13 RPMLA--ERLNIGYVEIKLlkgkpfyiETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYgasltPGSLTPYIHLAfnpkv 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  64 DDIVLDGEIVAlvdgapdFRTVMHRLAP-GGGRS-RMSATSPEDARRmartPVrFMAFDVLRAAGHDVVTMPWSARRALL 141
Cdd:cd07903    91 KSCILDGEMVV-------WDKETKRFLPfGTLKDvAKLREVEDSDLQ----PC-FVVFDILYLNGKSLTNLPLHERKKLL 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 142 EGAGVADGVAVEVPEAY-----EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLK 196
Cdd:cd07903   159 EKIITPIPGRLEVVKRTeastkEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIK 218
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 21-196 1.62e-15

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: 73.22  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  21 EVKWDGIRAIVTVSGGEMSIATRSGADATARFPEITGSH-LADFDDIVLDGEIVAlvdgapdfrtvmhrlapgggrsrms 99
Cdd:cd06846    24 QEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGRElLTLKPGFILDGELVV------------------------- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 100 atspeDARRMARTPVRFMAFDVLRAAGHDVVTMPWSARRALLE--GAGVADGVAVE------VPEAYEDGAALFAATLEQ 171
Cdd:cd06846    79 -----ENREVANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKslLKEFEGLDPVKlvplenAPSYDETLDDLLEKLKKK 153

                         170       180
                  ....*....|....*....|....*..
gi 1896675212 172 GVEGIVSKRVDAPY--RPGvRSEEWLK 196
Cdd:cd06846   154 GKEGLVFKHPDAPYkgRPG-SSGNQLK 179
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 3-196 2.60e-11

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: 61.43  E-value: 2.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   3 PMLASPAAAPPTGPSWRHEVKWDGIRAIVTvsGGEMsiATRSGAdatarfpEITGSH--LADFDDIVLDGEIVAlvdGAP 80
Cdd:cd07896     3 LLLAKTYDEGEDISGYLVSEKLDGVRAYWD--GKQL--LSRSGK-------PIAAPAwfTAGLPPFPLDGELWI---GRG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  81 DFRTVMhrlapggGRSRMSATSPEDARRmartpVRFMAFDVLRAaghdvvTMPWSAR----RALLEGAGVADGVAVE--V 154
Cdd:cd07896    69 QFEQTS-------SIVRSKKPDDEDWRK-----VKFMVFDLPSA------KGPFEERlerlKNLLEKIPNPHIKIVPqiP 130

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1896675212 155 PEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEWLK 196
Cdd:cd07896   131 VKSNEALDQYLDEVVAAGGEGLMLRRPDAPYETG-RSDNLLK 171
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 2-196 5.84e-11

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: 61.03  E-value: 5.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   2 RPMLASPA-----------AAPPTGpswrhEVKWDGIRAIVTVS-GGEMSIATRSGADATARFPEI----TGSHLADFDD 65
Cdd:cd07900    11 KPMLAKPTkgvsevldrfeDKEFTC-----EYKYDGERAQIHLLeDGKVKIFSRNLENNTEKYPDIvavlPKSLKPSVKS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  66 IVLDGEIVAlvdgapdFRTVMHRLAPG---GGRSRMSATSPEdarrmARTPVRFMAFDVLRAAGHDVVTMPWSARRALLE 142
Cdd:cd07900    86 FILDSEIVA-------YDRETGKILPFqvlSTRKRKDVDAND-----IKVQVCVFAFDLLYLNGESLLKKPLRERRELLH 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1896675212 143 GAgvadgvAVEVP-----------EAYEDGAALFAATLEQGVEGIVSK--RVDAPYRPGVRSEEWLK 196
Cdd:cd07900   154 SL------FKEVPgrfqfatskdsEDTEEIQEFLEEAVKNNCEGLMVKtlDSDATYEPSKRSHNWLK 214
OBF_DNA_ligase_family cd08040
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 206-307 6.91e-11

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: 58.42  E-value: 6.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 206 VVGGWRPVAGSLAQ-VGAILVGEVTDDGLRYRGRVGTGFSASSGRALLEWLTPMPQCPFTADDLPPEDLEGTHWVRPEIT 284
Cdd:cd08040     6 VIIGMRAGFGNRSDvMGSLLLGYYGEDGLQAVFSVGTGFSADERRDLWQNLEPLVTSFDDHPVWNVGKDLSFVPLYPGKV 85

                          90       100
                  ....*....|....*....|...
gi 1896675212 285 VDVTHLGRSAGGRLRQPSYKGLR 307
Cdd:cd08040    86 VEVKYFEMGSKDCLRFPVFIGIR 108
PRK09125 PRK09125
DNA ligase; Provisional
 23-244 7.59e-09

DNA ligase; Provisional


Pssm-ID: 181662 [Multi-domain]  Cd Length: 282  Bit Score: 55.64  E-value: 7.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  23 KWDGIRAIVTvsGGEMSiaTRSG------ADATARFPeitgshladfdDIVLDGEivalvdgapdfrtvmhrLAPGGGR- 95
Cdd:PRK09125   50 KLDGVRAYWD--GKQLL--TRQGnpiaapAWFTAGFP-----------PFPLDGE-----------------LWAGRGQf 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  96 SRMSAT----SPEDA--RRmartpVRFMAFDVLRAAGhdvvtmPWSAR----RALLEGAGVADGVAVEvPEAYEDGAALF 165
Cdd:PRK09125   98 EAISSIvrdkTPDDAawRK-----VRFMVFDLPDAPG------DFEERlavlKKLLAKLPSPYIKIIE-QIRVRSEAALQ 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 166 A---ATLEQGVEGIVSKRVDAPYRPGvRSEEWLK-SVHRQADSFVVgGWRPVAGSLA-QVGAILVgeVTDDGLRYrgRVG 240
Cdd:PRK09125  166 QfldQIVAAGGEGLMLHRPDAPYEAG-RSDDLLKlKPYYDAEATVI-GHLPGKGKFAgMLGALLV--ETPDGREF--KIG 239


                  ....
gi 1896675212 241 TGFS 244
Cdd:PRK09125  240 SGFS 243
PHA00454 PHA00454
ATP-dependent DNA ligase
 21-307 9.34e-09

ATP-dependent DNA ligase


Pssm-ID: 222798 [Multi-domain]  Cd Length: 315  Bit Score: 55.81  E-value: 9.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  21 EVKWDGIRAIVTVS-GGEMSIATRSGadatARFPEITgsHLADFDD----------------IVLDGEIvaLVDGApDFR 83
Cdd:PHA00454   32 DVKYDGVRGNIVVDnTADHGWLSREG----KTIPALE--HLNGFDRrwakllnddrcifpdgFMLDGEL--MVKGV-DFN 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  84 TvmhrlapGGGRSRMSATSPEDArrmARTPVRFMAFDVL------RAAGHDV--VTMPWSARRA---LLEGAGVADGVAV 152
Cdd:PHA00454  103 T-------GSGLLRRKWKVLFEL---HLKKLHVVVYDVTpldvleSGEDYDVmsLLMYEHVRAMvplLMEYFPEIDWFLS 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 153 EVPEAY--EDGAALFAATLEQGVEGIVSKRVDAPYRPGVRSEEWLKSVHRQADSFVVGgwrPVAGS--LAQVGAILVGEV 228
Cdd:PHA00454  173 ESYEVYdmESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSGWWKMKPECEADGTIVG---VVWGTpgLANEGKVIGFRV 249

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 229 tddgLRYRGRV--GTGFSassgRALLEWLTpmPQCPFTADDLPPEDLEGthWVrpeitVDVTHLGRSAGGRLRQPSYKGL 306
Cdd:PHA00454  250 ----LLEDGRVvnATGIS----RALMEEFT--ANVKEHGEDYEAMPYNG--RA-----CQVSYMERTPDGSLRHPSFDRF 312


                  .
gi 1896675212 307 R 307
Cdd:PHA00454  313 R 313
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 1-196 8.73e-07

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: 48.87  E-value: 8.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212   1 MRPMLASPAAAP-------PTGpsWRHEVKWDGIRAIVTVSGGEMSIATRSGADATARfpEItgSHLADF--------DD 65
Cdd:cd07902    14 VKPMLAEACKSVedamkkcPNG--MYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPH--KV--AHFKDYipkafphgHS 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  66 IVLDGEIVaLVDgapdfrTVMHRLAPGGGRSRMSATSPEDArrmarTPVRFMaFDVLRAAGHDVVTMPWSARRALLEgag 145
Cdd:cd07902    88 MILDSEVL-LVD------TKTGKPLPFGTLGIHKKSAFKDA-----NVCLFV-FDCLYYNGESLMDKPLRERRKILE--- 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1896675212 146 vaDGVAV-----------EVPEAyEDGAALFAATLEQGVEGIVSKRVDAPYRPGVRseEWLK 196
Cdd:cd07902   152 --DNMVEipnrimlsemkFVKKA-DDLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLK 208
30 PHA02587
DNA ligase; Provisional
 21-196 2.22e-06

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 48.93  E-value: 2.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  21 EVKWDGIRAIVTVSGGEMSIATRSG------ADATARFPEITGSHLADFDDIVLDGEIV------------ALVDGAPDF 82
Cdd:PHA02587  157 QLKADGARCFADIDADGIEIRSRNGneylglDLLKEELKKMTAEARQRPGGVVIDGELVyvevetkkpnglSFLFDDSKA 236

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  83 RTVMHRLAP---GGG---RSRMSATSPEDARRMArtpvrFMAFDVLRAaghDVV------TMPWSARRALLEG-AGVADG 149
Cdd:PHA02587  237 KEFVGVVADratGNGivnKSLKGTISKEEAQEIV-----FQVWDIVPL---EVYygkeksDMPYDDRFSKLAQmFEDCGY 308

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1896675212 150 VAVE-----VPEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPGvRSEEWLK 196
Cdd:PHA02587  309 DRVElienqVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIK 359
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 21-196 1.83e-04

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: 42.00  E-value: 1.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  21 EVKWDGIRA-I-VTVSGGE--MSIATRSGADATA-RFP---------EITGSHLADFDDIVLDGEIVALVDG----APDF 82
Cdd:cd08039    27 ETKYDGEYCqIhIDLSKDSspIRIFSKSGKDSTAdRAGvhsiirkalRIGKPGCKFSKNCILEGEMVVWSDRqgkiDPFH 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212  83 RTVMHRLAPGGGRSRMSATSPEDARRMArtpvrFMAFDVLRAAGHDVVTMPWSARRALLEG-AGVADGVAVEV------- 154
Cdd:cd08039   107 KIRKHVERSGSFIGTDNDSPPHEYEHLM-----IVFFDVLLLDDESLLSKPYSERRDLLESlVHVIPGYAGLSerfpidf 181

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1896675212 155 --PEAYEDGAALFAATLEQGVEGIVSKRVDAPYRPgVRSEE------WLK 196
Cdd:cd08039   182 srSSGYERLRQIFARAIAERWEGLVLKGDEEPYFD-LFLEQgsfsgcWIK 230
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 206-301 1.27e-03

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: 38.07  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896675212 206 VVGGWRpvaGSLAQVGAILVGEVTDDG-LRYRGRVGTgFSASSGRALLEWLTP-MPQCPFTAddlpPEDLEGTHW----- 278
Cdd:cd07970     6 VVGGVR---GHKDRPGSLLLGLYDDGGrLRHVGRTSP-LAAAERRELAELLEPaRAGHPWTG----RAPGFPSRWgtrks 77

                          90       100
                  ....*....|....*....|....*...
gi 1896675212 279 -----VRPEITVDVTHLGRSAGGRLRQP 301
Cdd:cd07970    78 lewvpVRPELVVEVSADTAEGGGRFRHP 105
 
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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