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Conserved domains on  [gi|1593021893|gb|TDF51913|]
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ATP-dependent DNA ligase [Streptomyces sp. WAC05374]

Protein Classification

ATP-dependent DNA ligase( domain architecture ID 10167743)

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
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 7-209 2.15e-77

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: 235.60  E-value: 2.15e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAAR-QLPPALVLDGEV 85
Cdd:cd07905     1 VEPMLARAVDALPEPG----GWQYEPKWDGFRCLAF---RDGDEVRLQSRSGKPLTRYFPELVAAARaLLPPGCVLDGEL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQDRLSFEALQRRASSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFreRGLSPPWTLCPMTT 165
Cdd:cd07905    74 VVWRGGRLDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALL--AGWGPPLHLSPATT 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1593021893 166 DPALAQEWLTSWtEVPGVEGLVIKGMGQRYLPGARGWFKVRRRD 209
Cdd:cd07905   152 DRAEAREWLEEF-EGAGLEGVVAKRLDGPYRPGERAMLKVKHRR 194
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 209-328 3.09e-43

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: 145.15  E-value: 3.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 209 DTTEAIIAGITGTLRRPQILVLGRYDEDGRLRAVGRTTPLRPDAAARLADHLHPAGPGHPWTG--VRFTATWGSREPLDP 286
Cdd:cd07970     1 RTADCVVGGVRGHKDRPGSLLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPARAGHPWTGraPGFPSRWGTRKSLEW 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1593021893 287 ILVVPDLVAEVSADTAIDRGAWRHPLRFVRPRLDVTVADVPM 328
Cdd:cd07970    81 VPVRPELVVEVSADTAEGGGRFRHPLRFLRWRPDKSPEDCTL 122
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 7-209 2.15e-77

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: 235.60  E-value: 2.15e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAAR-QLPPALVLDGEV 85
Cdd:cd07905     1 VEPMLARAVDALPEPG----GWQYEPKWDGFRCLAF---RDGDEVRLQSRSGKPLTRYFPELVAAARaLLPPGCVLDGEL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQDRLSFEALQRRASSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFreRGLSPPWTLCPMTT 165
Cdd:cd07905    74 VVWRGGRLDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALL--AGWGPPLHLSPATT 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1593021893 166 DPALAQEWLTSWtEVPGVEGLVIKGMGQRYLPGARGWFKVRRRD 209
Cdd:cd07905   152 DRAEAREWLEEF-EGAGLEGVVAKRLDGPYRPGERAMLKVKHRR 194
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
7-326 3.51e-70

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 224.80  E-value: 3.51e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPA-LVLDGEV 85
Cdd:COG1793   114 VPPMLATLVDSPPDGG----DWAYEPKWDGYRVQAH---RDGGEVRLYSRNGEDITDRFPELVEALRALPADdAVLDGEI 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQD-RLSFEALQRRASSsGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGlsPPWTLCPMT 164
Cdd:COG1793   187 VALDEDgRPPFQALQQRLGR-KRDVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAP--PPLRLSPHV 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 165 TDPALAQEWLTSWTEVpGVEGLVIKGMGQRYLPGARG--WFKVRRRDTTEAIIAGIT-GTLRRPQI---LVLGRYDEDGR 238
Cdd:COG1793   264 IDWGEGEALFAAAREA-GLEGVMAKRLDSPYRPGRRSgdWLKVKCPRTQDLVVGGATpGKGRRAGGfgsLLLGVYDPGGE 342

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 239 LRAVGRT-TPLRPDAAARLADHLHP-AGPGHPWTGVRFT--ATWgsrepldpilVVPDLVAEVSADTAIDRGAWRHPlRF 314
Cdd:COG1793   343 LVYVGKVgTGFTDAELAELTERLRPlTRERSPFAVPSDGrpVRW----------VRPELVAEVAFDEITRSGALRFP-RF 411

                         330
                  ....*....|..
gi 1593021893 315 VRPRLDVTVADV 326
Cdd:COG1793   412 LRLREDKPPEEA 423
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 3-320 1.64e-62

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 202.43  E-value: 1.64e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   3 LKPPVEPMLAQAretvtAPGVLPGN-LAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAAR-QLPPALV 80
Cdd:PRK08224    5 VMPPVEPMLAKS-----VDAIPPGDgWSYEPKWDGFRCLVF---RDGDEVELGSRNGKPLTRYFPELVAALRaELPERCV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  81 LDGEVVVWSQDRLSFEALQRRASSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFrerGLSPPWTL 160
Cdd:PRK08224   77 LDGEIVVARDGGLDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAA---AGSGPVHL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 161 CPMTTDPALAQEWLTSWtEVPGVEGLVIKGMGQRYLPGARGWFKVRRRDTTEAIIAGITGTLRRPQI--LVLGRYDEDGR 238
Cdd:PRK08224  154 TPATTDPATARRWFEEF-EGAGLDGVIAKPLDGPYQPGKRAMFKVKHERTADCVVAGYRYHKSGPVVgsLLLGLYDDDGQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 239 LRAVGRTTPLRPDAAARLADHLHP--AGPG-HPWTGVRFTAT-------WGSREPLDPILVVPDLVAEVSADtAIDRGAW 308
Cdd:PRK08224  233 LHHVGVTSAFPMARRRELTAELEPlrTPFGdHPWNWAAFTGRapggpsrWSAGKDLSWVPLRPERVVEVRYD-HMEGGRF 311

                         330
                  ....*....|..
gi 1593021893 309 RHPLRFVRPRLD 320
Cdd:PRK08224  312 RHTAQFLRWRPD 323
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 209-328 3.09e-43

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: 145.15  E-value: 3.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 209 DTTEAIIAGITGTLRRPQILVLGRYDEDGRLRAVGRTTPLRPDAAARLADHLHPAGPGHPWTG--VRFTATWGSREPLDP 286
Cdd:cd07970     1 RTADCVVGGVRGHKDRPGSLLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPARAGHPWTGraPGFPSRWGTRKSLEW 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1593021893 287 ILVVPDLVAEVSADTAIDRGAWRHPLRFVRPRLDVTVADVPM 328
Cdd:cd07970    81 VPVRPELVVEVSADTAEGGGRFRHPLRFLRWRPDKSPEDCTL 122
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 29-326 1.41e-34

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: 128.19  E-value: 1.41e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  29 AFEAKFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVTAARQLP--PAlVLDGEVVVW-SQDRLSFEALQRRASSS 105
Cdd:TIGR02779  15 RYEVKYDGYRCLARIE---GGKVRLISRNGHDWTEKFPILAAALAALPilPA-VLDGEIVVLdESGRSDFSALQNRLRAG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 106 GRTvaqladamPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLSPPWTL--CPMTTDPALAqewltsWTEVP-- 181
Cdd:TIGR02779  91 RDR--------PATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRysVHFEGDGQAL------LEAACrl 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 182 GVEGLVIKGMGQRYLPGA-RGWFKVRRRDTTEAIIAGIT---GTLRRPQILVLGRYdEDGRLRAVGR-TTPLRPDAAARL 256
Cdd:TIGR02779 157 GLEGVVAKRRDSPYRSGRsADWLKLKCRRRQEFVIGGYTppnGSRSGFGALLLGVY-EGGGLRYVGRvGTGFSEAELATI 235

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1593021893 257 ADHLHPAGPGHPWTGVRFTA--TWgsrepldpilVVPDLVAEVSADTAIDRGAWRHPLrFVRPRLDVTVADV 326
Cdd:TIGR02779 236 KERLKPLESKPDKPGAREKRgvHW----------VKPELVAEVEFAGWTRDGRLRQAS-FVGLREDKPASEV 296
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 9-205 1.78e-32

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: 120.08  E-value: 1.78e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   9 PMLAQARETV-TAPGVLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPA----LVLDG 83
Cdd:pfam01068   1 PMLAKSFKSIeEALKKFGGAFIAEYKYDGERAQIH---KDGDEVKLFSRNLENITRHYPEIVEALKEAFKPdeksFILDG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  84 EVVVWSQDR---LSFEALQRRASSSGRtVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERglSPPWTL 160
Cdd:pfam01068  78 EIVAVDPETgeiLPFQVLADRKKKKVD-VEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEI--PGRIQL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1593021893 161 CPM--TTDPALAQEWLtSWTEVPGVEGLVIKGMGQRYLPGARG--WFKV 205
Cdd:pfam01068 155 AESivTKDVEEAQEFL-EEAISEGLEGLVVKDPDSTYEPGKRGknWLKI 202
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 228-320 4.14e-05

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: 41.81  E-value: 4.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 228 LVLGRYDeDGRLRAVGRT-TPLRPDAAARLADHLHP-AGPGHPWTGVRFT---ATWgsrepldpilVVPDLVAEVSADTA 302
Cdd:pfam04679   8 LLLGVYD-DGRLVYVGKVgTGFTDADLEELRERLKPlERKKPPFAEPPPEargAVW----------VEPELVAEVEFAEW 76

                          90
                  ....*....|....*...
gi 1593021893 303 IDRGAWRHPlRFVRPRLD 320
Cdd:pfam04679  77 TRSGRLRFP-RFKGLRED 93
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 7-209 2.15e-77

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: 235.60  E-value: 2.15e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAAR-QLPPALVLDGEV 85
Cdd:cd07905     1 VEPMLARAVDALPEPG----GWQYEPKWDGFRCLAF---RDGDEVRLQSRSGKPLTRYFPELVAAARaLLPPGCVLDGEL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQDRLSFEALQRRASSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFreRGLSPPWTLCPMTT 165
Cdd:cd07905    74 VVWRGGRLDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALL--AGWGPPLHLSPATT 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1593021893 166 DPALAQEWLTSWtEVPGVEGLVIKGMGQRYLPGARGWFKVRRRD 209
Cdd:cd07905   152 DRAEAREWLEEF-EGAGLEGVVAKRLDGPYRPGERAMLKVKHRR 194
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
7-326 3.51e-70

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 224.80  E-value: 3.51e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPA-LVLDGEV 85
Cdd:COG1793   114 VPPMLATLVDSPPDGG----DWAYEPKWDGYRVQAH---RDGGEVRLYSRNGEDITDRFPELVEALRALPADdAVLDGEI 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQD-RLSFEALQRRASSsGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGlsPPWTLCPMT 164
Cdd:COG1793   187 VALDEDgRPPFQALQQRLGR-KRDVAKLAREVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAP--PPLRLSPHV 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 165 TDPALAQEWLTSWTEVpGVEGLVIKGMGQRYLPGARG--WFKVRRRDTTEAIIAGIT-GTLRRPQI---LVLGRYDEDGR 238
Cdd:COG1793   264 IDWGEGEALFAAAREA-GLEGVMAKRLDSPYRPGRRSgdWLKVKCPRTQDLVVGGATpGKGRRAGGfgsLLLGVYDPGGE 342

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 239 LRAVGRT-TPLRPDAAARLADHLHP-AGPGHPWTGVRFT--ATWgsrepldpilVVPDLVAEVSADTAIDRGAWRHPlRF 314
Cdd:COG1793   343 LVYVGKVgTGFTDAELAELTERLRPlTRERSPFAVPSDGrpVRW----------VRPELVAEVAFDEITRSGALRFP-RF 411

                         330
                  ....*....|..
gi 1593021893 315 VRPRLDVTVADV 326
Cdd:COG1793   412 LRLREDKPPEEA 423
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 3-320 1.64e-62

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 202.43  E-value: 1.64e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   3 LKPPVEPMLAQAretvtAPGVLPGN-LAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAAR-QLPPALV 80
Cdd:PRK08224    5 VMPPVEPMLAKS-----VDAIPPGDgWSYEPKWDGFRCLVF---RDGDEVELGSRNGKPLTRYFPELVAALRaELPERCV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  81 LDGEVVVWSQDRLSFEALQRRASSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFrerGLSPPWTL 160
Cdd:PRK08224   77 LDGEIVVARDGGLDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAA---AGSGPVHL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 161 CPMTTDPALAQEWLTSWtEVPGVEGLVIKGMGQRYLPGARGWFKVRRRDTTEAIIAGITGTLRRPQI--LVLGRYDEDGR 238
Cdd:PRK08224  154 TPATTDPATARRWFEEF-EGAGLDGVIAKPLDGPYQPGKRAMFKVKHERTADCVVAGYRYHKSGPVVgsLLLGLYDDDGQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 239 LRAVGRTTPLRPDAAARLADHLHP--AGPG-HPWTGVRFTAT-------WGSREPLDPILVVPDLVAEVSADtAIDRGAW 308
Cdd:PRK08224  233 LHHVGVTSAFPMARRRELTAELEPlrTPFGdHPWNWAAFTGRapggpsrWSAGKDLSWVPLRPERVVEVRYD-HMEGGRF 311

                         330
                  ....*....|..
gi 1593021893 309 RHPLRFVRPRLD 320
Cdd:PRK08224  312 RHTAQFLRWRPD 323
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 209-328 3.09e-43

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: 145.15  E-value: 3.09e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 209 DTTEAIIAGITGTLRRPQILVLGRYDEDGRLRAVGRTTPLRPDAAARLADHLHPAGPGHPWTG--VRFTATWGSREPLDP 286
Cdd:cd07970     1 RTADCVVGGVRGHKDRPGSLLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPARAGHPWTGraPGFPSRWGTRKSLEW 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1593021893 287 ILVVPDLVAEVSADTAIDRGAWRHPLRFVRPRLDVTVADVPM 328
Cdd:cd07970    81 VPVRPELVVEVSADTAEGGGRFRHPLRFLRWRPDKSPEDCTL 122
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 7-208 3.45e-38

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: 134.59  E-value: 3.45e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGvlpgNLAFEAKFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVTAARQLPP-ALVLDGEV 85
Cdd:cd07906     1 IEPMLATLVDEPPDGE----DWLYEIKWDGYRALARVD---GGRVRLYSRNGLDWTARFPELAEALAALPVrDAVLDGEI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQD-RLSFEALQRRasssGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERglSPPWTLCPMT 164
Cdd:cd07906    74 VVLDEGgRPDFQALQNR----LRLRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAG--SPRLRVSEHF 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1593021893 165 TDPALAqewLTSWTEVPGVEGLVIKGMGQRYLPGARG--WFKVRRR 208
Cdd:cd07906   148 EGGGAA---LFAAACELGLEGIVAKRADSPYRSGRRSrdWLKIKCR 190
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 29-326 1.41e-34

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: 128.19  E-value: 1.41e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  29 AFEAKFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVTAARQLP--PAlVLDGEVVVW-SQDRLSFEALQRRASSS 105
Cdd:TIGR02779  15 RYEVKYDGYRCLARIE---GGKVRLISRNGHDWTEKFPILAAALAALPilPA-VLDGEIVVLdESGRSDFSALQNRLRAG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 106 GRTvaqladamPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLSPPWTL--CPMTTDPALAqewltsWTEVP-- 181
Cdd:TIGR02779  91 RDR--------PATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRysVHFEGDGQAL------LEAACrl 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 182 GVEGLVIKGMGQRYLPGA-RGWFKVRRRDTTEAIIAGIT---GTLRRPQILVLGRYdEDGRLRAVGR-TTPLRPDAAARL 256
Cdd:TIGR02779 157 GLEGVVAKRRDSPYRSGRsADWLKLKCRRRQEFVIGGYTppnGSRSGFGALLLGVY-EGGGLRYVGRvGTGFSEAELATI 235

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1593021893 257 ADHLHPAGPGHPWTGVRFTA--TWgsrepldpilVVPDLVAEVSADTAIDRGAWRHPLrFVRPRLDVTVADV 326
Cdd:TIGR02779 236 KERLKPLESKPDKPGAREKRgvHW----------VKPELVAEVEFAGWTRDGRLRQAS-FVGLREDKPASEV 296
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 9-205 1.78e-32

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: 120.08  E-value: 1.78e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   9 PMLAQARETV-TAPGVLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPA----LVLDG 83
Cdd:pfam01068   1 PMLAKSFKSIeEALKKFGGAFIAEYKYDGERAQIH---KDGDEVKLFSRNLENITRHYPEIVEALKEAFKPdeksFILDG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  84 EVVVWSQDR---LSFEALQRRASSSGRtVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERglSPPWTL 160
Cdd:pfam01068  78 EIVAVDPETgeiLPFQVLADRKKKKVD-VEELAEKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEI--PGRIQL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1593021893 161 CPM--TTDPALAQEWLtSWTEVPGVEGLVIKGMGQRYLPGARG--WFKV 205
Cdd:pfam01068 155 AESivTKDVEEAQEFL-EEAISEGLEGLVVKDPDSTYEPGKRGknWLKI 202
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 5-327 1.83e-32

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 127.81  E-value: 1.83e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   5 PPVEPMLAQARetvTAPGVLPGNLAFEAKFDGYRALLftSARPGGSTLlQSRRGSLIQRHFPDLVTAARQLPP-ALVLDG 83
Cdd:PRK09632  459 DDLAPMLATAG---TVAGLKASQWAFEGKWDGYRLLA--EADHGALRL-RSRSGRDVTAEYPELAALAEDLADhHVVLDG 532

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  84 EVVVW-SQDRLSFEALQRRAsssgrtvaqlaDAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERglsppwtlCP 162
Cdd:PRK09632  533 EIVALdDSGVPSFGLLQNRG-----------RDTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG--------GS 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 163 MTTDPAL---AQEWLTSWTEVpGVEGLVIKGMGQRYLPGARG--WFKVRRRDTTEAIIAGI-TGTLRRPQ---ILVLGRY 233
Cdd:PRK09632  594 LTVPPLLpgdGAEALAYSREL-GWEGVVAKRRDSTYQPGRRSssWIKDKHWRTQEVVIGGWrPGEGGRSSgigSLLLGIP 672

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 234 DEDGrLRAVGRT-TPLRPDAAARLADHLHPAGPGHPwtgvRFTATWGSREPLDPILVVPDLVAEVSADTAIDRGAWRHPL 312
Cdd:PRK09632  673 DPGG-LRYVGRVgTGFTERELASLKETLAPLHRDTS----PFDADLPAADAKGATWVRPELVGEVRYSEWTPDGRLRQPS 747

                         330
                  ....*....|....*.
gi 1593021893 313 -RFVRPrlDVTVADVP 327
Cdd:PRK09632  748 wRGLRP--DKKPGDVV 761
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 7-207 4.80e-32

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: 118.59  E-value: 4.80e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPMLAQARETVTAPGVLPGNLA-FEAKFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVTAARQLPPALVLDGEV 85
Cdd:cd07898     1 IKPMLAHPEESAEAAKAKKPAAAwVEDKYDGIRAQVHKD---GGRVEIFSRSLEDITDQFPELAAAAKALPHEFILDGEI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQDR-LSFEALQRRASSSGRTVAQLADAmPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRErgLSPPWTLCPMT 164
Cdd:cd07898    78 LAWDDNRgLPFSELFKRLGRKFRDKFLDEDV-PVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVE--IPGRIRIAPAL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1593021893 165 -TDPA--LAQEWLTSWTEvpGVEGLVIKGMGQRYLPGARG--WFKVRR 207
Cdd:cd07898   155 pVESAeeLEAAFARARAR--GNEGLMLKDPDSPYEPGRRGlaWLKLKK 200
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 10-204 8.79e-31

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: 115.73  E-value: 8.79e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  10 MLAQARETVTAPGVLPGNLAFEAKFDGYRALLftsARPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPALVLDGEVVVWS 89
Cdd:cd07897     8 MLAHPLEDDPEDLGDPSDWQAEWKWDGIRGQL---IRRGGEVFLWSRGEELITGSFPELLAAAEALPDGTVLDGELLVWR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  90 QDR-LSFEALQRRAsssGR---TVAQLADAmPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERG-----LSPPWTL 160
Cdd:cd07897    85 DGRpLPFNDLQQRL---GRktvGKKLLAEA-PAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPpprldLSPLIAF 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1593021893 161 cpmTTDPALAQEWLTSwtEVPGVEGLVIKGMGQRYLPG-ARG-WFK 204
Cdd:cd07897   161 ---ADWEELAALRAQS--RERGAEGLMLKRRDSPYLVGrKKGdWWK 201
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 6-208 8.50e-28

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: 107.63  E-value: 8.50e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQARETV-TAPGVLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPA--LVLD 82
Cdd:cd07901     4 PVRPMLAQRAPSVeEALIKEGGEAAVEYKYDGIRVQIH---KDGDEVRIFSRRLEDITNALPEVVEAVRELVKAedAILD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  83 GEVVVWSQDR--LSF-EALQRRASSSGrtVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRErglSPPWT 159
Cdd:cd07901    81 GEAVAYDPDGrpLPFqETLRRFRRKYD--VEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPE---TEAIL 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1593021893 160 LCPM--TTDPALAQEWLtSWTEVPGVEGLVIKGMGQRYLPGARG--WFKVRRR 208
Cdd:cd07901   156 LAPRivTDDPEEAEEFF-EEALEAGHEGVMVKSLDSPYQAGRRGknWLKVKPD 207
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 10-204 9.43e-28

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 113.40  E-value: 9.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  10 MLAQARETVTAPGVLPGNLAFEAKFDGYRALLftsARPGGSTLLQSRRGSLIQRHFPDLVTAARQLPPALVLDGEVVVW- 88
Cdd:PRK09247  209 FLAHPLEDEDLTLGDPADWQAEWKWDGIRVQL---VRRGGEVRLWSRGEELITERFPELAEAAEALPDGTVLDGELLVWr 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  89 -SQDR-LSFEALQRRAsssGR---TVAQLADAmPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGlSPPWTLCPM 163
Cdd:PRK09247  286 pEDGRpQPFADLQQRI---GRktvGKKLLADY-PAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLP-DPRLDLSPL 360

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1593021893 164 TTdpalaqewLTSWTEV---------PGVEGLVIKGMGQRYLPG-ARG-WFK 204
Cdd:PRK09247  361 VP--------FSDWDELaalraaareRGVEGLMLKRRDSPYLVGrKKGpWWK 404
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 55-326 6.82e-21

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: 93.16  E-value: 6.82e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  55 SRRGSLIQRHFPDLVTAARQLPPA-LVLDGEVVVW-SQDRLSFEALQrrasssgrTVAQLADAMPAHFIAFDVLQIDGQE 132
Cdd:TIGR02776   1 TRNGHDWTKRFPEIVKALALLKLLpAWIDGEIVVLdERGRADFAALQ--------NALSAGASRPLTYYAFDLLFLSGED 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 133 LLAEPYERRRAALEGLFRERGLSPP-WTLCPMTTDPALaqewltsWTEVP--GVEGLVIKGMGQRYLPG-ARGWFKVRRR 208
Cdd:TIGR02776  73 LRDLPLEERKKRLKQLLKAQDEPAIrYSDHFESDGDAL-------LESACrlGLEGVVSKRLDSPYRSGrSKDWLKLKCR 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 209 DTTEAIIAGITGTLRRPQILVLGRYDeDGRLRAVGR-TTPLRPDAAARLADHLHPAGpghpwTGVRFTATWGSREPLDPI 287
Cdd:TIGR02776 146 RRQEFVITGYTPPNRRFGALLVGVYE-GGQLVYAGKvGTGFGADTLKTLLARLKALG-----AKASPFSGPAGAKTRGVH 219

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1593021893 288 LVVPDLVAEVSADTAIDRGAWRHPLrFVRPRLDVTVADV 326
Cdd:TIGR02776 220 WVRPSLVAEVEYAGITRDGILREAS-FKGLREDKPAEEV 257
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 6-210 1.41e-20

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 92.34  E-value: 1.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQARETVT-APGVLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQLP-PALVLDG 83
Cdd:PRK03180  183 PVRPMLAQTATSVAeALARLGGPAAVEAKLDGARVQVH---RDGDDVRVYTRTLDDITARLPEVVEAVRALPvRSLVLDG 259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  84 EVVVWSQDRLSfEALQRRASSSGRT--VAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLSPPWTlc 161
Cdd:PRK03180  260 EAIALRPDGRP-RPFQVTASRFGRRvdVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHRVPRLV-- 336

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1593021893 162 pmTTDPALAQEWLTSwTEVPGVEGLVIKGMGQRYLPGARG--WFKVRRRDT 210
Cdd:PRK03180  337 --TADPAAAAAFLAA-ALAAGHEGVMVKSLDAPYAAGRRGagWLKVKPVHT 384
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 6-207 1.81e-19

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 89.26  E-value: 1.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQ-ARETVTAPGVLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAARQL--PPALVLD 82
Cdd:PRK01109  227 PIRPMLAErLSSPKEILKKMGGEALVEYKYDGERAQIH---KKGDKVKIFSRRLENITHQYPDVVEYAKEAikAEEAIVE 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  83 GEVVVWSQDR---LSFEALQRRasssgRTVAQLADAM---PAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRErglSP 156
Cdd:PRK01109  304 GEIVAVDPETgemRPFQELMHR-----KRKYDIEEAIkeyPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKE---ND 375

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1593021893 157 PWTLCP--MTTDPALAQEWLTSWTEVpGVEGLVIKGMGQR--YLPGARG--WFKVRR 207
Cdd:PRK01109  376 KVKLAEriITDDVEELEKFFHRAIEE-GCEGLMAKSLGKDsiYQAGARGwlWIKYKR 431
ligD PRK09633
DNA ligase D;
30-322 1.68e-18

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 86.25  E-value: 1.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  30 FEAKFDGYRALLFTSARPggsTLLQSRRGSLIQRHFPDLVTAARQ--------LPpaLVLDGEVVVWSQD-RLSFEALQR 100
Cdd:PRK09633   20 YEVKYDGFRCLLIIDETG---ITLISRNGRELTNTFPEIIEFCESnfehlkeeLP--LTLDGELVCLVNPyRSDFEHVQQ 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 101 RA-SSSGRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLsppwtlcPMTTDPaLAQEWLTS--- 176
Cdd:PRK09633   95 RGrLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKL-------PASPDP-YAKARIQYips 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 177 -------WTEVPGV--EGLVIKGMGQRYLPGARG--WFKVRRRDTTEAIIAGITGTLRRPQILVLgrydEDGRLRAVGRT 245
Cdd:PRK09633  167 ttdfdalWEAVKRYdgEGIVAKKKTSKWLENKRSkdWLKIKNWRYVHVIVTGYDPSNGYFTGSVY----KDGQLTEVGSV 242

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1593021893 246 T-PLRPDAAARLadhlhpagpghpwtgVRFTATWGSREPLDPILVVPDLVAEVSADTaIDRGAWRHPlRFVRPRLDVT 322
Cdd:PRK09633  243 KhGMEDEERQTL---------------RAIFKQNGTKTKSGEYTLEPSICVTVACIT-FDGGTLREP-SFVSFLFDMD 303
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 6-326 4.06e-16

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: 78.90  E-value: 4.06e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQA----RETVTApgvLPGNLAFEAKFDGYRALLFtsaRPGGSTLLQSRRGSLIQRHFPDLVTAA--RQLPP-- 77
Cdd:TIGR00574 166 PFKPMLAERaksiEEALKK---KGNGFYVEYKYDGERVQVH---KDGDKFKIFSRRLENYTYQYPEIFTEFikEAFPGik 239

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  78 ALVLDGEVVVWSQDR---LSFEALQRRASSSGRTVAQLADAMPahFIAFDVLQIDGQELLAEPYERRRAALEGLFRER-- 152
Cdd:TIGR00574 240 SCILDGEMVAIDPETgkpLPFGTLLRRKRKYDIKAMDQKVPVC--LFVFDILYLNGKSLIDEPLIERREILESILKPIpn 317

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 153 --GLSPpwtlcPMTTDPALAQEWLTSWTEVPGVEGLVIKGMGQRYLPGARG--WFKVRRRDTTE-------AIIAGITGT 221
Cdd:TIGR00574 318 riEIAE-----MKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGwlWLKIKPEYLEGmgdtldlVVIGAYYGK 392

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 222 LRRPQIL---VLGRYDED-GRLRAVGR-TTPLRPDAAARLADHLHPAGPGHPWTGVRFTATWGSREPLDPILVVPDLVAE 296
Cdd:TIGR00574 393 GSRGGMYgsfLCACYDPEsEEFKTITKvGTGFTDADLQELGKKLPPLWIDPPGSRVPSILPDEPDIWPDPAIVWEVTGAE 472

                         330       340       350
                  ....*....|....*....|....*....|..
gi 1593021893 297 VSADTA--IDRGAWRHPlRFVRPRLDVTVADV 326
Cdd:TIGR00574 473 ITKSPAykANGISLRFP-RFSRIRDDKGPEDA 503
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 7-219 1.12e-15

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 75.95  E-value: 1.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   7 VEPML-AQARETVTApgvlpGNLAFEAKFDGYRALLftsARPGGSTLLQSRRGSLIQRHFPDLVTAarQLPPALVLDGEV 85
Cdd:PRK07636    3 ISPMLlESAKEPFNS-----ENYITEPKFDGIRLIA---SKNNGLIRLYTRHNNEVTAKFPELLNL--DIPDGTVLDGEL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  86 VVWSQD-RLSFEALQRRASSSGRTvaqlaDAMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRErglSPPWTLCPMT 164
Cdd:PRK07636   73 IVLGSTgAPDFEAVMERFQSKKST-----KIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLP---HPNVKIIEGI 144

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1593021893 165 TDPALAqewLTSWTEVPGVEGLVIKGMGQRYLPGARG--WFKVRRRDTTEAIIAGIT 219
Cdd:PRK07636  145 EGHGTA---YFELVEERELEGIVIKKANSPYEINKRSdnWLKVINYQYTDVLITGYR 198
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 6-205 5.46e-15

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: 73.00  E-value: 5.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQARETVTAPGVLPGNLAF--EAKFDGYRALLftsARPGGSTLLQSRR--------GSLIQRHF--PDLVTAAR 73
Cdd:cd07903    11 PFRPMLAERLNIGYVEIKLLKGKPFyiETKLDGERIQL---HKDGNEFKYFSRNgndytylyGASLTPGSltPYIHLAFN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  74 QLPPALVLDGEVVVWSQDRLSFEALqrrasSSGRTVAQLADAMPAH----FIAFDVLQIDGQELLAEPYERRRAALEGLF 149
Cdd:cd07903    88 PKVKSCILDGEMVVWDKETKRFLPF-----GTLKDVAKLREVEDSDlqpcFVVFDILYLNGKSLTNLPLHERKKLLEKII 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1593021893 150 RerglsppwtlcPMTTDPALAQEWLTSW-TEV---------PGVEGLVIKGMGQRYLPGAR--GWFKV 205
Cdd:cd07903   163 T-----------PIPGRLEVVKRTEASTkEEIeealneaidNREEGIVVKDLDSKYKPGKRggGWIKI 219
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 29-298 1.96e-13

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 71.09  E-value: 1.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  29 AFEAKFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVTAARQLP-PALVLDGEVVVWSQDRL-SFEALQRrASSSG 106
Cdd:PRK05972  252 IYEIKFDGYRILARIE---GGEVRLFTRNGLDWTAKLPALAKAAAALGlPDAWLDGEIVVLDEDGVpDFQALQN-AFDEG 327

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 107 RTVAQLadampahFIAFDVLQIDGQELLAEPYERRRAALEGLFRERglsPPWTLCPMTTDPALAQEWLTSWTEVpGVEGL 186
Cdd:PRK05972  328 RTEDLV-------YFAFDLPFLGGEDLRELPLEERRARLRALLEAA---RSDRIRFSEHFDAGGDAVLASACRL-GLEGV 396

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 187 VIKGMGQRYLPG-ARGWFKVRRRDTTEAIIAGIT---GTLRRPQILVLGRYDeDGRLRAVGRT-TPLRPDAAARLADHLH 261
Cdd:PRK05972  397 IGKRADSPYVSGrSEDWIKLKCRARQEFVIGGYTdpkGSRSGFGSLLLGVHD-DDHLRYAGRVgTGFGAATLKTLLPRLK 475

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1593021893 262 PAGPGHPwtgvRFTATWGSREPLDPILVVPDLVAEVS 298
Cdd:PRK05972  476 ALATDKS----PFAGKPAPRKARGVHWVKPELVAEVE 508
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 1-151 1.21e-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: 63.34  E-value: 1.21e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   1 MVLKP--PVEPMLAQARETVTApgVLP--GNLAF--EAKFDGYRALLftSARPGGSTLLQSRRGSLIQRHFPDLVTAA-R 73
Cdd:cd07900     2 CKLTPgiPVKPMLAKPTKGVSE--VLDrfEDKEFtcEYKYDGERAQI--HLLEDGKVKIFSRNLENNTEKYPDIVAVLpK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  74 QLPPA---LVLDGEVVVWSQDR---LSFEALQRRASssgRTVAQLADAMPAHFIAFDVLQIDGQELLAEPYERRRAALEG 147
Cdd:cd07900    78 SLKPSvksFILDSEIVAYDRETgkiLPFQVLSTRKR---KDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHS 154


                  ....
gi 1593021893 148 LFRE 151
Cdd:cd07900   155 LFKE 158
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 33-189 2.28e-11

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: 61.67  E-value: 2.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  33 KFDGYRALLFTSarpGGSTLLQSRRGSLIQRHFPDLVT-AARQLPPALVLDGEVVVWsqdrlsfealqrrasssGRTVAQ 111
Cdd:cd06846    26 KYDGKRALIVAL---NGGVFAISRTGLEVPLPSILIPGrELLTLKPGFILDGELVVE-----------------NREVAN 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 112 LADampaHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLSPPWTLCPMTTDPALAQEwLTSWTEV---PGVEGLVI 188
Cdd:cd06846    86 PKP----TYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLENAPSYDET-LDDLLEKlkkKGKEGLVF 160


                  .
gi 1593021893 189 K 189
Cdd:cd06846   161 K 161
PLN03113 PLN03113
DNA ligase 1; Provisional
 6-214 6.75e-10

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 60.38  E-value: 6.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893   6 PVEPMLAQARETVTAPGVLPGNLAF--EAKFDGYRALLftSARPGGSTLLQSRRGSLIQRHFPDLVTAARQLP----PAL 79
Cdd:PLN03113  369 PVGPMLAKPTKGVSEIVNKFQDMEFtcEYKYDGERAQI--HFLEDGSVEIYSRNAERNTGKYPDVVVAISRLKkpsvKSF 446

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  80 VLDGEVVVWSQDR---LSFEALQRRAsssgRTVAQLAD-AMPAHFIAFDVLQIDGQELLAEPYERRRAALEGLFRERGLS 155
Cdd:PLN03113  447 ILDCELVAYDREKkkiLPFQILSTRA----RKNVVMSDiKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGF 522

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1593021893 156 PPWTLCPMTTDPALAQEWLTSWTEVpGVEGLVIKGMGQ--RYLPGARG--WFKVrRRDTTEAI 214
Cdd:PLN03113  523 FQFATAITSNDLEEIQKFLDAAVDA-SCEGLIIKTLNKdaTYEPSKRSnnWLKL-KKDYMESI 583
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 80-207 7.30e-08

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: 52.40  E-value: 7.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893  80 VLDGEVVVWSQDR---LSFEALQRRASSSGRTVAQLADAMPA---HF--IAFDVLQIDGQELLAEPYERRRAALEGLFRE 151
Cdd:cd08039    87 ILEGEMVVWSDRQgkiDPFHKIRKHVERSGSFIGTDNDSPPHeyeHLmiVFFDVLLLDDESLLSKPYSERRDLLESLVHV 166

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1593021893 152 R----GLSP--PWTLcPMTTDP---------ALAQEWltswtevpgvEGLVIKGMGQRYLP-------GARGWFKVRR 207
Cdd:cd08039   167 IpgyaGLSErfPIDF-SRSSGYerlrqifarAIAERW----------EGLVLKGDEEPYFDlfleqgsFSGCWIKLKK 233
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 228-320 4.14e-05

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: 41.81  E-value: 4.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 228 LVLGRYDeDGRLRAVGRT-TPLRPDAAARLADHLHP-AGPGHPWTGVRFT---ATWgsrepldpilVVPDLVAEVSADTA 302
Cdd:pfam04679   8 LLLGVYD-DGRLVYVGKVgTGFTDADLEELRERLKPlERKKPPFAEPPPEargAVW----------VEPELVAEVEFAEW 76

                          90
                  ....*....|....*...
gi 1593021893 303 IDRGAWRHPlRFVRPRLD 320
Cdd:pfam04679  77 TRSGRLRFP-RFKGLRED 93
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 210-326 3.17e-04

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: 39.85  E-value: 3.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1593021893 210 TTEAIIAGIT-GTLRRPQI--LVLGRYDeDGRLRAVGRT-TPLRPDAAARLADHLHP---------AGPGHPWTGVRFta 276
Cdd:cd07971     2 RQEFVIGGYTpPKGSRGGFgsLLLGVYD-GGRLVYVGRVgTGFSAATLRELRERLAPlerktspfaDPPPADARGAVW-- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1593021893 277 twgsrepldpilVVPDLVAEVSADTAIDRGAWRHPlRFVRPRLDVTVADV 326
Cdd:cd07971    79 ------------VKPELVAEVEFAEWTPDGRLRHP-VFKGLREDKPAAEV 115
 
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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