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Conserved domains on  [gi|1670330484|gb|TLZ60180|]
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ATP-dependent DNA ligase, partial [Gammaproteobacteria bacterium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LigD COG3285
Eukaryotic-type DNA primase [Replication, recombination and repair];
155-489 7.20e-131

Eukaryotic-type DNA primase [Replication, recombination and repair];


:

Pssm-ID: 442515 [Multi-domain]  Cd Length: 300  Bit Score: 381.39  E-value: 7.20e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 155 PANRLDLTVGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWS 234
Cdd:COG3285     1 ASAAAELEVGGREVRLTNPDKVLFPE------AGITKGDLADYYAAVAPVMLPHLRDRPLSLVRYPDGIGGECFFQKHAP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 235 QELPEFVESITVFSEHKDEqHRYLLANNLPTLLWLGQVGTLEFHVWHSRAqlapeaagrptdyasslAALEasilnYPDY 314
Cdd:COG3285    75 KGAPDWVRTVPVPSPSGRT-ADYLVVDDLATLLWLAQLGALEFHPWGSRA-----------------DDLE-----HPDR 131

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 315 LVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETV 394
Cdd:COG3285   132 LVFDLDP-------GPGV-------GFADVVEAALLVRELLDELGLTSFPKTSGGKGLHVYVPLEPRYDWDEVRAFARAL 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 395 GRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEA-AEPMDFTIDSVPPRLE 473
Cdd:COG3285   198 ARELERRAPDLVTAEMSKEKRGGKIFIDYLQNARGATTVAPYSLRARPGAPVSTPLTWDELDDgLDPDDFTIRTVPERLA 277

                         330
                  ....*....|....*.
gi 1670330484 474 KRGDRWHDVLQRKQSL 489
Cdd:COG3285   278 ELGDPWADLLDAAQSL 293
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 3-116 7.27e-47

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: 158.49  E-value: 7.27e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFA-EPPPLHRPTVWLK 81
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDGGRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFAdPPPADARGAVWVK 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1670330484  82 PKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSV 116
Cdd:cd07971    81 PELVAEVEFAEWTPDGRLRHPVFKGLREDKPAAEV 115
 
Name Accession Description Interval E-value
LigD COG3285
Eukaryotic-type DNA primase [Replication, recombination and repair];
155-489 7.20e-131

Eukaryotic-type DNA primase [Replication, recombination and repair];


Pssm-ID: 442515 [Multi-domain]  Cd Length: 300  Bit Score: 381.39  E-value: 7.20e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 155 PANRLDLTVGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWS 234
Cdd:COG3285     1 ASAAAELEVGGREVRLTNPDKVLFPE------AGITKGDLADYYAAVAPVMLPHLRDRPLSLVRYPDGIGGECFFQKHAP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 235 QELPEFVESITVFSEHKDEqHRYLLANNLPTLLWLGQVGTLEFHVWHSRAqlapeaagrptdyasslAALEasilnYPDY 314
Cdd:COG3285    75 KGAPDWVRTVPVPSPSGRT-ADYLVVDDLATLLWLAQLGALEFHPWGSRA-----------------DDLE-----HPDR 131

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 315 LVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETV 394
Cdd:COG3285   132 LVFDLDP-------GPGV-------GFADVVEAALLVRELLDELGLTSFPKTSGGKGLHVYVPLEPRYDWDEVRAFARAL 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 395 GRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEA-AEPMDFTIDSVPPRLE 473
Cdd:COG3285   198 ARELERRAPDLVTAEMSKEKRGGKIFIDYLQNARGATTVAPYSLRARPGAPVSTPLTWDELDDgLDPDDFTIRTVPERLA 277

                         330
                  ....*....|....*.
gi 1670330484 474 KRGDRWHDVLQRKQSL 489
Cdd:COG3285   278 ELGDPWADLLDAAQSL 293
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 6-481 5.59e-115

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: 350.08  E-value: 5.59e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGArdpLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLHRPTV-WLKPKL 84
Cdd:TIGR02776 149 EFVITGYTPPNRR---FGALLVGVYEGGQLVYAGKVGTGFGADTLKTLLARLKALGAKASPFSGPAGAKTRGVhWVRPSL 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  85 VAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVrkrargagaaapaaggkdpddgdaeaaaaeaVLEQLKDP--ANRLDLT 162
Cdd:TIGR02776 226 VAEVEYAGITRDGILREASFKGLREDKPAEEV-------------------------------TLETPQRHaaAKRKRSA 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 163 VGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVE 242
Cdd:TIGR02776 275 ALVAGVRITHPDKVLWPK------EGITKLDLAVYYAEVGDWMLPFLKGRPLSLIRCPDGIGGECFFQKHAPDYAPPFVA 348

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 243 SITVfsehkDEQHRYLLANNLPTLLWLGQVGTLEFHVWhsraqlapeaaGRPTDYasslaaleasiLNYPDYLVFDIDPy 322
Cdd:TIGR02776 349 SFKD-----GDEKEYLVCNDAEGLLWLAQQGALEFHIW-----------GQTIDS-----------LDKPDRIVFDLDP- 400

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 323 iysgkeapgaEPELnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIER-TVTFDEARHICETVGRHLMRA 401
Cdd:TIGR02776 401 ----------PPGV---AFKLAVEAAQLMKQLLDELGLVSFVKTSGGKGLHVVVPLRPnTFTWDETKLFAKAIAEYLARQ 467

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 402 HPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAAEPMD--FTIDSVPPRLEKRGDRW 479
Cdd:TIGR02776 468 FPERFTTEMGKKNRVGRIFIDYLRNARGKTTVAPYSPRAREGGPVSTPLTWDELASLDLSPaqFTITNVPERLRESGDPW 547


                  ..
gi 1670330484 480 HD 481
Cdd:TIGR02776 548 AD 549
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 6-497 3.84e-107

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 338.42  E-value: 3.84e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLH--RPTVWLKPK 83
Cdd:PRK05972  423 EFVIGGYTDPKGSRSGFGSLLLGVHDDDHLRYAGRVGTGFGAATLKTLLPRLKALATDKSPFAGKPAPRkaRGVHWVKPE 502

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  84 LVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVRKRARGAGAAAPAAGGKDPDDGDaeaaaaeavleqlkdPANRLDLTV 163
Cdd:PRK05972  503 LVAEVEFAGWTRDGIVRQAVFKGLREDKPAREVVAERPAPPATAEPAAPAAAAAAA---------------ATAAAAAKA 567

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 164 GDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVES 243
Cdd:PRK05972  568 EVAGVRISHPDRVIDPD------SGVTKLDLARYYEAVADWMLPHLKGRPVSLVRAPDGIGGELFFQKHAMPGASPGIEL 641

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 244 ITVFSEHKdeqhRYLLANNLPTLLWLGQVGTLEFHVWHSRaqlapeaagrPTDYasslaaleasilNYPDYLVFDIDPyi 323
Cdd:PRK05972  642 LDVAPDHK----PLLQIDRVEGLVAAAQMGAVELHTWNAT----------PDRI------------EVPDRLVFDLDP-- 693

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 324 ysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHP 403
Cdd:PRK05972  694 -----GPGV-------PWKAVVEAARLMRTRLDELGLESFLKTSGGKGLHVVVPLARRLDWDEVKAFAQAVCQHMARDLP 761

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 404 KDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAA-EPMDFTIDSVPPRLEKRGDRWHDV 482
Cdd:PRK05972  762 ERFLAKMGKKNRVGKIFLDYLRNGRGATTVAALSPRARPGAPVSMPLTWEELKALlDPKQWTIRTVPARLAKLSDPWADY 841

                         490
                  ....*....|....*...
gi 1670330484 483 LQRKQSL---MKAFGLKR 497
Cdd:PRK05972  842 ADARQSLtaaMKRLGRKP 859
LigD_Pol_like cd04861
LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas ...
 191-455 6.30e-95

LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.


Pssm-ID: 240131 [Multi-domain]  Cd Length: 227  Bit Score: 287.10  E-value: 6.30e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVfsEHKDEQHRYLLANNLPTLLWLG 270
Cdd:cd04861     1 KGDLADYYAAVAPYMLPHLRGRPLTLVRYPDGIDGESFFQKHAPAGAPDWVRTVEV--ESEGGTINYLLVNDAAGLVWLA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAQlAPEaagrptdyasslaaleasilnYPDYLVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFW 350
Cdd:cd04861    79 NLGAIELHPWLSRAD-DLE---------------------RPDRLVFDLDP-------GPGV-------PFEDVVEAALL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04861   123 LRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAKAKRGGKIFVDYLQNARGK 202

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04861   203 TTVAPYSVRARPGAPVSTPLTWDEL 227
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 3-116 7.27e-47

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: 158.49  E-value: 7.27e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFA-EPPPLHRPTVWLK 81
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDGGRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFAdPPPADARGAVWVK 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1670330484  82 PKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSV 116
Cdd:cd07971    81 PELVAEVEFAEWTPDGRLRHPVFKGLREDKPAAEV 115
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
3-117 2.44e-33

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 131.20  E-value: 2.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGAR-DPLGALLLGYWE-GKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLhRPTVWL 80
Cdd:COG1793   309 RTQDLVVGGATPGKGRRaGGFGSLLLGVYDpGGELVYVGKVGTGFTDAELAELTERLRPLTRERSPFAVPSDG-RPVRWV 387

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1670330484  81 KPKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:COG1793   388 RPELVAEVAFDEITRSGALRFPRFLRLREDKPPEEAT 424
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 19-110 8.17e-33

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: 120.00  E-value: 8.17e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  19 RDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLHRPTVWLKPKLVAEVSFSDWTPGGA 98
Cdd:pfam04679   2 RGGFGSLLLGVYDDGRLVYVGKVGTGFTDADLEELRERLKPLERKKPPFAEPPPEARGAVWVEPELVAEVEFAEWTRSGR 81

                          90
                  ....*....|..
gi 1670330484  99 LRAPVFVRLRDD 110
Cdd:pfam04679  82 LRFPRFKGLRED 93
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 6-117 5.63e-31

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: 121.64  E-value: 5.63e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQR-DSPFAEPPplhRPTVWLKPKL 84
Cdd:TIGR02779 188 EFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGRVGTGFSEAELATIKERLKPLESKpDKPGAREK---RGVHWVKPEL 264

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1670330484  85 VAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:TIGR02779 265 VAEVEFAGWTRDGRLRQASFVGLREDKPASEVT 297
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 4-117 3.10e-23

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 103.54  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   4 TGEFLIGGYTRGKGAR-DPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAE--PPPLHRPTVWL 80
Cdd:PRK09632  645 TQEVVIGGWRPGEGGRsSGIGSLLLGIPDPGGLRYVGRVGTGFTERELASLKETLAPLHRDTSPFDAdlPAADAKGATWV 724

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1670330484  81 KPKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:PRK09632  725 RPELVGEVRYSEWTPDGRLRQPSWRGLRPDKKPGDVV 761
 
Name Accession Description Interval E-value
LigD COG3285
Eukaryotic-type DNA primase [Replication, recombination and repair];
155-489 7.20e-131

Eukaryotic-type DNA primase [Replication, recombination and repair];


Pssm-ID: 442515 [Multi-domain]  Cd Length: 300  Bit Score: 381.39  E-value: 7.20e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 155 PANRLDLTVGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWS 234
Cdd:COG3285     1 ASAAAELEVGGREVRLTNPDKVLFPE------AGITKGDLADYYAAVAPVMLPHLRDRPLSLVRYPDGIGGECFFQKHAP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 235 QELPEFVESITVFSEHKDEqHRYLLANNLPTLLWLGQVGTLEFHVWHSRAqlapeaagrptdyasslAALEasilnYPDY 314
Cdd:COG3285    75 KGAPDWVRTVPVPSPSGRT-ADYLVVDDLATLLWLAQLGALEFHPWGSRA-----------------DDLE-----HPDR 131

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 315 LVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETV 394
Cdd:COG3285   132 LVFDLDP-------GPGV-------GFADVVEAALLVRELLDELGLTSFPKTSGGKGLHVYVPLEPRYDWDEVRAFARAL 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 395 GRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEA-AEPMDFTIDSVPPRLE 473
Cdd:COG3285   198 ARELERRAPDLVTAEMSKEKRGGKIFIDYLQNARGATTVAPYSLRARPGAPVSTPLTWDELDDgLDPDDFTIRTVPERLA 277

                         330
                  ....*....|....*.
gi 1670330484 474 KRGDRWHDVLQRKQSL 489
Cdd:COG3285   278 ELGDPWADLLDAAQSL 293
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 6-481 5.59e-115

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: 350.08  E-value: 5.59e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGArdpLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLHRPTV-WLKPKL 84
Cdd:TIGR02776 149 EFVITGYTPPNRR---FGALLVGVYEGGQLVYAGKVGTGFGADTLKTLLARLKALGAKASPFSGPAGAKTRGVhWVRPSL 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  85 VAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVrkrargagaaapaaggkdpddgdaeaaaaeaVLEQLKDP--ANRLDLT 162
Cdd:TIGR02776 226 VAEVEYAGITRDGILREASFKGLREDKPAEEV-------------------------------TLETPQRHaaAKRKRSA 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 163 VGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVE 242
Cdd:TIGR02776 275 ALVAGVRITHPDKVLWPK------EGITKLDLAVYYAEVGDWMLPFLKGRPLSLIRCPDGIGGECFFQKHAPDYAPPFVA 348

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 243 SITVfsehkDEQHRYLLANNLPTLLWLGQVGTLEFHVWhsraqlapeaaGRPTDYasslaaleasiLNYPDYLVFDIDPy 322
Cdd:TIGR02776 349 SFKD-----GDEKEYLVCNDAEGLLWLAQQGALEFHIW-----------GQTIDS-----------LDKPDRIVFDLDP- 400

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 323 iysgkeapgaEPELnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIER-TVTFDEARHICETVGRHLMRA 401
Cdd:TIGR02776 401 ----------PPGV---AFKLAVEAAQLMKQLLDELGLVSFVKTSGGKGLHVVVPLRPnTFTWDETKLFAKAIAEYLARQ 467

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 402 HPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAAEPMD--FTIDSVPPRLEKRGDRW 479
Cdd:TIGR02776 468 FPERFTTEMGKKNRVGRIFIDYLRNARGKTTVAPYSPRAREGGPVSTPLTWDELASLDLSPaqFTITNVPERLRESGDPW 547


                  ..
gi 1670330484 480 HD 481
Cdd:TIGR02776 548 AD 549
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 6-497 3.84e-107

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 338.42  E-value: 3.84e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLH--RPTVWLKPK 83
Cdd:PRK05972  423 EFVIGGYTDPKGSRSGFGSLLLGVHDDDHLRYAGRVGTGFGAATLKTLLPRLKALATDKSPFAGKPAPRkaRGVHWVKPE 502

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  84 LVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVRKRARGAGAAAPAAGGKDPDDGDaeaaaaeavleqlkdPANRLDLTV 163
Cdd:PRK05972  503 LVAEVEFAGWTRDGIVRQAVFKGLREDKPAREVVAERPAPPATAEPAAPAAAAAAA---------------ATAAAAAKA 567

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 164 GDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVES 243
Cdd:PRK05972  568 EVAGVRISHPDRVIDPD------SGVTKLDLARYYEAVADWMLPHLKGRPVSLVRAPDGIGGELFFQKHAMPGASPGIEL 641

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 244 ITVFSEHKdeqhRYLLANNLPTLLWLGQVGTLEFHVWHSRaqlapeaagrPTDYasslaaleasilNYPDYLVFDIDPyi 323
Cdd:PRK05972  642 LDVAPDHK----PLLQIDRVEGLVAAAQMGAVELHTWNAT----------PDRI------------EVPDRLVFDLDP-- 693

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 324 ysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHP 403
Cdd:PRK05972  694 -----GPGV-------PWKAVVEAARLMRTRLDELGLESFLKTSGGKGLHVVVPLARRLDWDEVKAFAQAVCQHMARDLP 761

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 404 KDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAA-EPMDFTIDSVPPRLEKRGDRWHDV 482
Cdd:PRK05972  762 ERFLAKMGKKNRVGKIFLDYLRNGRGATTVAALSPRARPGAPVSMPLTWEELKALlDPKQWTIRTVPARLAKLSDPWADY 841

                         490
                  ....*....|....*...
gi 1670330484 483 LQRKQSL---MKAFGLKR 497
Cdd:PRK05972  842 ADARQSLtaaMKRLGRKP 859
LigD_Pol_like cd04861
LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas ...
 191-455 6.30e-95

LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.


Pssm-ID: 240131 [Multi-domain]  Cd Length: 227  Bit Score: 287.10  E-value: 6.30e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVfsEHKDEQHRYLLANNLPTLLWLG 270
Cdd:cd04861     1 KGDLADYYAAVAPYMLPHLRGRPLTLVRYPDGIDGESFFQKHAPAGAPDWVRTVEV--ESEGGTINYLLVNDAAGLVWLA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAQlAPEaagrptdyasslaaleasilnYPDYLVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFW 350
Cdd:cd04861    79 NLGAIELHPWLSRAD-DLE---------------------RPDRLVFDLDP-------GPGV-------PFEDVVEAALL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04861   123 LRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAKAKRGGKIFVDYLQNARGK 202

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04861   203 TTVAPYSVRARPGAPVSTPLTWDEL 227
ligD_pol TIGR02778
DNA ligase D, polymerase domain; DNA repair of double-stranded breaks by non-homologous end ...
 168-457 1.56e-82

DNA ligase D, polymerase 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 polymerase domain.


Pssm-ID: 274294 [Multi-domain]  Cd Length: 245  Bit Score: 256.07  E-value: 1.56e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 168 VRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVF 247
Cdd:TIGR02778   1 VRITNPDKVLWPA------EGITKLDLADYYAAVAPFMLPHLRGRPLSLLRCPDGIGGECFFQKHLPQGAPPFVVSAEVE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 248 SEHKDeqhRYLLANNLPTLLWLGQVGTLEFHVWHSRaqlaPEAAGRPtdyasslaaleasilnypDYLVFDIDPyiysgk 327
Cdd:TIGR02778  75 ESDGE---TYLVINDAEGLLWLVQQGALEFHIWGAR----IDAPEKP------------------DRIVFDLDP------ 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 328 eAPGAEpelnkrgFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDIT 407
Cdd:TIGR02778 124 -GPGVA-------WKLVVEAAQLIRELLDELGLESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQMPDRFT 195

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1670330484 408 LDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEA 457
Cdd:TIGR02778 196 AEMSKKNRVGKIFVDYLRNARGKTTVAPYSLRAREGATVSTPLTWDELDS 245
LigD_Pol_like_2 cd04865
LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas ...
 191-455 2.57e-82

LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.


Pssm-ID: 240135 [Multi-domain]  Cd Length: 228  Bit Score: 254.85  E-value: 2.57e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVFSEHKDEQHrYLLANNLPTLLWLG 270
Cdd:cd04865     1 KRDLIRYYRAVAPYLLPYLRDRPLVLKRYPDGIDGKGFYQKDVPAGAPDWLRTVRITSESGRTIN-YLIVQDPAALLWLA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAqlapeaagrptdyasslaaleaSILNYPDYLVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFW 350
Cdd:cd04865    80 NLGCIELHPWPSRA----------------------GDLDHPDELVIDLDP-------QPGT-------SFEDVVEVALL 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04865   124 VREVLDELGLRGYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREVERRLPDLATTERWKKERGGRVYLDYLQNARGK 203

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04865   204 TLAAPYSVRPLPGAPVSTPLEWEEL 228
PaeLigD_Pol_like cd04862
PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas ...
 191-455 7.18e-64

PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair.


Pssm-ID: 240132 [Multi-domain]  Cd Length: 227  Bit Score: 207.08  E-value: 7.18e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVFSEHKDEqhRYLLANNLPTLLWLG 270
Cdd:cd04862     1 KLDLARYYAAVAPWMLPHLAGRPLSLVRCPDGIGGECFFQKHAGAGLPPGVEQLEIEESGGTE--PYLYIEDAEGLLALV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAQlAPEaagrptdyasslaaleasilnYPDYLVFDIDPyiysgkeapgaEPELnkrGFAVGKRVAFW 350
Cdd:cd04862    79 QMGVLEFHTWGARID-RLE---------------------RPDRIVFDLDP-----------GPGV---PWKAVVEAALL 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04862   123 VRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLARTNPDRFVATMGKAKRVGKIFIDYLRNGRGA 202

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04862   203 TAVAPYSVRARPGAPVSVPVTWDEL 227
ligD PRK09633
DNA ligase D;
28-487 5.64e-62

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 212.98  E-value: 5.64e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  28 GYWEGK-----ALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPfaeppplhrPTVWLKPKLVAEVSFSDWTpGGALRAP 102
Cdd:PRK09633  224 GYFTGSvykdgQLTEVGSVKHGMEDEERQTLRAIFKQNGTKTKS---------GEYTLEPSICVTVACITFD-GGTLREP 293

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 103 VFVRLRDDIAPRSVrkrargagaaapaaggkdpddgdaeaaAAEAVLEQLKdpanrldlTVGDaRVRLTNLDRVYWPagp 182
Cdd:PRK09633  294 SFVSFLFDMDPTEC---------------------------TYQQLQRQLA--------PLPP-KVEITSLDKPIWP--- 334

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 183 gkdQPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESItvfsehKDEQHRYLLANN 262
Cdd:PRK09633  335 ---KIHKTKADYLLYLQEVSPFLLPFLRDRALTVIRYPHGSGGESFYQKNKPDYAPDFVQSA------RDDEIEYIVCND 405

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 263 LPTLLWLGQVGTLEFHVWHSRAQLApeaagRPTDyasslaaleasilnypdyLVFDIDPyiysgkeapgaePELNKRGFA 342
Cdd:PRK09633  406 LSTLLWLGNQLALEFHIPFQTIDST-----RPTE------------------IVFDLDP------------PSRDEFPLA 450

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 343 VgkRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPI-ERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFI 421
Cdd:PRK09633  451 V--EAALELKRLFDQFGLTSFVKTSGNKGLQLYIPLsKNAFTYEETRLFTEFIAEYLCSQFPELFTTERLKKNRGNRLYL 528

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 422 DYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAA-EPMDFTIDSVPPRLEKRGD---RWHDVLQRKQ 487
Cdd:PRK09633  529 DYVQHAEGKTIIAPYSTRGNELGTVATPLYWDEVNSDlSPDQFTIPAVIERIKEIGCpfaSFRRNPQDEP 598
LigD_Pol_like_1 cd04864
LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to ...
 191-455 4.42e-59

LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.


Pssm-ID: 240134 [Multi-domain]  Cd Length: 228  Bit Score: 194.63  E-value: 4.42e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVFSEHKDEQHRYLLANNLPTLLWLG 270
Cdd:cd04864     1 KGDLVDYYRAVAPVMLPHVRGRPITLERFPDGIGKPGFYQKEAPEHFPDWIERVEVPKRGDGGSVHHVLCDDAATLVYLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAqlapeaagrptdyasslaaleaSILNYPDYLVFDIDPyiysgkeapgaepelNKRGFAVGKRVAFW 350
Cdd:cd04864    81 DQASITPHVWLSRA----------------------DDLEHPDLMVFDLDP---------------SADDIEAVRTAALA 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04864   124 VRELLDELGLPSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAKRDPDLLTTEARKAKRGDRVFLDIGRNAYGQ 203

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04864   204 TAVAPYAVRARPGAPVAAPITWAEL 228
LigD_Pol_like_3 cd04866
LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas ...
 191-455 5.11e-59

LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.


Pssm-ID: 240136 [Multi-domain]  Cd Length: 223  Bit Score: 194.18  E-value: 5.11e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESItvfsehKDEQHRYLLANNLPTLLWLG 270
Cdd:cd04866     1 KIDYLHYLQEVSPYMLPFLKDRALTVIRYPHGIRGESFFQKNKPDYAPEFVETV------MLDEINYIVCNNLETLVWLG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAQlapeaagrptdyasslaaleasiLNYPDYLVFDIDPyiysgkeapgaePELNKRGFAVgkRVAFW 350
Cdd:cd04866    75 NQLALELHIPFQTIE-----------------------SNKPSEIVFDLDP------------PSRDHFSLAV--EAANL 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPI-ERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRG 429
Cdd:cd04866   118 LKEILDALGLTSFVKTSGNKGLQVYIPLpDNKFTYDETRLFTEFIAEYLCQQFPELFTTERLKKNRHNRLYLDYVQHAEG 197

                         250       260
                  ....*....|....*....|....*.
gi 1670330484 430 KTLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04866   198 KTIIAPYSARGNELGTVAAPLYWEEV 223
MtLigD_Pol_like cd04863
MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium ...
 191-455 2.51e-58

MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.


Pssm-ID: 240133 [Multi-domain]  Cd Length: 231  Bit Score: 192.61  E-value: 2.51e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 191 KRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWSQELPEFVESITVFSEHKDEQhRYLLANNLPTLLWLG 270
Cdd:cd04863     1 KGDVLDYYARVAPVLLPHLAGRPVTRKRWPDGVDGPFFFEKNCPSGAPDWLPTAEVRSEGSGTL-TYPLVNDLATLAWAA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 271 QVGTLEFHVWHSRAqlapEAAGRPTDyasslaaleasilnyPDYLVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFW 350
Cdd:cd04863    80 NLAALELHVPQWTV----DADGNPGP---------------PDRLVFDLDP-------GEPA-------GLVECARVALW 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 351 LRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICETVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGK 430
Cdd:cd04863   127 LRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELEREHPDLVVSRMTKSLRAGKVFVDWSQNDAAK 206

                         250       260
                  ....*....|....*....|....*
gi 1670330484 431 TLNVAYSPRGVPGAPVSMPLTWEEL 455
Cdd:cd04863   207 TTIAPYSLRAREVPTVATPVTWDEV 231
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 155-477 9.20e-54

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 193.30  E-value: 9.20e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 155 PANRLDLTVGDARVRLTNLDRVYWPAgpgkdqPAVTKRDFLRYLARVARFMLPHLADRPLTMIRMPEGIDGERFFQKHWS 234
Cdd:PRK09632    2 AADRETVEVDGHRVTLTNLDKVLYPA------TGTTKAEVIDYYAAIAPVMLPHIAGRPVTRKRWPNGVDGEVFFEKNLA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 235 QELPEFVESITVfsEHKDEQHRYLLANNLPTLLWLGQVGTLEFHV--WHSRAQLAPEAAGRPTDyasslaaleasilnyp 312
Cdd:PRK09632   76 SSAPDWLPRATI--QHSDGTTTYPLVDSAAGLAWLAQQAALEVHVpqWRFDAEGGELNPGPATR---------------- 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 313 dyLVFDIDPyiysgkeAPGAepelnkrGFAVGKRVAFWLRELLKEMSLEAVVKTSGKTGLHVFVPIERTVTFDEARHICE 392
Cdd:PRK09632  138 --LVFDLDP-------GEGV-------GLAECAEVARAVRDLLADIGLETFPVTSGSKGIHLYAPLDGPVSSEGASVVAK 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 393 TVGRHLMRAHPKDITLDWAIEKRTGKIFIDYNMNVRGKTLNVAYSPRGVPGAPVSMPLTWEELEAAEPMDFTIDSVPPRL 472
Cdd:PRK09632  202 EVARALEQDHPDLVTSTMTKSLRAGKVFVDWSQNNGSKTTIAPYSLRGREHPTVAAPRTWEELDDPGLRQLEYDEVLARV 281


                  ....*
gi 1670330484 473 EKRGD 477
Cdd:PRK09632  282 ARDGD 286
OBF_DNA_ligase_LigD cd07971
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ...
 3-116 7.27e-47

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: 158.49  E-value: 7.27e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFA-EPPPLHRPTVWLK 81
Cdd:cd07971     1 RRQEFVIGGYTPPKGSRGGFGSLLLGVYDGGRLVYVGRVGTGFSAATLRELRERLAPLERKTSPFAdPPPADARGAVWVK 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1670330484  82 PKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSV 116
Cdd:cd07971    81 PELVAEVEFAEWTPDGRLRHPVFKGLREDKPAAEV 115
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
3-117 2.44e-33

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 131.20  E-value: 2.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGAR-DPLGALLLGYWE-GKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLhRPTVWL 80
Cdd:COG1793   309 RTQDLVVGGATPGKGRRaGGFGSLLLGVYDpGGELVYVGKVGTGFTDAELAELTERLRPLTRERSPFAVPSDG-RPVRWV 387

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1670330484  81 KPKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:COG1793   388 RPELVAEVAFDEITRSGALRFPRFLRLREDKPPEEAT 424
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 19-110 8.17e-33

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: 120.00  E-value: 8.17e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  19 RDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPLHRPTVWLKPKLVAEVSFSDWTPGGA 98
Cdd:pfam04679   2 RGGFGSLLLGVYDDGRLVYVGKVGTGFTDADLEELRERLKPLERKKPPFAEPPPEARGAVWVEPELVAEVEFAEWTRSGR 81

                          90
                  ....*....|..
gi 1670330484  99 LRAPVFVRLRDD 110
Cdd:pfam04679  82 LRFPRFKGLRED 93
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 6-117 5.63e-31

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: 121.64  E-value: 5.63e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   6 EFLIGGYTRGKGARDPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQR-DSPFAEPPplhRPTVWLKPKL 84
Cdd:TIGR02779 188 EFVIGGYTPPNGSRSGFGALLLGVYEGGGLRYVGRVGTGFSEAELATIKERLKPLESKpDKPGAREK---RGVHWVKPEL 264

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1670330484  85 VAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:TIGR02779 265 VAEVEFAGWTRDGRLRQASFVGLREDKPASEVT 297
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 4-117 3.10e-23

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 103.54  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   4 TGEFLIGGYTRGKGAR-DPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPFAE--PPPLHRPTVWL 80
Cdd:PRK09632  645 TQEVVIGGWRPGEGGRsSGIGSLLLGIPDPGGLRYVGRVGTGFTERELASLKETLAPLHRDTSPFDAdlPAADAKGATWV 724

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1670330484  81 KPKLVAEVSFSDWTPGGALRAPVFVRLRDDIAPRSVR 117
Cdd:PRK09632  725 RPELVGEVRYSEWTPDGRLRQPSWRGLRPDKKPGDVV 761
AE_Prim_S_like cd00525
AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and ...
 212-450 4.96e-20

AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro.


Pssm-ID: 238291 [Multi-domain]  Cd Length: 136  Bit Score: 86.27  E-value: 4.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 212 RPLTMIRMPegidGERFFQKHWSqelpefvesitvfsehkdeqhRYLLANNLPTLLWLGQVGTLEFHVWHSRAQLapeaa 291
Cdd:cd00525     1 RPVSPIRPP----GKGPFQRHWP---------------------FGATTDDAEILAWLANLPPGNIGLSLGRYDK----- 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484 292 grptdyasslaaleasiLNYPDYLVFDIDPYIYSGKEApgaepelnkrgfavGKRVAFWLRELLKEMSLEAVVKTSGKTG 371
Cdd:cd00525    51 -----------------LWKPDLLVFDLDPDDYDCWED--------------VKEAALLLRELLDEDGLNTLVVTSGSRG 99

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1670330484 372 LHVFVPIertvtfdearhicetvgrhlmrahpkditldwaiekrtgkifIDYNMNVRGKTLNVAYSPRGVPGAPVSMPL 450
Cdd:cd00525   100 LHVYVRL------------------------------------------IDIRVNARGRLLVAPPSVHPRPGGPPSWPL 136
OBF_DNA_ligase_family cd08040
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 3-108 1.31e-15

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: 72.67  E-value: 1.31e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGAR-DPLGALLLGYWEGKALRYAGHVGSGLDDEIIETLLERAAKLGQRDSPF-AEPPPLHRPTVWL 80
Cdd:cd08040     1 KTAEAVIIGMRAGFGNRsDVMGSLLLGYYGEDGLQAVFSVGTGFSADERRDLWQNLEPLVTSFDDHpVWNVGKDLSFVPL 80

                          90       100
                  ....*....|....*....|....*...
gi 1670330484  81 KPKLVAEVSFSDWTPGGALRAPVFVRLR 108
Cdd:cd08040    81 YPGKVVEVKYFEMGSKDCLRFPVFIGIR 108
OBF_DNA_ligase_Arch_LigB cd07972
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ...
 8-113 6.68e-11

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases 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 Pyrococcus furiosus DNA ligase, Mycobacterium tuberculosis LigB, and similar archaeal and 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: 153441 [Multi-domain]  Cd Length: 122  Bit Score: 59.48  E-value: 6.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   8 LIGGyTRGKGAR-DPLGALLLGYWEGKALRYA--GHVGSGLDDEIIETLLERAAKLGQRDspfaeppplHRPTVWLKPKL 84
Cdd:cd07972     7 VIGA-EWGEGRRaGLLGSYTLAVRDEETGELVpvGKVATGLTDEELEELTERLRELIIEK---------FGPVVSVKPEL 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1670330484  85 VAEVSF-----SDWTPGG-ALRAPVFVRLRDDIAP 113
Cdd:cd07972    77 VFEVAFeeiqrSPRYKSGyALRFPRIVRIRDDKDP 111
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 9-116 8.74e-09

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: 57.71  E-value: 8.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   9 IGGYtRGKGAR-DPLGALLLGYWEGKALRY--AGHVGSGLDDEIIETLLERAAKLGQRDSPFAEPPPL-HRPTVWLKPKL 84
Cdd:TIGR00574 386 IGAY-YGKGSRgGMYGSFLCACYDPESEEFktITKVGTGFTDADLQELGKKLPPLWIDPPGSRVPSILpDEPDIWPDPAI 464

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1670330484  85 VAEVSFSDWTP-------GGALRAPVFVRLRDDIAPRSV 116
Cdd:TIGR00574 465 VWEVTGAEITKspaykanGISLRFPRFSRIRDDKGPEDA 503
OBF_DNA_ligase cd07893
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 4-113 3.23e-08

The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153435 [Multi-domain]  Cd Length: 129  Bit Score: 51.97  E-value: 3.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   4 TGEFLIGGYTRGKGARDPL-GALLLGYWEGKA--LRYAGHVGSGLDDEIIETLLERAAKLgQRDSPFAEPPPLHRPTVWL 80
Cdd:cd07893     2 TLDLVIVGAYYGKGRRGGGiGAFLCAVYDPERdeFQTICKVGSGFTDEELEELRELLKEL-KTPEKPPRVNSIEKPDFWV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1670330484  81 KPKLVAEVSFSDWT-------------PGGALRAPVFVRLRDDIAP 113
Cdd:cd07893    81 EPKVVVEVLADEITrspmhtagrgeeeEGYALRFPRFVRIRDDKGP 126
OBF_DNA_ligase_LigC cd07970
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC ...
 4-117 3.63e-08

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: 51.93  E-value: 3.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   4 TGEFLIGGYTrgkGARDPLGALLLGYW-EGKALRYAGHVgSGLDDEIIETLLERAAKLGQRDsPFAEPPP-------LHR 75
Cdd:cd07970     2 TADCVVGGVR---GHKDRPGSLLLGLYdDGGRLRHVGRT-SPLAAAERRELAELLEPARAGH-PWTGRAPgfpsrwgTRK 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1670330484  76 PTVW--LKPKLVAEVSFSDWTPGGALRAPV-FVRLRDDIAPRSVR 117
Cdd:cd07970    77 SLEWvpVRPELVVEVSADTAEGGGRFRHPLrFLRWRPDKSPEDCT 121
OBF_DNA_ligase_I cd07969
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ...
 9-110 8.00e-06

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I 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. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). 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: 153438 [Multi-domain]  Cd Length: 144  Bit Score: 45.55  E-value: 8.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   9 IGGYtRGKGARDP-LGALLLGYW--EGKALRYAGHVGSGLDDEIIETLLERAAKLGQRdspfaEPPP----LHRPTVWLK 81
Cdd:cd07969     9 IGAY-YGKGKRTGvYGAFLLACYdpETEEFQTVCKIGTGFSDEFLEELYESLKEHVIP-----KKPYrvdsSLEPDVWFE 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1670330484  82 PKLVAEVSFSDWT--P-------------GGALRAPVFVRLRDD 110
Cdd:cd07969    83 PKEVWEVKAADLTlsPvhtaaiglvdeekGISLRFPRFIRVRDD 126
PLN03113 PLN03113
DNA ligase 1; Provisional
 9-113 4.21e-05

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 46.13  E-value: 4.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   9 IGGYtRGKGARDPL-GALLLGYWEGKALRYAG--HVGSGLDDEIIEtllERAAKLgqRDSPFAEPPPLHR------PTVW 79
Cdd:PLN03113  592 IAAF-HGRGKRTGVyGAFLLACYDSNKEEFQSicKIGTGFSEAVLE---ERSASL--RSQVIPTPKSYYRygdsikPDVW 665

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1670330484  80 LKPKLVAEVSFSDWT---------------PGGALRAPVFVRLRDDIAP 113
Cdd:PLN03113  666 FEPTEVWEVKAADLTispvhraavgivdpdKGISLRFPRLVRVREDKSP 714
OBF_kDNA_ligase_like cd08041
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent ...
 3-108 9.92e-05

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases 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. The mitochondrial DNA of parasitic protozoan 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 DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and 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 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: 153443 [Multi-domain]  Cd Length: 77  Bit Score: 40.58  E-value: 9.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   3 KTGEFLIGGYTRGKGA-RDPLGALLLGYWEGKALRyaghVGSGLDDEiietlleraaklgQRDspfaEPPPLHRptvwlk 81
Cdd:cd08041     1 QDAEARVVGYEEGKGKyEGMLGALVVETKDGIRFK----IGSGFSDE-------------QRR----NPPPIGS------ 53

                          90       100
                  ....*....|....*....|....*..
gi 1670330484  82 pklVAEVSFSDWTPGGALRAPVFVRLR 108
Cdd:cd08041    54 ---IITYKYQGLTKNGLPRFPVFLRVR 77
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 15-113 1.91e-04

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 44.19  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484  15 GKGARD-PLGALLLGYWEGK--ALRYAGHVGSGLDDEIIETLLEraaKLGQRDSPfaEPPP----LHRPTVWLKPKLVAE 87
Cdd:PRK01109  451 GRGRRGgKYGSLLMAAYDPKtdTFETVCKVGSGFTDEDLDELPK---MLKPYKID--HKHPrvvsKMEPDVWVEPKLVAE 525

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1670330484  88 VSFSDWT--P-------------GGALRAPVFVRLRDDIAP 113
Cdd:PRK01109  526 IIGAEITlsPlhtcclgvvekgaGLAIRFPRFIRWRDDKSP 566
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 2-115 3.73e-03

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 39.49  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1670330484   2 AKTGEFLIGGYTRGKGaRDPLGALLLG-YWEGKALRYAGHVGSGLDDEIIEtLLERAAKLgqrDSPFAEPPPLHR----- 75
Cdd:PRK08224  200 ERTADCVVAGYRYHKS-GPVVGSLLLGlYDDDGQLHHVGVTSAFPMARRRE-LTAELEPL---RTPFGDHPWNWAaftgr 274

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1670330484  76 ----PTVW----------LKPKLVAEVSFsDWTPGGALRAPV-FVRLRDDIAPRS 115
Cdd:PRK08224  275 apggPSRWsagkdlswvpLRPERVVEVRY-DHMEGGRFRHTAqFLRWRPDRDPRS 328
 
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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