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Conserved domains on  [gi|499777958|ref|WP_011458692|]
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ATP-dependent DNA ligase [Rhodoferax ferrireducens]

Protein Classification

ATP-dependent DNA ligase( domain architecture ID 10168734)

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
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 38-115 1.93e-29

WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.


:

Pssm-ID: 153427  Cd Length: 77  Bit Score: 109.32  E-value: 1.93e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499777958  38 KNTSLYSRHNGADKVYHAYLRK-KDDGWTVDYAHGGRGKALKVGTRTETPVAYVKALKIFESLVNSKKNGdsHYQEGEA 115
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEvSDDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNK--GYREGEG 77
CDC9 super family cl43518
ATP-dependent DNA ligase [Replication, recombination and repair];
209-335 6.16e-14

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


The actual alignment was detected with superfamily member COG1793:

Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 73.03  E-value: 6.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVIECYYTADEKQALLQRAEDIRLEGIVAKNARGVY 288
Cdd:COG1793  220 VFYAFDLLYLDGEDLRDLPLSERRALLEEL------LAGAPPPLRLSPHVIDWGEGEALFAAAREAGLEGVMAKRLDSPY 293

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499777958 289 AQG-RGPDSLKFVFREVSTCIVMA--------RNVQRSVQVGLLNSEGDLVSRGNV 335
Cdd:COG1793  294 RPGrRSGDWLKVKCPRTQDLVVGGatpgkgrrAGGFGSLLLGVYDPGGELVYVGKV 349
 
Name Accession Description Interval E-value
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 38-115 1.93e-29

WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153427  Cd Length: 77  Bit Score: 109.32  E-value: 1.93e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499777958  38 KNTSLYSRHNGADKVYHAYLRK-KDDGWTVDYAHGGRGKALKVGTRTETPVAYVKALKIFESLVNSKKNGdsHYQEGEA 115
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEvSDDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNK--GYREGEG 77
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
209-335 6.16e-14

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 73.03  E-value: 6.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVIECYYTADEKQALLQRAEDIRLEGIVAKNARGVY 288
Cdd:COG1793  220 VFYAFDLLYLDGEDLRDLPLSERRALLEEL------LAGAPPPLRLSPHVIDWGEGEALFAAAREAGLEGVMAKRLDSPY 293

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499777958 289 AQG-RGPDSLKFVFREVSTCIVMA--------RNVQRSVQVGLLNSEGDLVSRGNV 335
Cdd:COG1793  294 RPGrRSGDWLKVKCPRTQDLVVGGatpgkgrrAGGFGSLLLGVYDPGGELVYVGKV 349
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 133-299 7.50e-12

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: 63.71  E-value: 7.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 133 PQEPTAIQRAALkalifDNDWCFQVK----------ANGENRLLS------------IKGDCARGGNKK----GQVVSIP 186
Cdd:cd07906    3 PMLATLVDEPPD-----GEDWLYEIKwdgyralarvDGGRVRLYSrngldwtarfpeLAEALAALPVRDavldGEIVVLD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 187 THWLTEFKALGNFVANGEHVGDR----FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDVANVTPSFgviecyytAD 262
Cdd:cd07906   78 EGGRPDFQALQNRLRLRRRLARTvpvvYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF--------EG 149

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 499777958 263 EKQALLQRAEDIRLEGIVAKNARGVYAQGR-GPDSLKF 299
Cdd:cd07906  150 GGAALFAAACELGLEGIVAKRADSPYRSGRrSRDWLKI 187
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 152-335 8.28e-11

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: 62.32  E-value: 8.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  152 DWCFQVKANGENRLLSIKGDCARGGNKKGQVVS--IPTH-WLTEFKALGNFVANGEHV--------------------GD 208
Cdd:TIGR02779  13 DWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTekFPILaAALAALPILPAVLDGEIVvldesgrsdfsalqnrlragRD 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  209 R---FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNdvANVTPSFGVIECYytaDEKQALLQRAEDIRLEGIVAKNAR 285
Cdd:TIGR02779  93 RpatYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIK--GPLAPDRYSVHFE---GDGQALLEAACRLGLEGVVAKRRD 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 499777958  286 GVYAQGRGPDSLKF-VFREVSTCIV------MARNVQRSVQVGLLnSEGDLVSRGNV 335
Cdd:TIGR02779 168 SPYRSGRSADWLKLkCRRRQEFVIGgytppnGSRSGFGALLLGVY-EGGGLRYVGRV 223
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 210-299 1.55e-07

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: 51.52  E-value: 1.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  210 FIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVIECY--YTADEKQALLQRAEDIRLEGIVAKNARGV 287
Cdd:pfam01068 116 LFVFDLLYLDGEDLTDLPLRERRKLLEEI------FKEIPGRIQLAESIvtKDVEEAQEFLEEAISEGLEGLVVKDPDST 189

                          90
                  ....*....|...
gi 499777958  288 YAQG-RGPDSLKF 299
Cdd:pfam01068 190 YEPGkRGKNWLKI 202
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 180-298 2.74e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 52.60  E-value: 2.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 180 GQVVSIPTHWLTEFKALGNFVANGEHVGDRFIAFDLLEYEGIDMRGWP--QRR-RFAKLLEmyDSMNDVANVTPSFGVie 256
Cdd:PRK05972 304 GEIVVLDEDGVPDFQALQNAFDEGRTEDLVYFAFDLPFLGGEDLRELPleERRaRLRALLE--AARSDRIRFSEHFDA-- 379

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 499777958 257 cyytadEKQALLQRAEDIRLEGIVAKNARGVYAQGRGPDSLK 298
Cdd:PRK05972 380 ------GGDAVLASACRLGLEGVIGKRADSPYVSGRSEDWIK 415
 
Name Accession Description Interval E-value
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 38-115 1.93e-29

WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153427  Cd Length: 77  Bit Score: 109.32  E-value: 1.93e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499777958  38 KNTSLYSRHNGADKVYHAYLRK-KDDGWTVDYAHGGRGKALKVGTRTETPVAYVKALKIFESLVNSKKNGdsHYQEGEA 115
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEvSDDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNK--GYREGEG 77
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
209-335 6.16e-14

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 73.03  E-value: 6.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVIECYYTADEKQALLQRAEDIRLEGIVAKNARGVY 288
Cdd:COG1793  220 VFYAFDLLYLDGEDLRDLPLSERRALLEEL------LAGAPPPLRLSPHVIDWGEGEALFAAAREAGLEGVMAKRLDSPY 293

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 499777958 289 AQG-RGPDSLKFVFREVSTCIVMA--------RNVQRSVQVGLLNSEGDLVSRGNV 335
Cdd:COG1793  294 RPGrRSGDWLKVKCPRTQDLVVGGatpgkgrrAGGFGSLLLGVYDPGGELVYVGKV 349
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 133-299 7.50e-12

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: 63.71  E-value: 7.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 133 PQEPTAIQRAALkalifDNDWCFQVK----------ANGENRLLS------------IKGDCARGGNKK----GQVVSIP 186
Cdd:cd07906    3 PMLATLVDEPPD-----GEDWLYEIKwdgyralarvDGGRVRLYSrngldwtarfpeLAEALAALPVRDavldGEIVVLD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 187 THWLTEFKALGNFVANGEHVGDR----FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDVANVTPSFgviecyytAD 262
Cdd:cd07906   78 EGGRPDFQALQNRLRLRRRLARTvpvvYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF--------EG 149

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 499777958 263 EKQALLQRAEDIRLEGIVAKNARGVYAQGR-GPDSLKF 299
Cdd:cd07906  150 GGAALFAAACELGLEGIVAKRADSPYRSGRrSRDWLKI 187
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 152-335 8.28e-11

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: 62.32  E-value: 8.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  152 DWCFQVKANGENRLLSIKGDCARGGNKKGQVVS--IPTH-WLTEFKALGNFVANGEHV--------------------GD 208
Cdd:TIGR02779  13 DWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTekFPILaAALAALPILPAVLDGEIVvldesgrsdfsalqnrlragRD 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  209 R---FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNdvANVTPSFGVIECYytaDEKQALLQRAEDIRLEGIVAKNAR 285
Cdd:TIGR02779  93 RpatYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIK--GPLAPDRYSVHFE---GDGQALLEAACRLGLEGVVAKRRD 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 499777958  286 GVYAQGRGPDSLKF-VFREVSTCIV------MARNVQRSVQVGLLnSEGDLVSRGNV 335
Cdd:TIGR02779 168 SPYRSGRSADWLKLkCRRRQEFVIGgytppnGSRSGFGALLLGVY-EGGGLRYVGRV 223
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 180-336 2.59e-10

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: 61.95  E-value: 2.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  180 GQVVSIPTHWLTEFKALGNFVANGehVGDR--FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSmNDVANVTPSFGViec 257
Cdd:TIGR02776  30 GEIVVLDERGRADFAALQNALSAG--ASRPltYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKA-QDEPAIRYSDHF--- 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  258 yytADEKQALLQRAEDIRLEGIVAKNARGVYAQGRGPDSLKF-VFREVSTCIV---MARNVQRSVQVGLLnSEGDLVSRG 333
Cdd:TIGR02776 104 ---ESDGDALLESACRLGLEGVVSKRLDSPYRSGRSKDWLKLkCRRRQEFVITgytPPNRRFGALLVGVY-EGGQLVYAG 179


                  ...
gi 499777958  334 NVT 336
Cdd:TIGR02776 180 KVG 182
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 209-292 1.21e-09

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: 57.64  E-value: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVieCYYTADEKQAL--LQRAEDIRLEGIVAKNARG 286
Cdd:cd07905  107 SFVAFDLLALGGRDLRGRPLRERRAALEAL------LAGWGPPLHL--SPATTDRAEARewLEEFEGAGLEGVVAKRLDG 178


                 ....*.
gi 499777958 287 VYAQGR 292
Cdd:cd07905  179 PYRPGE 184
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 133-301 4.37e-08

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: 52.81  E-value: 4.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 133 PQEPTAIQRAALKALIFDNDWCFQVKANGENRLLSIKGDCARGGNKKGQVVSIPTHWLTE---FKALGNFVANGEHVGDR 209
Cdd:cd06846    1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGrelLTLKPGFILDGELVVEN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 210 ---------FIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDVANVtPSFGVI--ECYYtaDEKQALLQRAEDIRLEG 278
Cdd:cd06846   81 revanpkptYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPV-KLVPLEnaPSYD--ETLDDLLEKLKKKGKEG 157

                        170       180
                 ....*....|....*....|....*
gi 499777958 279 IVAKNARGVYAQ--GRGPDSLKFVF 301
Cdd:cd06846  158 LVFKHPDAPYKGrpGSSGNQLKLKP 182
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 210-299 1.55e-07

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: 51.52  E-value: 1.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958  210 FIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndVANVTPSFGVIECY--YTADEKQALLQRAEDIRLEGIVAKNARGV 287
Cdd:pfam01068 116 LFVFDLLYLDGEDLTDLPLRERRKLLEEI------FKEIPGRIQLAESIvtKDVEEAQEFLEEAISEGLEGLVVKDPDST 189

                          90
                  ....*....|...
gi 499777958  288 YAQG-RGPDSLKF 299
Cdd:pfam01068 190 YEPGkRGKNWLKI 202
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 180-298 2.74e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 52.60  E-value: 2.74e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 180 GQVVSIPTHWLTEFKALGNFVANGEHVGDRFIAFDLLEYEGIDMRGWP--QRR-RFAKLLEmyDSMNDVANVTPSFGVie 256
Cdd:PRK05972 304 GEIVVLDEDGVPDFQALQNAFDEGRTEDLVYFAFDLPFLGGEDLRELPleERRaRLRALLE--AARSDRIRFSEHFDA-- 379

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 499777958 257 cyytadEKQALLQRAEDIRLEGIVAKNARGVYAQGRGPDSLK 298
Cdd:PRK05972 380 ------GGDAVLASACRLGLEGVIGKRADSPYVSGRSEDWIK 415
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 133-292 1.42e-06

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 50.39  E-value: 1.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 133 PQEPTAIQRAALKAlifdNDWCFQVKANGENRLLSIKGDCARGGNKKGQVVSiPTH----WLTEFKALGNFVANGEHV-- 206
Cdd:PRK09632 463 PMLATAGTVAGLKA----SQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVT-AEYpelaALAEDLADHHVVLDGEIVal 537

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 207 GD------------------RFIAFDLLEYEGIDMRGWPQRRRfAKLLEMYDSMNDVANVTPSFgviecyytADEKQALL 268
Cdd:PRK09632 538 DDsgvpsfgllqnrgrdtrvEFWAFDLLYLDGRSLLRKPYRDR-RKLLEALAPSGGSLTVPPLL--------PGDGAEAL 608

                        170       180
                 ....*....|....*....|....
gi 499777958 269 QRAEDIRLEGIVAKNARGVYAQGR 292
Cdd:PRK09632 609 AYSRELGWEGVVAKRRDSTYQPGR 632
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 209-292 2.26e-05

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 46.37  E-value: 2.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDvANVTPSFGViecyyTADEKQALLQRAEDIR---LEGIVAKNAR 285
Cdd:PRK09247 317 FLRAYDLLEDGGEDLRALPLAERRARLEALIARLPD-PRLDLSPLV-----PFSDWDELAALRAAARergVEGLMLKRRD 390


                 ....*..
gi 499777958 286 GVYAQGR 292
Cdd:PRK09247 391 SPYLVGR 397
ligD PRK09633
DNA ligase D;
209-308 3.62e-05

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 45.80  E-value: 3.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDVANVTP-SFGVIECYYTADEKQALLQRAEDIRLEGIVAKNARGV 287
Cdd:PRK09633 114 QLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPASPDPyAKARIQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSK 193

                         90       100
                 ....*....|....*....|...
gi 499777958 288 YAQG-RGPDSLKFV-FREVSTCI 308
Cdd:PRK09633 194 WLENkRSKDWLKIKnWRYVHVIV 216
30 PHA02587
DNA ligase; Provisional
 231-307 9.63e-05

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 44.31  E-value: 9.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499777958 231 RFAKLLEMYDSMnDVANVTPsfgvIEC--YYTADEKQALLQRAEDIRLEGIVAKNARGVYAQGRGPDSLKfvFREVSTC 307
Cdd:PHA02587 295 RFSKLAQMFEDC-GYDRVEL----IENqvVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDGRSKDQIK--FKEVIDI 366
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 210-298 1.01e-04

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: 43.34  E-value: 1.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 210 FIAFDLLEYEGIDMRGWPQRRRFAKLLEMydsmndvanVTPSFGVIEC-----YYTADEKQALLQRAEDIRLEGIVAKNA 284
Cdd:cd07903  133 FVVFDILYLNGKSLTNLPLHERKKLLEKI---------ITPIPGRLEVvkrteASTKEEIEEALNEAIDNREEGIVVKDL 203

                         90
                 ....*....|....*
gi 499777958 285 RGVYAQG-RGPDSLK 298
Cdd:cd07903  204 DSKYKPGkRGGGWIK 218
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 209-292 2.80e-04

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: 41.77  E-value: 2.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSM-NDVANVTPsfgVIEcYYTADEKQALLQRAEDIRLEGIVAKNARGV 287
Cdd:cd07897  114 AFRAYDLLELNGEDLRALPLRERRARLEALLARLpPPRLDLSP---LIA-FADWEELAALRAQSRERGAEGLMLKRRDSP 189


                 ....*
gi 499777958 288 YAQGR 292
Cdd:cd07897  190 YLVGR 194
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 210-307 2.83e-04

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 42.44  E-value: 2.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 210 FIAFDLLEYEGIDMRGWPqrrrfakLLEMYDSMNDVANVTPSFGVIEcyYTADEKQALLQRAEDIRLEGIVAKNARGVYA 289
Cdd:PRK07636 103 FCVFDVLYINGVSLTALP-------LSERKEILASLLLPHPNVKIIE--GIEGHGTAYFELVEERELEGIVIKKANSPYE 173

                         90       100
                 ....*....|....*....|..
gi 499777958 290 QGRGPDS-LKFV---FREVSTC 307
Cdd:PRK07636 174 INKRSDNwLKVInyqYTDVLIT 195
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 193-299 8.76e-04

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: 40.40  E-value: 8.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 193 FKALGN-----FVANGEHVgdRFIAFDLLEYEGIDMRGWPQRRRfAKLLEmydsmndvANVTPSFGVIEC-----YYTAD 262
Cdd:cd07898   92 FKRLGRkfrdkFLDEDVPV--VLMAFDLLYLNGESLLDRPLRER-RQLLE--------ELFVEIPGRIRIapalpVESAE 160

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499777958 263 EKQALLQRAEDIRLEGIVAKNARGVYAQG-RGPDSLKF 299
Cdd:cd07898  161 ELEAAFARARARGNEGLMLKDPDSPYEPGrRGLAWLKL 198
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 212-299 2.08e-03

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: 39.06  E-value: 2.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 212 AFDLLEYEGIDMRGWPQRRRFAKLLEmydsmndVANVTPSFGVIECYYTADEK--QALLQRAEDIRLEGIVAKNARGVYA 289
Cdd:cd07901  121 LFDILYLDGEDLLDLPLSERRKILEE-------IVPETEAILLAPRIVTDDPEeaEEFFEEALEAGHEGVMVKSLDSPYQ 193

                         90
                 ....*....|.
gi 499777958 290 QG-RGPDSLKF 299
Cdd:cd07901  194 AGrRGKNWLKV 204
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 209-292 2.25e-03

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 39.88  E-value: 2.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499777958 209 RFIAFDLLEYEGIDMRGWPQRRRFAKLLEMYDSMNDVaNVTPSfgviecyyTADEKQA--LLQRAEDIRLEGIVAKNARG 286
Cdd:PRK08224 115 SFVAFDLLALGDRDLTGRPFAERRAALEAAAAGSGPV-HLTPA--------TTDPATArrWFEEFEGAGLDGVIAKPLDG 185


                 ....*.
gi 499777958 287 VYAQGR 292
Cdd:PRK08224 186 PYQPGK 191
 
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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