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Conserved domains on  [gi|446939140|ref|WP_001016396|]
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WGR domain-containing protein [Leptospira interrogans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 247-413 7.22e-52

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: 174.14  E-value: 7.22e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 247 CQLLNPIDEEELSTYVEDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLIIAISQILHD--HSLSFSEDFILDGEVIGD- 323
Cdd:cd06846    1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPgrELLTLKPGFILDGELVVEn 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------VFFPFDIFSKDGKDIQHLPYQERYAILESILK-----DQDEIFHIVKLVKSTKGKKVLLEELREKQKEGIVF 390
Cdd:cd06846   81 revanpkpTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKefeglDPVKLVPLENAPSYDETLDDLLEKLKKKGKEGLVF 160

                        170       180
                 ....*....|....*....|...
gi 446939140 391 KDLNAPYKaGRPSSKGSQIKFKF 413
Cdd:cd06846  161 KHPDAPYK-GRPGSSGNQLKLKP 182
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 154-229 2.38e-31

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: 115.49  E-value: 2.38e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446939140 154 NKISLYYQGDGSDKVYHVNIDPEGD-GYVVHFAFGRRGSSLQTGTKTSKPVSYEAAQKIMRQLVNSKMAKGYTEIES 229
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEVSDdGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNKGYREGEG 77
WGR COG3831
WGR domain, predicted DNA-binding domain in MolR [Transcription];
4-67 2.16e-19

WGR domain, predicted DNA-binding domain in MolR [Transcription];


:

Pssm-ID: 443043  Cd Length: 83  Bit Score: 82.34  E-value: 2.16e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446939140   4 QLIFRDDKSDKFWNIETS-----GNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:COG3831    6 ERIDPAGNSARFYELEVEpdlfgGWSLTRRWGRIGTKGQTKTKTFASEEEALAALEKLVAEKLRKGYRE 74
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 247-413 7.22e-52

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: 174.14  E-value: 7.22e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 247 CQLLNPIDEEELSTYVEDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLIIAISQILHD--HSLSFSEDFILDGEVIGD- 323
Cdd:cd06846    1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPgrELLTLKPGFILDGELVVEn 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------VFFPFDIFSKDGKDIQHLPYQERYAILESILK-----DQDEIFHIVKLVKSTKGKKVLLEELREKQKEGIVF 390
Cdd:cd06846   81 revanpkpTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKefeglDPVKLVPLENAPSYDETLDDLLEKLKKKGKEGLVF 160

                        170       180
                 ....*....|....*....|...
gi 446939140 391 KDLNAPYKaGRPSSKGSQIKFKF 413
Cdd:cd06846  161 KHPDAPYK-GRPGSSGNQLKLKP 182
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 154-229 2.38e-31

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: 115.49  E-value: 2.38e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446939140 154 NKISLYYQGDGSDKVYHVNIDPEGD-GYVVHFAFGRRGSSLQTGTKTSKPVSYEAAQKIMRQLVNSKMAKGYTEIES 229
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEVSDdGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNKGYREGEG 77
WGR COG3831
WGR domain, predicted DNA-binding domain in MolR [Transcription];
4-67 2.16e-19

WGR domain, predicted DNA-binding domain in MolR [Transcription];


Pssm-ID: 443043  Cd Length: 83  Bit Score: 82.34  E-value: 2.16e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446939140   4 QLIFRDDKSDKFWNIETS-----GNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:COG3831    6 ERIDPAGNSARFYELEVEpdlfgGWSLTRRWGRIGTKGQTKTKTFASEEEALAALEKLVAEKLRKGYRE 74
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
263-497 3.39e-18

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 86.90  E-value: 3.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 263 EDDQYGAQEKLDGNRMMIRKIGDNVEGINRKG---------LIIAISQILHDhslsfseDFILDGEVI---GD------- 323
Cdd:COG1793  127 DGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGeditdrfpeLVEALRALPAD-------DAVLDGEIValdEDgrppfqa 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGKKVLLEELREK 383
Cdd:COG1793  200 lqqrlgrkrdvaklarevpvVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVIDWGEGEALFAAAREA 279

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 384 QKEGIVFKDLNAPYKAGRPSskGSQIKFKFYETatvsVETV------------NLKRSVSMRLYN-GNEWVSVGNV---- 446
Cdd:COG1793  280 GLEGVMAKRLDSPYRPGRRS--GDWLKVKCPRT----QDLVvggatpgkgrraGGFGSLLLGVYDpGGELVYVGKVgtgf 353

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446939140 447 ---------------TI---PINFAIPKEND-------IIEVRYLYAYKGGSLYQPTYLGARTDADENDCDLKQLK 497
Cdd:COG1793  354 tdaelaelterlrplTRersPFAVPSDGRPVrwvrpelVAEVAFDEITRSGALRFPRFLRLREDKPPEEATLEELE 429
WGR_MMR_like cd07996
WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in ...
 5-67 2.13e-17

WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153425  Cd Length: 74  Bit Score: 76.49  E-value: 2.13e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140   5 LIFRD--DKSDKFWNIETSGNSF-----TVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:cd07996    4 LERIDpeRNSARFYEIELEGDLFgewslVRRWGRIGTKGQSRTKTFDSEEEALKAAEKLIREKLKRGYRE 73
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 269-412 6.62e-16

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: 76.17  E-value: 6.62e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  269 AQEKLDGNRMMIRKIGDNVEGINRKG---------LIIAISQILHDHSLSfsedFILDGEVI-----GDVFFP------- 327
Cdd:pfam01068  23 AEYKYDGERAQIHKDGDEVKLFSRNLenitrhypeIVEALKEAFKPDEKS----FILDGEIVavdpeTGEILPfqvladr 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  328 --------------------FDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIV--KLVKSTKGKKVLLEELREKQK 385
Cdd:pfam01068  99 kkkkvdveelaekvpvclfvFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAesIVTKDVEEAQEFLEEAISEGL 178

                         170       180
                  ....*....|....*....|....*..
gi 446939140  386 EGIVFKDLNAPYKAGRPSSKgsQIKFK 412
Cdd:pfam01068 179 EGLVVKDPDSTYEPGKRGKN--WLKIK 203
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 272-493 1.74e-15

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: 76.96  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  272 KLDGNRMMIRKIGDNVEGINRKGLIIAISQILHDHSLSFSE--DFILDGEVI----------------GD-------VFF 326
Cdd:TIGR02779  19 KYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAALAALPilPAVLDGEIVvldesgrsdfsalqnrLRagrdrpaTYY 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  327 PFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGK-KVLLEELREKQKEGIVFKDLNAPYKAGRpssK 405
Cdd:TIGR02779  99 AFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRYSVHFEGDgQALLEAACRLGLEGVVAKRRDSPYRSGR---S 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  406 GSQIKFKFYETATVSV---ETVNLKRSVS----MRLYNGNEWVSVGNVT---------------------IPINFAIPKE 457
Cdd:TIGR02779 176 ADWLKLKCRRRQEFVIggyTPPNGSRSGFgallLGVYEGGGLRYVGRVGtgfseaelatikerlkpleskPDKPGAREKR 255

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 446939140  458 ND-------IIEVRYLYAYKGGSLYQPTYLGARTDADENDCDL 493
Cdd:TIGR02779 256 GVhwvkpelVAEVEFAGWTRDGRLRQASFVGLREDKPASEVTR 298
WGR pfam05406
WGR domain; This domain is found in a variety of polyA polymerases as well as the E. coli ...
 11-67 1.89e-14

WGR domain; This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.


Pssm-ID: 398851  Cd Length: 79  Bit Score: 68.42  E-value: 1.89e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446939140   11 KSDKFWNIET-----SGNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:pfam05406  13 NSNKFYEIQVeddlfGGYSLFRRWGRIGTRGQTKLKSFDSLEEAIKEFEKLFAEKTKKGYRE 74
WGR smart00773
Proposed nucleic acid binding domain; This domain is named after its most conserved central ...
 1-71 2.24e-14

Proposed nucleic acid binding domain; This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.


Pssm-ID: 214814  Cd Length: 84  Bit Score: 68.47  E-value: 2.24e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446939140     1 MNHQLIFRDDKSD--KFWNIET-----SGNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIEGNDR 71
Cdd:smart00773   6 YDVYLNFTDLASNnnKFYIIQLleddfGGYSVYRRWGRIGTKGQTKLKTFDSLEDAIKEFEKLFKEKTKNGYEERGKF 83
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 249-403 1.15e-10

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 62.08  E-value: 1.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 249 LLNPIDEEelstyVEDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLIIAiSQILHDHSLSFSEDFILDGEVI------- 321
Cdd:PRK07636   7 LLESAKEP-----FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVT-AKFPELLNLDIPDGTVLDGELIvlgstga 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 322 GD-------------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEifhiVKLVKSTKGK-KVLLEELR 381
Cdd:PRK07636  81 PDfeavmerfqskkstkihpvVFCVFDVLYINGVSLTALPLSERKEILASLLLPHPN----VKIIEGIEGHgTAYFELVE 156

                        170       180
                 ....*....|....*....|..
gi 446939140 382 EKQKEGIVFKDLNAPYKAGRPS 403
Cdd:PRK07636 157 ERELEGIVIKKANSPYEINKRS 178
WGR COG3831
WGR domain, predicted DNA-binding domain in MolR [Transcription];
155-232 4.34e-10

WGR domain, predicted DNA-binding domain in MolR [Transcription];


Pssm-ID: 443043  Cd Length: 83  Bit Score: 56.15  E-value: 4.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 155 KISLYYQ--GDGSDKVYHVNIDP-EGDGYVVHFAFGRRGSSLQTGTKTSkpVSYEAAQKIMRQLVNSKMAKGYTEIESGA 231
Cdd:COG3831    2 RLYLERIdpAGNSARFYELEVEPdLFGGWSLTRRWGRIGTKGQTKTKTF--ASEEEALAALEKLVAEKLRKGYREVGAGA 79


                 .
gi 446939140 232 P 232
Cdd:COG3831   80 A 80
WGR smart00773
Proposed nucleic acid binding domain; This domain is named after its most conserved central ...
 162-230 1.06e-03

Proposed nucleic acid binding domain; This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.


Pssm-ID: 214814  Cd Length: 84  Bit Score: 38.04  E-value: 1.06e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140   162 GDGSDKVYHVNIDPEGDG-YVVHFAFGRRGSSLQTgtKTSKPVSYEAAQKIMRQLVNSKMAKGYTEIESG 230
Cdd:smart00773  16 ASNNNKFYIIQLLEDDFGgYSVYRRWGRIGTKGQT--KLKTFDSLEDAIKEFEKLFKEKTKNGYEERGKF 83
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 247-413 7.22e-52

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: 174.14  E-value: 7.22e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 247 CQLLNPIDEEELSTYVEDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLIIAISQILHD--HSLSFSEDFILDGEVIGD- 323
Cdd:cd06846    1 PQLLNPILEEALSEYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPgrELLTLKPGFILDGELVVEn 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------VFFPFDIFSKDGKDIQHLPYQERYAILESILK-----DQDEIFHIVKLVKSTKGKKVLLEELREKQKEGIVF 390
Cdd:cd06846   81 revanpkpTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKefeglDPVKLVPLENAPSYDETLDDLLEKLKKKGKEGLVF 160

                        170       180
                 ....*....|....*....|...
gi 446939140 391 KDLNAPYKaGRPSSKGSQIKFKF 413
Cdd:cd06846  161 KHPDAPYK-GRPGSSGNQLKLKP 182
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 154-229 2.38e-31

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: 115.49  E-value: 2.38e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446939140 154 NKISLYYQGDGSDKVYHVNIDPEGD-GYVVHFAFGRRGSSLQTGTKTSKPVSYEAAQKIMRQLVNSKMAKGYTEIES 229
Cdd:cd07998    1 KSTSLYFQEGNSDKVYEVDLFEVSDdGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLVKSKTNKGYREGEG 77
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 263-414 1.61e-19

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: 86.44  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 263 EDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGL--------IIAISQILHDHslsfseDFILDGEVI--GD--------- 323
Cdd:cd07906   14 DGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLdwtarfpeLAEALAALPVR------DAVLDGEIVvlDEggrpdfqal 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 ----------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVksTKGKKVLLEELREKQKEG 387
Cdd:cd07906   88 qnrlrlrrrlartvpvVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHF--EGGGAALFAAACELGLEG 165

                        170       180
                 ....*....|....*....|....*..
gi 446939140 388 IVFKDLNAPYKAGRPSskGSQIKFKFY 414
Cdd:cd07906  166 IVAKRADSPYRSGRRS--RDWLKIKCR 190
WGR COG3831
WGR domain, predicted DNA-binding domain in MolR [Transcription];
4-67 2.16e-19

WGR domain, predicted DNA-binding domain in MolR [Transcription];


Pssm-ID: 443043  Cd Length: 83  Bit Score: 82.34  E-value: 2.16e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446939140   4 QLIFRDDKSDKFWNIETS-----GNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:COG3831    6 ERIDPAGNSARFYELEVEpdlfgGWSLTRRWGRIGTKGQTKTKTFASEEEALAALEKLVAEKLRKGYRE 74
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
263-497 3.39e-18

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 86.90  E-value: 3.39e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 263 EDDQYGAQEKLDGNRMMIRKIGDNVEGINRKG---------LIIAISQILHDhslsfseDFILDGEVI---GD------- 323
Cdd:COG1793  127 DGGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGeditdrfpeLVEALRALPAD-------DAVLDGEIValdEDgrppfqa 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGKKVLLEELREK 383
Cdd:COG1793  200 lqqrlgrkrdvaklarevpvVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSPHVIDWGEGEALFAAAREA 279

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 384 QKEGIVFKDLNAPYKAGRPSskGSQIKFKFYETatvsVETV------------NLKRSVSMRLYN-GNEWVSVGNV---- 446
Cdd:COG1793  280 GLEGVMAKRLDSPYRPGRRS--GDWLKVKCPRT----QDLVvggatpgkgrraGGFGSLLLGVYDpGGELVYVGKVgtgf 353

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446939140 447 ---------------TI---PINFAIPKEND-------IIEVRYLYAYKGGSLYQPTYLGARTDADENDCDLKQLK 497
Cdd:COG1793  354 tdaelaelterlrplTRersPFAVPSDGRPVrwvrpelVAEVAFDEITRSGALRFPRFLRLREDKPPEEATLEELE 429
WGR_MMR_like cd07996
WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in ...
 5-67 2.13e-17

WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153425  Cd Length: 74  Bit Score: 76.49  E-value: 2.13e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140   5 LIFRD--DKSDKFWNIETSGNSF-----TVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:cd07996    4 LERIDpeRNSARFYEIELEGDLFgewslVRRWGRIGTKGQSRTKTFDSEEEALKAAEKLIREKLKRGYRE 73
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 269-412 6.62e-16

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: 76.17  E-value: 6.62e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  269 AQEKLDGNRMMIRKIGDNVEGINRKG---------LIIAISQILHDHSLSfsedFILDGEVI-----GDVFFP------- 327
Cdd:pfam01068  23 AEYKYDGERAQIHKDGDEVKLFSRNLenitrhypeIVEALKEAFKPDEKS----FILDGEIVavdpeTGEILPfqvladr 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  328 --------------------FDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIV--KLVKSTKGKKVLLEELREKQK 385
Cdd:pfam01068  99 kkkkvdveelaekvpvclfvFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAesIVTKDVEEAQEFLEEAISEGL 178

                         170       180
                  ....*....|....*....|....*..
gi 446939140  386 EGIVFKDLNAPYKAGRPSSKgsQIKFK 412
Cdd:pfam01068 179 EGLVVKDPDSTYEPGKRGKN--WLKIK 203
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 272-493 1.74e-15

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: 76.96  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  272 KLDGNRMMIRKIGDNVEGINRKGLIIAISQILHDHSLSFSE--DFILDGEVI----------------GD-------VFF 326
Cdd:TIGR02779  19 KYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAALAALPilPAVLDGEIVvldesgrsdfsalqnrLRagrdrpaTYY 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  327 PFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGK-KVLLEELREKQKEGIVFKDLNAPYKAGRpssK 405
Cdd:TIGR02779  99 AFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRYSVHFEGDgQALLEAACRLGLEGVVAKRRDSPYRSGR---S 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  406 GSQIKFKFYETATVSV---ETVNLKRSVS----MRLYNGNEWVSVGNVT---------------------IPINFAIPKE 457
Cdd:TIGR02779 176 ADWLKLKCRRRQEFVIggyTPPNGSRSGFgallLGVYEGGGLRYVGRVGtgfseaelatikerlkpleskPDKPGAREKR 255

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 446939140  458 ND-------IIEVRYLYAYKGGSLYQPTYLGARTDADENDCDL 493
Cdd:TIGR02779 256 GVhwvkpelVAEVEFAGWTRDGRLRQASFVGLREDKPASEVTR 298
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 248-412 3.73e-15

Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185713 [Multi-domain]  Cd Length: 225  Bit Score: 74.54  E-value: 3.73e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 248 QLLN--PIDEEELSTyVEDDQYGAQEKLDGNRMMIRKIGDNV---------------EGINRKGLIIAISQILHDHslsf 310
Cdd:cd07903   15 MLAErlNIGYVEIKL-LKGKPFYIETKLDGERIQLHKDGNEFkyfsrngndytylygASLTPGSLTPYIHLAFNPK---- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 311 SEDFILDGEVIG---------------DV--------------FFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIF 361
Cdd:cd07903   90 VKSCILDGEMVVwdketkrflpfgtlkDVaklrevedsdlqpcFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPGRL 169

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446939140 362 HIVKLVKSTKGKKV--LLEELREKQKEGIVFKDLNAPYKAGrpSSKGSQIKFK 412
Cdd:cd07903  170 EVVKRTEASTKEEIeeALNEAIDNREEGIVVKDLDSKYKPG--KRGGGWIKIK 220
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 269-412 8.69e-15

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: 72.96  E-value: 8.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 269 AQEKLDGNRMMIRKIGDNVEGINRK---------GLIIAISQILHdhslsfSEDFILDGEVIG----------------- 322
Cdd:cd07901   29 VEYKYDGIRVQIHKDGDEVRIFSRRleditnalpEVVEAVRELVK------AEDAILDGEAVAydpdgrplpfqetlrrf 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 323 ----DV----------FFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKST--KGKKVLLEELREKQkE 386
Cdd:cd07901  103 rrkyDVeeaaeeipltLFLFDILYLDGEDLLDLPLSERRKILEEIVPETEAILLAPRIVTDDpeEAEEFFEEALEAGH-E 181

                        170       180
                 ....*....|....*....|....*.
gi 446939140 387 GIVFKDLNAPYKAGRPSSkgSQIKFK 412
Cdd:cd07901  182 GVMVKSLDSPYQAGRRGK--NWLKVK 205
WGR pfam05406
WGR domain; This domain is found in a variety of polyA polymerases as well as the E. coli ...
 11-67 1.89e-14

WGR domain; This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.


Pssm-ID: 398851  Cd Length: 79  Bit Score: 68.42  E-value: 1.89e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446939140   11 KSDKFWNIET-----SGNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:pfam05406  13 NSNKFYEIQVeddlfGGYSLFRRWGRIGTRGQTKLKSFDSLEEAIKEFEKLFAEKTKKGYRE 74
WGR smart00773
Proposed nucleic acid binding domain; This domain is named after its most conserved central ...
 1-71 2.24e-14

Proposed nucleic acid binding domain; This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.


Pssm-ID: 214814  Cd Length: 84  Bit Score: 68.47  E-value: 2.24e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446939140     1 MNHQLIFRDDKSD--KFWNIET-----SGNSFTVTYGKTGTAGTSQTKTFETEETCIKEARKLLSEKLKKGYIEGNDR 71
Cdd:smart00773   6 YDVYLNFTDLASNnnKFYIIQLleddfGGYSVYRRWGRIGTKGQTKLKTFDSLEDAIKEFEKLFKEKTKNGYEERGKF 83
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 253-412 2.44e-12

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: 65.82  E-value: 2.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 253 IDEEELSTYVEDdqygaqeKLDGNRMMIRKIGDNVEGINRKGLIIAISQI-LHDHSLSFSEDFILDGE--VIGD------ 323
Cdd:cd07898   16 KAKKPAAAWVED-------KYDGIRAQVHKDGGRVEIFSRSLEDITDQFPeLAAAAKALPHEFILDGEilAWDDnrglpf 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 ----------------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKdqdEIFHIVKLVKSTKGKKV-----L 376
Cdd:cd07898   89 selfkrlgrkfrdkfldedvpvVLMAFDLLYLNGESLLDRPLRERRQLLEELFV---EIPGRIRIAPALPVESAeeleaA 165

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 446939140 377 LEELREKQKEGIVFKDLNAPYKAGRPSskGSQIKFK 412
Cdd:cd07898  166 FARARARGNEGLMLKDPDSPYEPGRRG--LAWLKLK 199
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 249-403 1.15e-10

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 62.08  E-value: 1.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 249 LLNPIDEEelstyVEDDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLIIAiSQILHDHSLSFSEDFILDGEVI------- 321
Cdd:PRK07636   7 LLESAKEP-----FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVT-AKFPELLNLDIPDGTVLDGELIvlgstga 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 322 GD-------------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEifhiVKLVKSTKGK-KVLLEELR 381
Cdd:PRK07636  81 PDfeavmerfqskkstkihpvVFCVFDVLYINGVSLTALPLSERKEILASLLLPHPN----VKIIEGIEGHgTAYFELVE 156

                        170       180
                 ....*....|....*....|..
gi 446939140 382 EKQKEGIVFKDLNAPYKAGRPS 403
Cdd:PRK07636 157 ERELEGIVIKKANSPYEINKRS 178
WGR COG3831
WGR domain, predicted DNA-binding domain in MolR [Transcription];
155-232 4.34e-10

WGR domain, predicted DNA-binding domain in MolR [Transcription];


Pssm-ID: 443043  Cd Length: 83  Bit Score: 56.15  E-value: 4.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 155 KISLYYQ--GDGSDKVYHVNIDP-EGDGYVVHFAFGRRGSSLQTGTKTSkpVSYEAAQKIMRQLVNSKMAKGYTEIESGA 231
Cdd:COG3831    2 RLYLERIdpAGNSARFYELEVEPdLFGGWSLTRRWGRIGTKGQTKTKTF--ASEEEALAALEKLVAEKLRKGYREVGAGA 79


                 .
gi 446939140 232 P 232
Cdd:COG3831   80 A 80
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 324-496 1.24e-09

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: 60.41  E-value: 1.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  324 VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFhIVKLVKSTKGKKVLLEELREKQKEGIVFKDLNAPYKAGRPS 403
Cdd:TIGR02776  59 TYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDEPA-IRYSDHFESDGDALLESACRLGLEGVVSKRLDSPYRSGRSK 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  404 skgSQIKFKFYETATVSV----ETVNLKRSVSMRLYNGNEWVSVGNV----------------------TIPINFAIPKE 457
Cdd:TIGR02776 138 ---DWLKLKCRRRQEFVItgytPPNRRFGALLVGVYEGGQLVYAGKVgtgfgadtlktllarlkalgakASPFSGPAGAK 214

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 446939140  458 NDII---------EVRYLYAYKGGSLYQPTYLGARTDADENDCDLKQL 496
Cdd:TIGR02776 215 TRGVhwvrpslvaEVEYAGITRDGILREASFKGLREDKPAEEVTLETP 262
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 257-404 7.44e-09

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 58.38  E-value: 7.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 257 ELSTYVE----DDQYGAQEKLDGNRMMIRKIGDNVEGINRKGL-----IIAISQILHDHSLsfsEDFILDGEVI------ 321
Cdd:PRK05972 237 QLATLVDrppsGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLdwtakLPALAKAAAALGL---PDAWLDGEIVvldedg 313

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 322 -----------------GDVFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEifHIVKLVKS-TKGKKVLLEELREK 383
Cdd:PRK05972 314 vpdfqalqnafdegrteDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARS--DRIRFSEHfDAGGDAVLASACRL 391

                        170       180
                 ....*....|....*....|.
gi 446939140 384 QKEGIVFKDLNAPYKAGRPSS 404
Cdd:PRK05972 392 GLEGVIGKRADSPYVSGRSED 412
Adenylation_RNA_ligase cd07894
Adenylation domain of RNA circularization proteins; RNA circularization proteins are capable ...
 264-411 2.04e-08

Adenylation domain of RNA circularization proteins; RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.


Pssm-ID: 185705 [Multi-domain]  Cd Length: 342  Bit Score: 56.03  E-value: 2.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 264 DDQYGAQEKLDGNRMMIRKIGDNVEGINRKGLI----------IAISQILHDHslsfsEDFILDGEVIG----------- 322
Cdd:cd07894   47 KGPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFIcpfttdrlrdLIDPEFFDDH-----PDLVLCGEVVGpenpyvpgsyp 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 323 ---DV-FFPFDIFSKDGKdiQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGKKvLLEELREKQKEGIVFKDlnapyk 398
Cdd:cd07894  122 eveDVgFFVFDIRKKNTG--RPLPVEERRELLEKYGLPTVRLFGEFTADEIEELKE-IIRELDKEGREGVVLKD------ 192

                        170
                 ....*....|...
gi 446939140 399 agrPSSKGSQIKF 411
Cdd:cd07894  193 ---PDMRVPPLKY 202
WGR cd07994
WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases ...
 5-67 9.07e-07

WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153424  Cd Length: 73  Bit Score: 46.50  E-value: 9.07e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140   5 LIFRDDKSDKFWNIETSGNS------FTVTYGKTGTA-GTSQTKTFETEETCIKEARKLLSEKLKKGYIE 67
Cdd:cd07994    4 LGFQDIGSNKYYKLQLLEDDkenrywVFRSYGRVGTViGSTKLEQMPSKEEAEEHFMKLYEEKTGKGYYP 73
COG1423 COG1423
ATP-dependent RNA circularization protein, DNA/RNA ligase (PAB1020) family [Replication, ...
 269-392 1.10e-06

ATP-dependent RNA circularization protein, DNA/RNA ligase (PAB1020) family [Replication, recombination and repair];


Pssm-ID: 441033 [Multi-domain]  Cd Length: 373  Bit Score: 50.59  E-value: 1.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 269 AQEKLDGNRMMIRKIGDNVEGINRKGLIIAIS----------QILHDHslsfsEDFILDGEVIG--------------DV 324
Cdd:COG1423   83 VEEKMNGYNVRIAKIGGEILAFTRGGYVCPFTtdrardlldlEFFDDH-----PDLVLCGEMVGpenpyvphdypevdDL 157

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446939140 325 -FFPFDIFSKDGKDiqHLPYQERYAILESILKDQDEIFHIVKlVKSTKGKKVLLEELREKQKEGIVFKD 392
Cdd:COG1423  158 aFFVFDIRDKETGR--PLPVEERRELAEEYGLPQVRLFGEFD-PDDVEEIKEIIERLDKEGREGVVLKD 223
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 272-401 1.53e-06

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: 48.78  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 272 KLDGNRMMIRKIGDNVEGINRKG---------LIIAISQILhdhslsfSEDFILDGEVI----GDVFFP----------- 327
Cdd:cd07905   23 KWDGFRCLAFRDGDEVRLQSRSGkpltryfpeLVAAARALL-------PPGCVLDGELVvwrgGRLDFDalqqrihpaas 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 328 ---------------FDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHivkLVKSTKGKKVL---LEELREKQKEGIV 389
Cdd:cd07905   96 rvrrlaeetpasfvaFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLH---LSPATTDRAEArewLEEFEGAGLEGVV 172

                        170
                 ....*....|..
gi 446939140 390 FKDLNAPYKAGR 401
Cdd:cd07905  173 AKRLDGPYRPGE 184
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 271-401 1.64e-06

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 50.35  E-value: 1.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 271 EKLDGNRMMIRKIGDNVEGINRkGL---------IIAISQILHdhslsfSEDFILDGEVI---GD--------------- 323
Cdd:PRK03180 210 AKLDGARVQVHRDGDDVRVYTR-TLdditarlpeVVEAVRALP------VRSLVLDGEAIalrPDgrprpfqvtasrfgr 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 --------------VFFpFDIFSKDGKDIQHLPYQERYAILESILKDQdeifHIV-KLVKST-KGKKVLLEELREKQKEG 387
Cdd:PRK03180 283 rvdvaaaratqplsPFF-FDALHLDGRDLLDAPLSERLAALDALVPAA----HRVpRLVTADpAAAAAFLAAALAAGHEG 357

                        170
                 ....*....|....
gi 446939140 388 IVFKDLNAPYKAGR 401
Cdd:PRK03180 358 VMVKSLDAPYAAGR 371
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 303-412 6.28e-06

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: 47.16  E-value: 6.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 303 LHDHSLSFSEDFILDGEVI---GDVFFPF---------------------------DIFSKDGKDIQHLPYQERYAILES 352
Cdd:cd07897   63 LLAAAEALPDGTVLDGELLvwrDGRPLPFndlqqrlgrktvgkkllaeapaafrayDLLELNGEDLRALPLRERRARLEA 142

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446939140 353 ILKD-QDEIFHIVKLVKSTKGKKvlLEELR----EKQKEGIVFKDLNAPYKAGRPssKGSQIKFK 412
Cdd:cd07897  143 LLARlPPPRLDLSPLIAFADWEE--LAALRaqsrERGAEGLMLKRRDSPYLVGRK--KGDWWKWK 203
Adenylation_mRNA_capping cd07895
Adenylation domain of GTP-dependent mRNA capping enzymes; RNA capping enzymes transfer GMP ...
 266-413 6.74e-06

Adenylation domain of GTP-dependent mRNA capping enzymes; RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.


Pssm-ID: 185706 [Multi-domain]  Cd Length: 215  Bit Score: 47.24  E-value: 6.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 266 QYGAQEKLDGNR-MMIRKIGDNVEGINRKGLIIAISQIL---HDHSLSFSEDFILDGEVIGD--------VFFPFDIFSK 333
Cdd:cd07895   42 DYFVCEKSDGVRyLLLITGRGEVYLIDRKNDVFKVPGLFfprRKNLEPHHQGTLLDGELVIDkvpgkkrpRYLIFDILAF 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 334 DGKDIQHLPYQERYAILE-------------SILKDQDEIFHIV--KLVKSTKGKKvLLEELREKQK---EGIVFKDLNA 395
Cdd:cd07895  122 NGQSVTEKPLSERLKYIKkevieprnellkkGPIDKAKEPFSVRlkDFFPLYKIEK-LFEKIIPKLPhenDGLIFTPNDE 200

                        170
                 ....*....|....*...
gi 446939140 396 PYKAGRPSskgSQIKFKF 413
Cdd:cd07895  201 PYVPGTDK---NLLKWKP 215
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 247-401 9.23e-06

Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues.


Pssm-ID: 185707 [Multi-domain]  Cd Length: 174  Bit Score: 46.02  E-value: 9.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 247 CQLLNPIDEEELSTyveddQYGAQEKLDGNRMMIrkigDNVEGINRKGLIIaisqilhdHSLS-FSEDF---ILDGE-VI 321
Cdd:cd07896    3 LLLAKTYDEGEDIS-----GYLVSEKLDGVRAYW----DGKQLLSRSGKPI--------AAPAwFTAGLppfPLDGElWI 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 322 GD-----------------------VFFPFDIFSKDGkdiqhlPYQERYAILESILKDQDEIF-HIVKLVKsTKGKKVLL 377
Cdd:cd07896   66 GRgqfeqtssivrskkpddedwrkvKFMVFDLPSAKG------PFEERLERLKNLLEKIPNPHiKIVPQIP-VKSNEALD 138

                        170       180
                 ....*....|....*....|....*..
gi 446939140 378 EELR---EKQKEGIVFKDLNAPYKAGR 401
Cdd:cd07896  139 QYLDevvAAGGEGLMLRRPDAPYETGR 165
WGR_MMR_like cd07996
WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in ...
 155-227 1.47e-05

WGR domain of molybdate metabolism regulator and related proteins; The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153425  Cd Length: 74  Bit Score: 42.98  E-value: 1.47e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446939140 155 KISLYYQ--GDGSDKVYHVNIDPEGDGYV-VHFAFGRRGSSLQTGTKTSkpVSYEAAQKIMRQLVNSKMAKGYTEI 227
Cdd:cd07996    1 MTRLERIdpERNSARFYEIELEGDLFGEWsLVRRWGRIGTKGQSRTKTF--DSEEEALKAAEKLIREKLKRGYREA 74
WGR cd07994
WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases ...
 155-226 3.69e-05

WGR domain; The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.


Pssm-ID: 153424  Cd Length: 73  Bit Score: 41.88  E-value: 3.69e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446939140 155 KISLYYQGDGSDKVYHVNI--DPEGDGYVVHFAFGRRGSSLQtGTKTSKPVSYEAAQKIMRQLVNSKMAKGYTE 226
Cdd:cd07994    1 KATLGFQDIGSNKYYKLQLleDDKENRYWVFRSYGRVGTVIG-STKLEQMPSKEEAEEHFMKLYEEKTGKGYYP 73
WGR_DNA_ligase cd07998
WGR domain of bacterial DNA ligases; The WGR domain is found in a small family of predicted ...
 5-70 5.08e-05

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: 41.53  E-value: 5.08e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446939140   5 LIFRDDKSDKFWNI---ETSGNSFTVT--YGKTGTAGTSQTKTFE--TEETCIKEARKLLSEKLKKGYIEGND 70
Cdd:cd07998    5 LYFQEGNSDKVYEVdlfEVSDDGYVVNfrYGRRGSALREGTKTVApvTLEAAEKIFDKLVKSKTNKGYREGEG 77
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 303-412 6.40e-05

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 45.60  E-value: 6.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 303 LHDHSLSFSEDFILDGEVI-----GDVFFPF---------------------------DIFSKDGKDIQHLPYQERYAIL 350
Cdd:PRK09247 264 LAEAAEALPDGTVLDGELLvwrpeDGRPQPFadlqqrigrktvgkklladypaflrayDLLEDGGEDLRALPLAERRARL 343

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446939140 351 ESILKD-QDEIFHIVKLV--KSTKGKKVLLEELREKQKEGIVFKDLNAPYKAGRPssKGSQIKFK 412
Cdd:PRK09247 344 EALIARlPDPRLDLSPLVpfSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRK--KGPWWKWK 406
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 269-401 6.42e-05

Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185712 [Multi-domain]  Cd Length: 213  Bit Score: 44.25  E-value: 6.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 269 AQEKLDGNRMMIRKIGDNVEGINRkgliiAISQILhDHSLSFSEDFI-----------LDGEVI------------GDV- 324
Cdd:cd07902   38 AEIKYDGERVQVHKQGDNFKFFSR-----SLKPVL-PHKVAHFKDYIpkafphghsmiLDSEVLlvdtktgkplpfGTLg 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 325 -------------FFPFDIFSKDGKDIQHLPYQERYAILESILKdqdEI-----FHIVKLVKSTKGKKVLLEELREKQKE 386
Cdd:cd07902  112 ihkksafkdanvcLFVFDCLYYNGESLMDKPLRERRKILEDNMV---EIpnrimLSEMKFVKKADDLSAMIARVIKEGLE 188

                        170
                 ....*....|....*
gi 446939140 387 GIVFKDLNAPYKAGR 401
Cdd:cd07902  189 GLVLKDLKSVYEPGK 203
30 PHA02587
DNA ligase; Provisional
 341-416 1.67e-04

DNA ligase; Provisional


Pssm-ID: 222893 [Multi-domain]  Cd Length: 488  Bit Score: 43.93  E-value: 1.67e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446939140 341 LPYQERYAILESILKDQDE--IFHIVKLVKSTKGK-KVLLEELREKQKEGIVFKDLNAPYKAGRPSskgSQIKFKFYET 416
Cdd:PHA02587 290 MPYDDRFSKLAQMFEDCGYdrVELIENQVVNNLEEaKEIYKRYVDQGLEGIILKNTDGLWEDGRSK---DQIKFKEVID 365
RNA_ligase pfam09414
RNA ligase; This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked ...
 314-392 2.60e-04

RNA ligase; This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes.


Pssm-ID: 430596 [Multi-domain]  Cd Length: 120  Bit Score: 40.80  E-value: 2.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140  314 FILDGEVIG-----------DVFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIFHIVKLVKSTKGKKVLLEELRE 382
Cdd:pfam09414  18 LVLFGELVGakhqinydglpHGFYVFDVFDIDDETGRFLSPDEVEALAEGLGLPTVPVLGGVFDEEALEELLELLSGLEG 97

                          90
                  ....*....|
gi 446939140  383 KQKEGIVFKD 392
Cdd:pfam09414  98 NLREGVVIKP 107
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 272-426 7.72e-04

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 41.88  E-value: 7.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 272 KLDGNRMMIRKIGDNV-------EGINRK--GLIIAISQILHdhslsfSEDFILDGEVI------GD------------- 323
Cdd:PRK01109 255 KYDGERAQIHKKGDKVkifsrrlENITHQypDVVEYAKEAIK------AEEAIVEGEIVavdpetGEmrpfqelmhrkrk 328

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 324 ------------VFFPFDIFSKDGKDIQHLPYQERYAILESILKDQDEIfhivKLVKSTKGKKVllEELR-------EKQ 384
Cdd:PRK01109 329 ydieeaikeypvNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKENDKV----KLAERIITDDV--EELEkffhraiEEG 402

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446939140 385 KEGIVFKDL--NAPYKAGrpsSKGSQ-IKFKF-YETATvsVETVNL 426
Cdd:PRK01109 403 CEGLMAKSLgkDSIYQAG---ARGWLwIKYKRdYQSEM--ADTVDL 443
ligD PRK09633
DNA ligase D;
325-496 1.01e-03

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 41.56  E-value: 1.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 325 FFPFDIFSKDGKDIQHLPYQERYAILESILKDQD-------EIFHIVKLVKSTKGKKVLLEELREKQKEGIVFKDLNAPY 397
Cdd:PRK09633 115 LLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKlpaspdpYAKARIQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSKW 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140 398 KAGRPSSkgSQIKFKFYETATVSVETVNLK-RSVSMRLYNGNEWVSVGNV----------TIpinFAIPKEND------- 459
Cdd:PRK09633 195 LENKRSK--DWLKIKNWRYVHVIVTGYDPSnGYFTGSVYKDGQLTEVGSVkhgmedeerqTL---RAIFKQNGtktksge 269

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446939140 460 -------IIEVRYLYAYkGGSLYQPTYLGARTDADENDCDLKQL 496
Cdd:PRK09633 270 ytlepsiCVTVACITFD-GGTLREPSFVSFLFDMDPTECTYQQL 312
WGR smart00773
Proposed nucleic acid binding domain; This domain is named after its most conserved central ...
 162-230 1.06e-03

Proposed nucleic acid binding domain; This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain.


Pssm-ID: 214814  Cd Length: 84  Bit Score: 38.04  E-value: 1.06e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446939140   162 GDGSDKVYHVNIDPEGDG-YVVHFAFGRRGSSLQTgtKTSKPVSYEAAQKIMRQLVNSKMAKGYTEIESG 230
Cdd:smart00773  16 ASNNNKFYIIQLLEDDFGgYSVYRRWGRIGTKGQT--KLKTFDSLEDAIKEFEKLFKEKTKNGYEERGKF 83
 
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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