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Conserved domains on  [gi|1678130702|gb|TMW43975|]
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hypothetical protein DOY81_010945, partial [Sarcophaga bullata]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 23-241 2.68e-143

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


:

Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 403.86  E-value: 2.68e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  23 RCPMIPGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHCNENGVVSIFSRNQENNTLKYPDILTRITSFAK 102
Cdd:cd07900     1 HCKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 103 PNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:cd07900    81 PSVKSFILDSEIVAYDRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVP 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 183 GCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDY 241
Cdd:cd07900   161 GRFQFATSKDSEDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219
OBF_DNA_ligase_family super family cl08424
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 246-290 4.59e-27

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


The actual alignment was detected with superfamily member cd07969:

Pssm-ID: 447632 [Multi-domain]  Cd Length: 144  Bit Score: 103.71  E-value: 4.59e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1678130702 246 GDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:cd07969     1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGT 45
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 23-241 2.68e-143

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 403.86  E-value: 2.68e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  23 RCPMIPGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHCNENGVVSIFSRNQENNTLKYPDILTRITSFAK 102
Cdd:cd07900     1 HCKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 103 PNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:cd07900    81 PSVKSFILDSEIVAYDRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVP 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 183 GCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDY 241
Cdd:cd07900   161 GRFQFATSKDSEDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219
PLN03113 PLN03113
DNA ligase 1; Provisional
 3-301 2.14e-138

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 410.14  E-value: 2.14e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702   3 PNYNKIIPTLLKYGVEQLQERCPMIPGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHCNENGVVSIFSRN 82
Cdd:PLN03113  341 PVYDKIVPALLSGGVWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRN 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  83 QENNTLKYPDILTRITSFAKPNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGKPL 162
Cdd:PLN03113  421 AERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYDREKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPL 500

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 163 VRNTFAERRQLMKDNFTELEGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDYL 242
Cdd:PLN03113  501 IQEQLKIRREHLYESFEEDPGFFQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLKKDYM 580

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 243 SGCGDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGTaGLWEGLENDR 301
Cdd:PLN03113  581 ESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNKEEFQSICKIGT-GFSEAVLEER 638
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 1-290 1.75e-112

DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 336.60  E-value: 1.75e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702   1 QCPNYNKIIPTLLKYGVEQLQERCPMIPGIPIKPMLAQPTTGVSDVLERFDGlNITCEWKYDGERAQIHCNeNGVVSIFS 80
Cdd:TIGR00574 136 LTNDLGKVAKILLEPGLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-GFYVEYKYDGERVQVHKD-GDKFKIFS 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  81 RNQENNTLKYPDILTRITSFAKPNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRK-NVDVKDIKVQVCVYAFDLLYLNG 159
Cdd:TIGR00574 214 RRLENYTYQYPEIFTEFIKEAFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKRKyDIKAMDQKVPVCLFVFDILYLNG 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 160 KPLVRNTFAERRQLMKDNFTELEGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLKK 239
Cdd:TIGR00574 294 KSLIDEPLIERREILESILKPIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDL--KSIYEPGKRGWLWLKIKP 371

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1678130702 240 DYLSGCGDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:TIGR00574 372 EYLEGMGDTLDLVVIGAYYGKGSRGGMYGSFLCACYDPESEEFKTITKVGT 422
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 34-238 1.92e-83

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: 251.43  E-value: 1.92e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  34 PMLAQPTTGVSDVLERFDGLnITCEWKYDGERAQIHcNENGVVSIFSRNQENNTLKYPDILTRITSFAKPNVKSYIMDSE 113
Cdd:pfam01068   1 PMLAKSFKSIEEALKKFGGA-FIAEYKYDGERAQIH-KDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 114 IVAWDADQKIILPFQVLSTRKRKNVDVKDI--KVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFATAV 191
Cdd:pfam01068  79 IVAVDPETGEILPFQVLADRKKKKVDVEELaeKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1678130702 192 DTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLK 238
Cdd:pfam01068 159 VTKDVEEAQEFLEEAISEGLEGLVVKDP--DSTYEPGKRGKNWLKIK 203
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
32-290 9.23e-66

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 213.63  E-value: 9.23e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLAQPTTGVsdvlerFDGLNITCEWKYDGERAQIHCnENGVVSIFSRNQENNTLKYPDILTRITSFAKPNVksyIMD 111
Cdd:COG1793   114 VPPMLATLVDSP------PDGGDWAYEPKWDGYRVQAHR-DGGEVRLYSRNGEDITDRFPELVEALRALPADDA---VLD 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQKiiLPFQVLSTRKRKNVDVKDI--KVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFAT 189
Cdd:COG1793   184 GEIVALDEDGR--PPFQALQQRLGRKRDVAKLarEVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSP 261

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 190 AVdtRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLKkdylsgCGDSLDLVVIGGYRGKGKRTGSYGG 269
Cdd:COG1793   262 HV--IDWGEGEALFAAAREAGLEGVMAK--RLDSPYRPGRRSGDWLKVK------CPRTQDLVVGGATPGKGRRAGGFGS 331

                         250       260
                  ....*....|....*....|.
gi 1678130702 270 FLLACYDnENEEYQSICKIGT 290
Cdd:COG1793   332 LLLGVYD-PGGELVYVGKVGT 351
OBF_DNA_ligase_I cd07969
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ...
 246-290 4.59e-27

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153438 [Multi-domain]  Cd Length: 144  Bit Score: 103.71  E-value: 4.59e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1678130702 246 GDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:cd07969     1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGT 45
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 263-290 1.18e-03

ATP dependent DNA ligase C terminal region; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase.


Pssm-ID: 398383 [Multi-domain]  Cd Length: 94  Bit Score: 37.57  E-value: 1.18e-03
                          10        20
                  ....*....|....*....|....*...
gi 1678130702 263 RTGSYGGFLLACYDneNEEYQSICKIGT 290
Cdd:pfam04679   1 RRGGFGSLLLGVYD--DGRLVYVGKVGT 26
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 23-241 2.68e-143

Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases.


Pssm-ID: 185710 [Multi-domain]  Cd Length: 219  Bit Score: 403.86  E-value: 2.68e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  23 RCPMIPGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHCNENGVVSIFSRNQENNTLKYPDILTRITSFAK 102
Cdd:cd07900     1 HCKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 103 PNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:cd07900    81 PSVKSFILDSEIVAYDRETGKILPFQVLSTRKRKDVDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVP 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 183 GCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDY 241
Cdd:cd07900   161 GRFQFATSKDSEDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219
PLN03113 PLN03113
DNA ligase 1; Provisional
 3-301 2.14e-138

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 410.14  E-value: 2.14e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702   3 PNYNKIIPTLLKYGVEQLQERCPMIPGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHCNENGVVSIFSRN 82
Cdd:PLN03113  341 PVYDKIVPALLSGGVWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRN 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  83 QENNTLKYPDILTRITSFAKPNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGKPL 162
Cdd:PLN03113  421 AERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYDREKKKILPFQILSTRARKNVVMSDIKVDVCIFAFDMLYLNGQPL 500

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 163 VRNTFAERRQLMKDNFTELEGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDYL 242
Cdd:PLN03113  501 IQEQLKIRREHLYESFEEDPGFFQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLKKDYM 580

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 243 SGCGDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGTaGLWEGLENDR 301
Cdd:PLN03113  581 ESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNKEEFQSICKIGT-GFSEAVLEER 638
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 1-290 1.75e-112

DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273147 [Multi-domain]  Cd Length: 514  Bit Score: 336.60  E-value: 1.75e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702   1 QCPNYNKIIPTLLKYGVEQLQERCPMIPGIPIKPMLAQPTTGVSDVLERFDGlNITCEWKYDGERAQIHCNeNGVVSIFS 80
Cdd:TIGR00574 136 LTNDLGKVAKILLEPGLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-GFYVEYKYDGERVQVHKD-GDKFKIFS 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  81 RNQENNTLKYPDILTRITSFAKPNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRK-NVDVKDIKVQVCVYAFDLLYLNG 159
Cdd:TIGR00574 214 RRLENYTYQYPEIFTEFIKEAFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKRKyDIKAMDQKVPVCLFVFDILYLNG 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 160 KPLVRNTFAERRQLMKDNFTELEGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLKK 239
Cdd:TIGR00574 294 KSLIDEPLIERREILESILKPIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDL--KSIYEPGKRGWLWLKIKP 371

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1678130702 240 DYLSGCGDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:TIGR00574 372 EYLEGMGDTLDLVVIGAYYGKGSRGGMYGSFLCACYDPESEEFKTITKVGT 422
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 16-290 1.43e-84

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 266.84  E-value: 1.43e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  16 GVEQLQERCPMiPGIPIKPMLAQPTTGVSDVLERFDGlNITCEWKYDGERAQIHCNENGVVsIFSRNQENNTLKYPDILT 95
Cdd:PRK01109  213 GIEALKKVKPQ-VGIPIRPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKKGDKVK-IFSRRLENITHQYPDVVE 289

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  96 RITSFAKPNvkSYIMDSEIVAWDADQKIILPFQVLSTRKRK-NVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLM 174
Cdd:PRK01109  290 YAKEAIKAE--EAIVEGEIVAVDPETGEMRPFQELMHRKRKyDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKL 367

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 175 KDNFTELEGcWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHKNATYEIAKRSRNWLKLKKDYLSGCGDSLDLVVI 254
Cdd:PRK01109  368 EEIVKENDK-VKLAERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVVV 446

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1678130702 255 GGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:PRK01109  447 GAFYGRGRRGGKYGSLLMAAYDPKTDTFETVCKVGS 482
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 34-238 1.92e-83

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: 251.43  E-value: 1.92e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  34 PMLAQPTTGVSDVLERFDGLnITCEWKYDGERAQIHcNENGVVSIFSRNQENNTLKYPDILTRITSFAKPNVKSYIMDSE 113
Cdd:pfam01068   1 PMLAKSFKSIEEALKKFGGA-FIAEYKYDGERAQIH-KDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 114 IVAWDADQKIILPFQVLSTRKRKNVDVKDI--KVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFATAV 191
Cdd:pfam01068  79 IVAVDPETGEILPFQVLADRKKKKVDVEELaeKVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESI 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1678130702 192 DTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLK 238
Cdd:pfam01068 159 VTKDVEEAQEFLEEAISEGLEGLVVKDP--DSTYEPGKRGKNWLKIK 203
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
32-290 9.23e-66

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 213.63  E-value: 9.23e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLAQPTTGVsdvlerFDGLNITCEWKYDGERAQIHCnENGVVSIFSRNQENNTLKYPDILTRITSFAKPNVksyIMD 111
Cdd:COG1793   114 VPPMLATLVDSP------PDGGDWAYEPKWDGYRVQAHR-DGGEVRLYSRNGEDITDRFPELVEALRALPADDA---VLD 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQKiiLPFQVLSTRKRKNVDVKDI--KVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFAT 189
Cdd:COG1793   184 GEIVALDEDGR--PPFQALQQRLGRKRDVAKLarEVPVVFYAFDLLYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSP 261

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 190 AVdtRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLKkdylsgCGDSLDLVVIGGYRGKGKRTGSYGG 269
Cdd:COG1793   262 HV--IDWGEGEALFAAAREAGLEGVMAK--RLDSPYRPGRRSGDWLKVK------CPRTQDLVVGGATPGKGRRAGGFGS 331

                         250       260
                  ....*....|....*....|.
gi 1678130702 270 FLLACYDnENEEYQSICKIGT 290
Cdd:COG1793   332 LLLGVYD-PGGELVYVGKVGT 351
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 32-240 2.00e-64

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: 202.95  E-value: 2.00e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLAQPTTGVSDVLeRFDGLNITCEWKYDGERAQIHCNEnGVVSIFSRNQENNTLKYPDILTRitsfAKPNVKSYIMD 111
Cdd:cd07898     1 IKPMLAHPEESAEAAK-AKKPAAAWVEDKYDGIRAQVHKDG-GRVEIFSRSLEDITDQFPELAAA----AKALPHEFILD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQKI--ILPFQVLSTRKRKnvDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFAT 189
Cdd:cd07898    75 GEILAWDDNRGLpfSELFKRLGRKFRD--KFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAP 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1678130702 190 AVDTRDVDEVQHCLEESIKGNCEGLMVKTLHknATYEIAKRSRNWLKLKKD 240
Cdd:cd07898   153 ALPVESAEELEAAFARARARGNEGLMLKDPD--SPYEPGRRGLAWLKLKKE 201
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 28-240 4.88e-58

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: 186.59  E-value: 4.88e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  28 PGIPIKPMLAQPTTGVSDVLERfDGLNITCEWKYDGERAQIHCNENGVVsIFSRNQENNTLKYPDILTRITsfAKPNVKS 107
Cdd:cd07901     1 VGRPVRPMLAQRAPSVEEALIK-EGGEAAVEYKYDGIRVQIHKDGDEVR-IFSRRLEDITNALPEVVEAVR--ELVKAED 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 108 YIMDSEIVAWDADQKIiLPFQVLSTRKRKNVDVKDI--KVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGcW 185
Cdd:cd07901    77 AILDGEAVAYDPDGRP-LPFQETLRRFRRKYDVEEAaeEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPETEA-I 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1678130702 186 QFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHknATYEIAKRSRNWLKLKKD 240
Cdd:cd07901   155 LLAPRIVTDDPEEAEEFFEEALEAGHEGVMVKSLD--SPYQAGRRGKNWLKVKPD 207
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 28-242 2.12e-40

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: 141.56  E-value: 2.12e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  28 PGIPIKPMLAQPTTGVSDVLERFDGLNITCEWKYDGERAQIHcNENGVVSIFSRNQENNTLKY-----PDILT-RITSFA 101
Cdd:cd07903     8 LFSPFRPMLAERLNIGYVEIKLLKGKPFYIETKLDGERIQLH-KDGNEFKYFSRNGNDYTYLYgasltPGSLTpYIHLAF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 102 KPNVKSYIMDSEIVAWDADQKIILPFQVLSTRKrKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTEL 181
Cdd:cd07903    87 NPKVKSCILDGEMVVWDKETKRFLPFGTLKDVA-KLREVEDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPI 165

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1678130702 182 EGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLKKDYL 242
Cdd:cd07903   166 PGRLEVVKRTEASTKEEIEEALNEAIDNREEGIVVKDL--DSKYKPGKRGGGWIKIKPEYL 224
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 30-241 7.92e-39

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: 137.08  E-value: 7.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  30 IPIKPMLAQPTTGVSDVLERF-DGlnITCEWKYDGERAQIHCNENGVvSIFSRNqenntLKyPDILTRITSF------AK 102
Cdd:cd07902    12 TPVKPMLAEACKSVEDAMKKCpNG--MYAEIKYDGERVQVHKQGDNF-KFFSRS-----LK-PVLPHKVAHFkdyipkAF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 103 PNVKSYIMDSEIVAWDADQKIILPFQVLSTRKRKnvDVKDikVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:cd07902    83 PHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKS--AFKD--ANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIP 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1678130702 183 GCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLHknATYEIAKrsRNWLKLKKDY 241
Cdd:cd07902   159 NRIMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLK--SVYEPGK--RHWLKVKKDY 213
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 32-238 7.07e-35

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: 126.11  E-value: 7.07e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLAQPTTgvsdvlERFDGLNITCEWKYDGERAQIHCnENGVVSIFSRNQENNTLKYPDIltrITSFAKPNVKSYIMD 111
Cdd:cd07906     1 IEPMLATLVD------EPPDGEDWLYEIKWDGYRALARV-DGGRVRLYSRNGLDWTARFPEL---AEALAALPVRDAVLD 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQKiilP-FQVLSTRkRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFATA 190
Cdd:cd07906    71 GEIVVLDEGGR---PdFQALQNR-LRLRRRLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEH 146

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1678130702 191 VDtrdvDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLK 238
Cdd:cd07906   147 FE----GGGAALFAAACELGLEGIVAK--RADSPYRSGRRSRDWLKIK 188
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 29-265 1.29e-31

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 123.92  E-value: 1.29e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  29 GIPIKPMLAQPTTGVSDVLERFDGlNITCEWKYDGERAQIHcNENGVVSIFSRNQENNTLKYPDI--LTRitsfAKPnVK 106
Cdd:PRK03180  181 GRPVRPMLAQTATSVAEALARLGG-PAAVEAKLDGARVQVH-RDGDDVRVYTRTLDDITARLPEVveAVR----ALP-VR 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 107 SYIMDSEIVAWDADQKiILPFQVLSTR--KRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERrqlmkdnFTELEGC 184
Cdd:PRK03180  254 SLVLDGEAIALRPDGR-PRPFQVTASRfgRRVDVAAARATQPLSPFFFDALHLDGRDLLDAPLSER-------LAALDAL 325

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 185 WQFATAVD---TRDVDEVQHCLEESIKGNCEGLMVKTLHknATYEIAKRSRNWLKLKKDYlsgcgdSLDLVVIGGYRGKG 261
Cdd:PRK03180  326 VPAAHRVPrlvTADPAAAAAFLAAALAAGHEGVMVKSLD--APYAAGRRGAGWLKVKPVH------TLDLVVLAAEWGSG 397


                  ....
gi 1678130702 262 KRTG 265
Cdd:PRK03180  398 RRTG 401
OBF_DNA_ligase_I cd07969
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ...
 246-290 4.59e-27

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153438 [Multi-domain]  Cd Length: 144  Bit Score: 103.71  E-value: 4.59e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1678130702 246 GDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:cd07969     1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGT 45
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 33-239 5.14e-25

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: 99.80  E-value: 5.14e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  33 KPMLAQPTTGVSDVLERFDGlnITCEWKYDGERAQIHcNENGVVSIFSRNQENNTLKYPDILTRITSFAKPNvksYIMDS 112
Cdd:cd06846     1 PQLLNPILEEALSEYDEQDE--YYVQEKYDGKRALIV-ALNGGVFAISRTGLEVPLPSILIPGRELLTLKPG---FILDG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 113 EIVAWDADQkiilpfqvlstrkrknvdvkdIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQF----A 188
Cdd:cd06846    75 ELVVENREV---------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVklvpL 133

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1678130702 189 TAVDTRDvDEVQHCLEESIKGNCEGLMVKtlHKNATY-EIAKRSRNWLKLKK 239
Cdd:cd06846   134 ENAPSYD-ETLDDLLEKLKKKGKEGLVFK--HPDAPYkGRPGSSGNQLKLKP 182
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 31-290 6.94e-24

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 102.77  E-value: 6.94e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  31 PIKPMLAQPTTgvsdvLERFDGLNITCEWKYDGERAQIHCNEnGVVSIFSRNQENNTLKYPdiltRITSFAKP-NVKSYI 109
Cdd:PRK09632  460 DLAPMLATAGT-----VAGLKASQWAFEGKWDGYRLLAEADH-GALRLRSRSGRDVTAEYP----ELAALAEDlADHHVV 529

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 110 MDSEIVAWDADQKiilP-FQVLSTRkRKNVDVKdikvqvcVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCwqfa 188
Cdd:PRK09632  530 LDGEIVALDDSGV---PsFGLLQNR-GRDTRVE-------FWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSGGSL---- 594

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 189 tAVDTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRNWLKLKkdylsgcgDSLDL-VVIGGYR-GKGKRTGS 266
Cdd:PRK09632  595 -TVPPLLPGDGAEALAYSRELGWEGVVAKRR--DSTYQPGRRSSSWIKDK--------HWRTQeVVIGGWRpGEGGRSSG 663

                         250       260
                  ....*....|....*....|....
gi 1678130702 267 YGGFLLACYDNENEEYqsICKIGT 290
Cdd:PRK09632  664 IGSLLLGIPDPGGLRY--VGRVGT 685
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 28-240 5.77e-23

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: 94.93  E-value: 5.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  28 PGIPIKPMLAQPTTGvsdvlERFDGLNIT---CEWKYDGERAQIhCNENGVVSIFSRNQENNTLKYPDILTRITSFAKPN 104
Cdd:cd07897     1 ASRPYPFMLAHPLED-----DPEDLGDPSdwqAEWKWDGIRGQL-IRRGGEVFLWSRGEELITGSFPELLAAAEALPDGT 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 105 VksyiMDSEIVAWDADQkiILPFQVLSTR-KRKNVDVKDIK-VQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:cd07897    75 V----LDGELLVWRDGR--PLPFNDLQQRlGRKTVGKKLLAeAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLP 148

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 183 GcWQF--ATAVDTRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLKKD 240
Cdd:cd07897   149 P-PRLdlSPLIAFADWEELAALRAQSRERGAEGLMLK--RRDSPYLVGRKKGDWWKWKID 205
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 28-283 1.44e-22

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 98.37  E-value: 1.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  28 PGIPIKPMLAQPttgVSDvlERFDGLNIT---CEWKYDGERAQIhCNENGVVSIFSRNQENNTLKYPDILTRITSFAKPN 104
Cdd:PRK09247  202 PGQPYPFFLAHP---LED--EDLTLGDPAdwqAEWKWDGIRVQL-VRRGGEVRLWSRGEELITERFPELAEAAEALPDGT 275

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 105 VksyiMDSEIVAWDADQKIILPFQVLSTR-KRKNVDVKDIK-VQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELE 182
Cdd:PRK09247  276 V----LDGELLVWRPEDGRPQPFADLQQRiGRKTVGKKLLAdYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLP 351

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 183 -GCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLKKDYLsgcgdSLDLVVIGGYRGKG 261
Cdd:PRK09247  352 dPRLDLSPLVPFSDWDELAALRAAARERGVEGLMLK--RRDSPYLVGRKKGPWWKWKRDPL-----TIDAVLMYAQRGHG 424

                         250       260
                  ....*....|....*....|..
gi 1678130702 262 KRTGSYGGFLLACYDNENEEYQ 283
Cdd:PRK09247  425 RRASLYTDYTFGVWDGPEGGRQ 446
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 58-290 2.14e-21

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: 92.36  E-value: 2.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  58 EWKYDGERAQIHCnENGVVSIFSRNQENNTLKYPDIltrITSFAKPNVKSYIMDSEIVAWD----ADqkiilpFQVLSTR 133
Cdd:TIGR02779  17 EVKYDGYRCLARI-EGGKVRLISRNGHDWTEKFPIL---AAALAALPILPAVLDGEIVVLDesgrSD------FSALQNR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 134 KRknvdvkDIKVQVCVY-AFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGcwqfaTAVDTRDVDEV----QHCLEESIK 208
Cdd:TIGR02779  87 LR------AGRDRPATYyAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKG-----PLAPDRYSVHFegdgQALLEAACR 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 209 GNCEGLMVKtlHKNATYEIaKRSRNWLKLKKdylsgcgDSLDLVVIGGYR-GKGKRTGsYGGFLLACYDNENEEYqsICK 287
Cdd:TIGR02779 156 LGLEGVVAK--RRDSPYRS-GRSADWLKLKC-------RRRQEFVIGGYTpPNGSRSG-FGALLLGVYEGGGLRY--VGR 222


                  ...
gi 1678130702 288 IGT 290
Cdd:TIGR02779 223 VGT 225
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 57-241 4.42e-19

Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. This model characterizes the adenylation domain of this group of uncharacterized fungal proteins. It is not known whether these proteins also contain an OB-fold domain.


Pssm-ID: 185716 [Multi-domain]  Cd Length: 235  Bit Score: 84.76  E-value: 4.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  57 CEWKYDGERAQIHC---NENGVVSIFSRNQENNTL-KYP--DILTRITSFAKPN---VKSYIMDSEIVAWDADQKIILPF 127
Cdd:cd08039    26 VETKYDGEYCQIHIdlsKDSSPIRIFSKSGKDSTAdRAGvhSIIRKALRIGKPGckfSKNCILEGEMVVWSDRQGKIDPF 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 128 QVL--------STRKRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGcwqFATAVDTRDVD-- 197
Cdd:cd08039   106 HKIrkhversgSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPG---YAGLSERFPIDfs 182

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1678130702 198 --EVQHCLEE----SIKGNCEGLMVKTLHK---NATYEIAKRSRNWLKLKKDY 241
Cdd:cd08039   183 rsSGYERLRQifarAIAERWEGLVLKGDEEpyfDLFLEQGSFSGCWIKLKKDY 235
OBF_DNA_ligase cd07893
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 247-290 1.73e-17

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


Pssm-ID: 153435 [Multi-domain]  Cd Length: 129  Bit Score: 77.77  E-value: 1.73e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1678130702 247 DSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGT 290
Cdd:cd07893     1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPERDEFQTICKVGS 44
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 58-290 6.44e-16

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 78.79  E-value: 6.44e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  58 EWKYDGERAQIHCnENGVVSIFSRNQENNTLKYPDIltrITSFAKPNVKSYIMDSEIVAWDADQkiiLP-FQVL----ST 132
Cdd:PRK05972  254 EIKFDGYRILARI-EGGEVRLFTRNGLDWTAKLPAL---AKAAAALGLPDAWLDGEIVVLDEDG---VPdFQALqnafDE 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 133 RKRKNVdvkdikvqVCvYAFDLLYLNGKPLVRNTFAERRQLMKDNFTE-LEGCWQFATAVDTrDVDEVqhcLEESIKGNC 211
Cdd:PRK05972  327 GRTEDL--------VY-FAFDLPFLGGEDLRELPLEERRARLRALLEAaRSDRIRFSEHFDA-GGDAV---LASACRLGL 393

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 212 EGLMVKTLhkNATYeIAKRSRNWLKLKkdylsgCGDSLDlVVIGGYRG-KGKRTGsYGGFLLACYDNENEEYqsICKIGT 290
Cdd:PRK05972  394 EGVIGKRA--DSPY-VSGRSEDWIKLK------CRARQE-FVIGGYTDpKGSRSG-FGSLLLGVHDDDHLRY--AGRVGT 460
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 32-238 6.70e-14

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: 69.20  E-value: 6.70e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLAQPTtgvsDVLERFDGLNItcEWKYDGERAQIHCNENGVVsIFSRNQENNTLKYPDILTRITSFAKPnvkSYIMD 111
Cdd:cd07905     1 VEPMLARAV----DALPEPGGWQY--EPKWDGFRCLAFRDGDEVR-LQSRSGKPLTRYFPELVAAARALLPP---GCVLD 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQkiiLPFQVLSTR---KRKNVDVKDIKVQVCVYAFDLLYLNGKPLVRNTFAERRQLMKDNFTELEGCWQFA 188
Cdd:cd07905    71 GELVVWRGGR---LDFDALQQRihpAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLS 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1678130702 189 TAvdTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSrnWLKLK 238
Cdd:cd07905   148 PA--TTDRAEAREWLEEFEGAGLEGVVAKRL--DGPYRPGERA--MLKVK 191
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 32-260 9.13e-14

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 70.56  E-value: 9.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  32 IKPMLaqpttgVSDVLERFDGLNITCEWKYDGERAqIHCNENGVVSIFSRNQENNTLKYPDILTritsfaKPNVKSYIMD 111
Cdd:PRK07636    3 ISPML------LESAKEPFNSENYITEPKFDGIRL-IASKNNGLIRLYTRHNNEVTAKFPELLN------LDIPDGTVLD 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 112 SEIVAWDADQKiilP-FQVLSTRKRKNVDVKDIKVQVCVyaFDLLYLNGKPLVRNTFAERRQLMK------DNFTELEGC 184
Cdd:PRK07636   70 GELIVLGSTGA---PdFEAVMERFQSKKSTKIHPVVFCV--FDVLYINGVSLTALPLSERKEILAslllphPNVKIIEGI 144

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1678130702 185 WQFATAVDTRdvdevqhcLEESikgNCEGLMVKtlHKNATYEIAKRSRNWLK-LKKDYLSgcgdsldlVVIGGYRGK 260
Cdd:PRK07636  145 EGHGTAYFEL--------VEER---ELEGIVIK--KANSPYEINKRSDNWLKvINYQYTD--------VLITGYRKE 200
ligD PRK09633
DNA ligase D;
33-238 2.38e-13

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 70.84  E-value: 2.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  33 KPMLAQPTTGVSDvlerfdGLNITCEWKYDGERAQIHCNENGVvSIFSRNQENNTLKYPDIltriTSFAKPN---VKSY- 108
Cdd:PRK09633    2 KPMQPTLTTSIPI------GDEWRYEVKYDGFRCLLIIDETGI-TLISRNGRELTNTFPEI----IEFCESNfehLKEEl 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 109 --IMDSEIV----AWDADqkiilpFQVLSTRKR-KNVDV---KDIKVQVCVYAFDLLYLNGKPLVRNTFAERR----QLM 174
Cdd:PRK09633   71 plTLDGELVclvnPYRSD------FEHVQQRGRlKNTEViakSANARPCQLLAFDLLELKGESLTSLPYLERKkqldKLM 144

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 175 KD----NFTELEG--CWQFatavdTRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEIAKRSRNWLKLK 238
Cdd:PRK09633  145 KAaklpASPDPYAkaRIQY-----IPSTTDFDALWEAVKRYDGEGIVAK--KKTSKWLENKRSKDWLKIK 207
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
 80-289 3.27e-11

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: 64.27  E-value: 3.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  80 SRNQENNTLKYPDIltrITSFAKPNVKSYIMDSEIVAwdADQKIILPFQVLstrkrKNVDVKDIKVQVCVYAFDLLYLNG 159
Cdd:TIGR02776   1 TRNGHDWTKRFPEI---VKALALLKLLPAWIDGEIVV--LDERGRADFAAL-----QNALSAGASRPLTYYAFDLLFLSG 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 160 KPLVRNTFAERR----QLMKDNfteLEGCWQFATAVDtrdvDEVQHCLEESIKGNCEGLMVKtlHKNATYEiAKRSRNWL 235
Cdd:TIGR02776  71 EDLRDLPLEERKkrlkQLLKAQ---DEPAIRYSDHFE----SDGDALLESACRLGLEGVVSK--RLDSPYR-SGRSKDWL 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1678130702 236 KLKkdylsgCgDSLDLVVIGGYRGKGKRTGSyggFLLACYDNENEEYQSICKIG 289
Cdd:TIGR02776 141 KLK------C-RRRQEFVITGYTPPNRRFGA---LLVGVYEGGQLVYAGKVGTG 184
OBF_DNA_ligase_Arch_LigB cd07972
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ...
 247-293 8.68e-09

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DNA ligase, Mycobacterium tuberculosis LigB, and similar archaeal and bacterial proteins. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153441 [Multi-domain]  Cd Length: 122  Bit Score: 52.94  E-value: 8.68e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1678130702 247 DSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIGTaGL 293
Cdd:cd07972     1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEETGELVPVGKVAT-GL 46
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
 33-239 1.44e-08

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: 53.72  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  33 KPMLA---QPTTGVSDVL--ERFDGlnITCEWkyDGERaqihcnengvvsIFSRNqeNNTLKYPDILTRitsfakpNVKS 107
Cdd:cd07896     2 ELLLAktyDEGEDISGYLvsEKLDG--VRAYW--DGKQ------------LLSRS--GKPIAAPAWFTA-------GLPP 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 108 YIMDSEIvaWDADQKiilpFQVLSTRKRKNVDVKDIKVQVCVYAFDLLYLNGkplvrnTFAERRQLMKDNFTELEGCW-- 185
Cdd:cd07896    57 FPLDGEL--WIGRGQ----FEQTSSIVRSKKPDDEDWRKVKFMVFDLPSAKG------PFEERLERLKNLLEKIPNPHik 124

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1678130702 186 ---QFATavdtRDVDEVQHCLEESIKGNCEGLMVKtlHKNATYEiAKRSRNWLKLKK 239
Cdd:cd07896   125 ivpQIPV----KSNEALDQYLDEVVAAGGEGLMLR--RPDAPYE-TGRSDNLLKLKP 174
PRK09125 PRK09125
DNA ligase; Provisional
 150-265 4.63e-07

DNA ligase; Provisional


Pssm-ID: 181662 [Multi-domain]  Cd Length: 282  Bit Score: 50.63  E-value: 4.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 150 YAFDLlylngkPLVRNTFAERRQLMKDNFTELEGCW-----QFATavdtRDVDEVQHCLEESIKGNCEGLMVKtlHKNAT 224
Cdd:PRK09125  120 MVFDL------PDAPGDFEERLAVLKKLLAKLPSPYikiieQIRV----RSEAALQQFLDQIVAAGGEGLMLH--RPDAP 187

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1678130702 225 YEiAKRSRNWLKLKKDYLSGCgdsldlVVIGGYRGKGKRTG 265
Cdd:PRK09125  188 YE-AGRSDDLLKLKPYYDAEA------TVIGHLPGKGKFAG 221
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 25-278 7.91e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 50.28  E-value: 7.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702  25 PMIPgiPIKPMLAQPTTGVSDvlerfdGLNITCEWKYDGERAQIHCNENGVVsIFSRNQENNTLKYPDILTRITSfAKPn 104
Cdd:PRK08224    4 PVMP--PVEPMLAKSVDAIPP------GDGWSYEPKWDGFRCLVFRDGDEVE-LGSRNGKPLTRYFPELVAALRA-ELP- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 105 vKSYIMDSEIV-AWDADqkiiLPFQVLSTR-----KRknvdVKDIKVQ--VCVYAFDLLYLNGKPLVRNTFAERRQLMKD 176
Cdd:PRK08224   73 -ERCVLDGEIVvARDGG----LDFEALQQRihpaaSR----VRKLAEEtpASFVAFDLLALGDRDLTGRPFAERRAALEA 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 177 nftELEGCWQFATAVDTRDVDEVQHCLEESIKGNCEGLMVKTLhkNATYEIAKRSRnwLKLKKDYLSGCgdsldlvVIGG 256
Cdd:PRK08224  144 ---AAAGSGPVHLTPATTDPATARRWFEEFEGAGLDGVIAKPL--DGPYQPGKRAM--FKVKHERTADC-------VVAG 209

                         250       260
                  ....*....|....*....|..
gi 1678130702 257 YRgKGKRTGSYGGFLLACYDNE 278
Cdd:PRK08224  210 YR-YHKSGPVVGSLLLGLYDDD 230
OBF_DNA_ligase_IV cd07968
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is ...
 246-290 1.89e-06

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). 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 oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153437  Cd Length: 140  Bit Score: 46.78  E-value: 1.89e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1678130702 246 GDSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEE------YQSICKIGT 290
Cdd:cd07968     1 GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPEsdkpsvFYSFCKVGS 51
OBF_DNA_ligase_family cd08040
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 247-341 2.07e-06

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


Pssm-ID: 153442  Cd Length: 108  Bit Score: 46.09  E-value: 2.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1678130702 247 DSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEeyQSICKIGTA-------GLWEGLE------------NDREVRGKS 307
Cdd:cd08040     1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGEDGL--QAVFSVGTGfsaderrDLWQNLEplvtsfddhpvwNVGKDLSFV 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1678130702 308 LLDISVMcgrigLELNRSSIGPERGVVKIRFRNL 341
Cdd:cd08040    79 PLYPGKV-----VEVKYFEMGSKDCLRFPVFIGI 107
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
 247-289 2.58e-06

The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). 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 oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain.


Pssm-ID: 153436  Cd Length: 139  Bit Score: 46.20  E-value: 2.58e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1678130702 247 DSLDLVVIGGYRGKGKRTGSYGGFLLACYDNENEEYQSICKIG 289
Cdd:cd07967     3 DTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNSKKWCTVTKCG 45
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
 263-290 1.18e-03

ATP dependent DNA ligase C terminal region; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase.


Pssm-ID: 398383 [Multi-domain]  Cd Length: 94  Bit Score: 37.57  E-value: 1.18e-03
                          10        20
                  ....*....|....*....|....*...
gi 1678130702 263 RTGSYGGFLLACYDneNEEYQSICKIGT 290
Cdd:pfam04679   1 RRGGFGSLLLGVYD--DGRLVYVGKVGT 26
 
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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