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Conserved domains on  [gi|2059423981|gb|KAG7217137|]
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hypothetical protein INR49_027678 [Caranx melampygus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 471-677 5.90e-155

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: 447.17  E-value: 5.90e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 471 RKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQ 550
Cdd:cd07902     1 KKKLSVRASLMTPVKPMLAEACKSVEDAMKKCPNGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AFPGGHSMILDAEVLLIDTKTSKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNR 624
Cdd:cd07902    81 AFPHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDkplrerRKILEDNMVEIPNR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059423981 625 ILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKDY 677
Cdd:cd07902   161 IMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVKKDY 213
DNA_ligase_A_N pfam04675
DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase ...
 265-436 9.86e-40

DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I, and in Saccharomyces cerevisiae, this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation.


:

Pssm-ID: 461387 [Multi-domain]  Cd Length: 174  Bit Score: 143.87  E-value: 9.86e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 265 LFREFRKLCATVAEN-SSYNVKTQIIEKYLKK-GSAGDKfhgDLYLTVKLLLPGVVKSVYNLNDKQIVKLFSRIFRCNQD 342
Cdd:pfam04675   1 PFSLLAELFEKIEATtSSRLEKTAILANFFRSvIGAGPE---DLYPALRLLLPDYDGREYGIGEKLLAKAIAEALGLSKD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 343 DMVRDL-EQGDVSETVRMFFEESKafPPAAKSLLTIQEVDASLTRLAQLT---KEDEQQTELESIAKKCTSNDLKCIIRL 418
Cdd:pfam04675  78 SIKDAYrKAGDLGEVAEEVLSKRS--TLFKPSPLTIDEVNELLDKLAAASgkgSQDEKIKILKKLLKRATPEEAKYLIRI 155

                         170
                  ....*....|....*...
gi 2059423981 419 IKHDLKMNAGAKHVLDAL 436
Cdd:pfam04675 156 ILGDLRIGLGEKTVLDAL 173
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
 97-182 2.95e-34

Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.


:

Pssm-ID: 459887 [Multi-domain]  Cd Length: 87  Bit Score: 125.51  E-value: 2.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  97 EYAKRGTAGCKKCKDKIQKGIVRIGKIVPN-PFSESAGEMKEWYHVKCIFEKLERARATTKKIEDITDLEGWEELQDEDK 175
Cdd:pfam00645   1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80


                  ....*..
gi 2059423981 176 DLINKHV 182
Cdd:pfam00645  81 EKIRKAI 87
OBF_DNA_ligase_family super family cl08424
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 683-702 3.54e-07

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 cd07967:

Pssm-ID: 447632  Cd Length: 139  Bit Score: 50.05  E-value: 3.54e-07
                          10        20
                  ....*....|....*....|
gi 2059423981 683 MADTADLVVLGAFYGKGSNG 702
Cdd:cd07967     1 MADTADLVVLGAYYGTGSKG 20
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 471-677 5.90e-155

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: 447.17  E-value: 5.90e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 471 RKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQ 550
Cdd:cd07902     1 KKKLSVRASLMTPVKPMLAEACKSVEDAMKKCPNGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AFPGGHSMILDAEVLLIDTKTSKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNR 624
Cdd:cd07902    81 AFPHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDkplrerRKILEDNMVEIPNR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059423981 625 ILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKDY 677
Cdd:cd07902   161 IMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVKKDY 213
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 321-702 2.70e-147

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: 439.06  E-value: 2.70e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 321 VYNLNDKQIVKLFSRIFRCNQDDMVRD-LEQGDVSETVRMFFEESK--AFPPAAKSLLTIQEVDASLTRLAQLTKEDEQQ 397
Cdd:TIGR00574   1 EYGIGEKLLIKAISEILGIPKDEIEEKvLEDGDLGEGIEGLFSKQKqtSFFPAPLTVKEVYEVLKFIARLSGEGSQDKKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 398 TELESIAKKCTSNDLKCIIRLIKHDLKMNAGAKHVLDALDPNA-------YDAFKASRNLGDVVERVLrnhqessNGSGP 470
Cdd:TIGR00574  81 KSLKSLLKRASPLEAKYLIRLILGDLRIGIAEKTILDALAKAFllsppdvERAFNLTNDLGKVAKILL-------EPGLR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 471 RKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQ 550
Cdd:TIGR00574 154 GLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKE 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AFPGGHSMILDAEVLLIDTKTSKPLPFGTLGVHK-----KAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMV 619
Cdd:TIGR00574 234 AFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKrkydiKAMDQKVPVCLFVFDILYLNGKSLIDeplierREILESILK 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 620 EVHNRILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGKG 699
Cdd:TIGR00574 314 PIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEGMGDTLDLVVIGAYYGKG 393


                  ...
gi 2059423981 700 SNG 702
Cdd:TIGR00574 394 SRG 396
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 486-674 1.07e-76

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: 244.89  E-value: 1.07e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 486 PMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMILDAEVL 565
Cdd:pfam01068   1 PMLAKSFKSIEEALKKFGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 566 LIDTKTSKPLPFGTLGVHKKAAFQD------ANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNRILFSEMKHV 633
Cdd:pfam01068  81 AVDPETGEILPFQVLADRKKKKVDVeelaekVPVCLFVFDLLYLDGEDLTDlplrerRKLLEEIFKEIPGRIQLAESIVT 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2059423981 634 TRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVK 674
Cdd:pfam01068 161 KDVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRgkNWLKIK 203
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 287-699 3.00e-51

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 187.87  E-value: 3.00e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 287 QIIEK--YLKKGSAGDKFHG-DLYLTVKLLLPGVVKsVYNLNDKQIVKLFSRIfrcnqddmvrdleqGDVSETVRMFFEE 363
Cdd:PRK01109   36 EIIDKvvYLIQGKLWPDWLGlELGVGEKLLIKAISM-ATGISEKEVENLYKKT--------------GDLGEVARRLKSK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 364 SKAFPPAA---KSLLTIQEVDASLTRLAQLTKEDEQQTELESIA---KKCTSNDLKCIIRLIKHDLKMNAGAKHVLDALD 437
Cdd:PRK01109  101 KKQKSLLAffsKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAgllKDASPLEAKYIARFVEGRLRLGVGDATILDALA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 438 pnayDAFKASRNLgDVVER----------VLRNHQESsngsGPRKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMY 507
Cdd:PRK01109  181 ----IAFGGAVAR-ELVERaynlradlgyIAKILAEG----GIEALKKVKPQVGIPIRPMLAERLSSPKEILKKMGGEAL 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 508 SEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKDYIPqafpgGHSMILDAEVLLIDTKTSKPLPFGTLgVHK 584
Cdd:PRK01109  252 VEYKYDGERAQIHKKGDKVKIFSRRLENIthqYPDVVEYAKEAIK-----AEEAIVEGEIVAVDPETGEMRPFQEL-MHR 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 585 K------AAFQDANVCLFVFDCIYFNGVSL-----MERKFLHDNMVEVHNRILFSEMKHVTRAGDLADMITRVIREGLEG 653
Cdd:PRK01109  326 KrkydieEAIKEYPVNVFLFDLLYVDGEDLtdkplPERRKKLEEIVKENDKVKLAERIITDDVEELEKFFHRAIEEGCEG 405

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 2059423981 654 LVLKDIKGT--YEPGKRHWL--KVKKDYLNEgaMADTADLVVLGAFYGKG 699
Cdd:PRK01109  406 LMAKSLGKDsiYQAGARGWLwiKYKRDYQSE--MADTVDLVVVGAFYGRG 453
DNA_ligase_A_N pfam04675
DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase ...
 265-436 9.86e-40

DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I, and in Saccharomyces cerevisiae, this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation.


Pssm-ID: 461387 [Multi-domain]  Cd Length: 174  Bit Score: 143.87  E-value: 9.86e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 265 LFREFRKLCATVAEN-SSYNVKTQIIEKYLKK-GSAGDKfhgDLYLTVKLLLPGVVKSVYNLNDKQIVKLFSRIFRCNQD 342
Cdd:pfam04675   1 PFSLLAELFEKIEATtSSRLEKTAILANFFRSvIGAGPE---DLYPALRLLLPDYDGREYGIGEKLLAKAIAEALGLSKD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 343 DMVRDL-EQGDVSETVRMFFEESKafPPAAKSLLTIQEVDASLTRLAQLT---KEDEQQTELESIAKKCTSNDLKCIIRL 418
Cdd:pfam04675  78 SIKDAYrKAGDLGEVAEEVLSKRS--TLFKPSPLTIDEVNELLDKLAAASgkgSQDEKIKILKKLLKRATPEEAKYLIRI 155

                         170
                  ....*....|....*...
gi 2059423981 419 IKHDLKMNAGAKHVLDAL 436
Cdd:pfam04675 156 ILGDLRIGLGEKTVLDAL 173
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
476-700 1.53e-39

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 151.23  E-value: 1.53e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 476 VEASLMtpVQPMLAEACKSIEYamkkcPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKdyipqAF 552
Cdd:COG1793   108 VSDWLL--VPPMLATLVDSPPD-----GGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDItdrFPELVEALR-----AL 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 553 PGgHSMILDAEVLLIDtKTSKPlPFGTL------GVHKKAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMVE 620
Cdd:COG1793   176 PA-DDAVLDGEIVALD-EDGRP-PFQALqqrlgrKRDVAKLAREVPVVFYAFDLLYLDGEDLRDlplserRALLEELLAG 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 621 VHNRILFSEmkHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKKdylnegamADTADLVVLGAFYGK 698
Cdd:COG1793   253 APPPLRLSP--HVIDWGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRsgDWLKVKC--------PRTQDLVVGGATPGK 322


                  ..
gi 2059423981 699 GS 700
Cdd:COG1793   323 GR 324
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
 97-182 2.95e-34

Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.


Pssm-ID: 459887 [Multi-domain]  Cd Length: 87  Bit Score: 125.51  E-value: 2.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  97 EYAKRGTAGCKKCKDKIQKGIVRIGKIVPN-PFSESAGEMKEWYHVKCIFEKLERARATTKKIEDITDLEGWEELQDEDK 175
Cdd:pfam00645   1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80


                  ....*..
gi 2059423981 176 DLINKHV 182
Cdd:pfam00645  81 EKIRKAI 87
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
 97-182 1.19e-11

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 68.28  E-value: 1.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  97 EYAKRGTAGCKKCKDKIQKGIVRIGKIVPNPfsESAGEMKEWYHVKCIFEKleraratTKKIEDITDLEGWEELQDEDKD 176
Cdd:PLN03123   11 EYAKSSRSSCKTCKSPIDKDELRLGKMVQST--QFDGFMPMWNHASCILKK-------KNQIKSIDDVEGIDSLRWEDQQ 81


                  ....*.
gi 2059423981 177 LINKHV 182
Cdd:PLN03123   82 KIRKYV 87
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
 683-702 3.54e-07

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: 50.05  E-value: 3.54e-07
                          10        20
                  ....*....|....*....|
gi 2059423981 683 MADTADLVVLGAFYGKGSNG 702
Cdd:cd07967     1 MADTADLVVLGAYYGTGSKG 20
 
Name Accession Description Interval E-value
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
 471-677 5.90e-155

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: 447.17  E-value: 5.90e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 471 RKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQ 550
Cdd:cd07902     1 KKKLSVRASLMTPVKPMLAEACKSVEDAMKKCPNGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AFPGGHSMILDAEVLLIDTKTSKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNR 624
Cdd:cd07902    81 AFPHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDkplrerRKILEDNMVEIPNR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059423981 625 ILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKDY 677
Cdd:cd07902   161 IMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVKKDY 213
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
 321-702 2.70e-147

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: 439.06  E-value: 2.70e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 321 VYNLNDKQIVKLFSRIFRCNQDDMVRD-LEQGDVSETVRMFFEESK--AFPPAAKSLLTIQEVDASLTRLAQLTKEDEQQ 397
Cdd:TIGR00574   1 EYGIGEKLLIKAISEILGIPKDEIEEKvLEDGDLGEGIEGLFSKQKqtSFFPAPLTVKEVYEVLKFIARLSGEGSQDKKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 398 TELESIAKKCTSNDLKCIIRLIKHDLKMNAGAKHVLDALDPNA-------YDAFKASRNLGDVVERVLrnhqessNGSGP 470
Cdd:TIGR00574  81 KSLKSLLKRASPLEAKYLIRLILGDLRIGIAEKTILDALAKAFllsppdvERAFNLTNDLGKVAKILL-------EPGLR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 471 RKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQ 550
Cdd:TIGR00574 154 GLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKE 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AFPGGHSMILDAEVLLIDTKTSKPLPFGTLGVHK-----KAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMV 619
Cdd:TIGR00574 234 AFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKrkydiKAMDQKVPVCLFVFDILYLNGKSLIDeplierREILESILK 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 620 EVHNRILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGKG 699
Cdd:TIGR00574 314 PIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEGMGDTLDLVVIGAYYGKG 393


                  ...
gi 2059423981 700 SNG 702
Cdd:TIGR00574 394 SRG 396
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
 486-674 1.07e-76

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: 244.89  E-value: 1.07e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 486 PMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMILDAEVL 565
Cdd:pfam01068   1 PMLAKSFKSIEEALKKFGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 566 LIDTKTSKPLPFGTLGVHKKAAFQD------ANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNRILFSEMKHV 633
Cdd:pfam01068  81 AVDPETGEILPFQVLADRKKKKVDVeelaekVPVCLFVFDLLYLDGEDLTDlplrerRKLLEEIFKEIPGRIQLAESIVT 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2059423981 634 TRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVK 674
Cdd:pfam01068 161 KDVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRgkNWLKIK 203
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
 484-676 3.47e-69

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: 224.91  E-value: 3.47e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 484 VQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHKVAHFKDYIpqafPGGHSMILDAE 563
Cdd:cd07898     1 IKPMLAHPEESAEAAKAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAK----ALPHEFILDGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 564 VLLID--TKTSKPLPFGTLGVHKKAAF--QDANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHNRILFSEMKHV 633
Cdd:cd07898    77 ILAWDdnRGLPFSELFKRLGRKFRDKFldEDVPVVLMAFDLLYLNGESLLDrplrerRQLLEELFVEIPGRIRIAPALPV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2059423981 634 TRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKKD 676
Cdd:cd07898   157 ESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRglAWLKLKKE 201
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
 287-699 3.00e-51

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 187.87  E-value: 3.00e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 287 QIIEK--YLKKGSAGDKFHG-DLYLTVKLLLPGVVKsVYNLNDKQIVKLFSRIfrcnqddmvrdleqGDVSETVRMFFEE 363
Cdd:PRK01109   36 EIIDKvvYLIQGKLWPDWLGlELGVGEKLLIKAISM-ATGISEKEVENLYKKT--------------GDLGEVARRLKSK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 364 SKAFPPAA---KSLLTIQEVDASLTRLAQLTKEDEQQTELESIA---KKCTSNDLKCIIRLIKHDLKMNAGAKHVLDALD 437
Cdd:PRK01109  101 KKQKSLLAffsKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAgllKDASPLEAKYIARFVEGRLRLGVGDATILDALA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 438 pnayDAFKASRNLgDVVER----------VLRNHQESsngsGPRKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMY 507
Cdd:PRK01109  181 ----IAFGGAVAR-ELVERaynlradlgyIAKILAEG----GIEALKKVKPQVGIPIRPMLAERLSSPKEILKKMGGEAL 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 508 SEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKDYIPqafpgGHSMILDAEVLLIDTKTSKPLPFGTLgVHK 584
Cdd:PRK01109  252 VEYKYDGERAQIHKKGDKVKIFSRRLENIthqYPDVVEYAKEAIK-----AEEAIVEGEIVAVDPETGEMRPFQEL-MHR 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 585 K------AAFQDANVCLFVFDCIYFNGVSL-----MERKFLHDNMVEVHNRILFSEMKHVTRAGDLADMITRVIREGLEG 653
Cdd:PRK01109  326 KrkydieEAIKEYPVNVFLFDLLYVDGEDLtdkplPERRKKLEEIVKENDKVKLAERIITDDVEELEKFFHRAIEEGCEG 405

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 2059423981 654 LVLKDIKGT--YEPGKRHWL--KVKKDYLNEgaMADTADLVVLGAFYGKG 699
Cdd:PRK01109  406 LMAKSLGKDsiYQAGARGWLwiKYKRDYQSE--MADTVDLVVVGAFYGRG 453
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
 482-677 1.10e-42

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: 153.87  E-value: 1.10e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 482 TPVQPMLAEACKSIEYAMKKCPNGMYS-EIKYDGERVQVHKNGD-VFSYFSRSLKPV---LPHKVAHFKDYIPqafPGGH 556
Cdd:cd07900     8 IPVKPMLAKPTKGVSEVLDRFEDKEFTcEYKYDGERAQIHLLEDgKVKIFSRNLENNtekYPDIVAVLPKSLK---PSVK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 557 SMILDAEVLLIDTKTSKPLPFGTLGVHKK----AAFQDANVCLFVFDCIYFNGVSLM------ERKFLHDNMVEVHNRIL 626
Cdd:cd07900    85 SFILDSEIVAYDRETGKILPFQVLSTRKRkdvdANDIKVQVCVFAFDLLYLNGESLLkkplreRRELLHSLFKEVPGRFQ 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2059423981 627 FSEMKHVTRAGDLADMITRVIREGLEGLVLK--DIKGTYEPGKR--HWLKVKKDY 677
Cdd:cd07900   165 FATSKDSEDTEEIQEFLEEAVKNNCEGLMVKtlDSDATYEPSKRshNWLKLKKDY 219
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
 480-676 3.48e-42

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: 151.92  E-value: 3.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 480 LMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKDYIPqafpgGH 556
Cdd:cd07901     1 VGRPVRPMLAQRAPSVEEALIKEGGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDItnaLPEVVEAVRELVK-----AE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 557 SMILDAEVLLIDtKTSKPLPFGTL-----GVHKKAAFQDA-NVCLFVFDCIYFNGVSLM-----ERKFLHDNMVEVHNRI 625
Cdd:cd07901    76 DAILDGEAVAYD-PDGRPLPFQETlrrfrRKYDVEEAAEEiPLTLFLFDILYLDGEDLLdlplsERRKILEEIVPETEAI 154

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2059423981 626 LFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKKD 676
Cdd:cd07901   155 LLAPRIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRgkNWLKVKPD 207
DNA_ligase_A_N pfam04675
DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase ...
 265-436 9.86e-40

DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I, and in Saccharomyces cerevisiae, this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation.


Pssm-ID: 461387 [Multi-domain]  Cd Length: 174  Bit Score: 143.87  E-value: 9.86e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 265 LFREFRKLCATVAEN-SSYNVKTQIIEKYLKK-GSAGDKfhgDLYLTVKLLLPGVVKSVYNLNDKQIVKLFSRIFRCNQD 342
Cdd:pfam04675   1 PFSLLAELFEKIEATtSSRLEKTAILANFFRSvIGAGPE---DLYPALRLLLPDYDGREYGIGEKLLAKAIAEALGLSKD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 343 DMVRDL-EQGDVSETVRMFFEESKafPPAAKSLLTIQEVDASLTRLAQLT---KEDEQQTELESIAKKCTSNDLKCIIRL 418
Cdd:pfam04675  78 SIKDAYrKAGDLGEVAEEVLSKRS--TLFKPSPLTIDEVNELLDKLAAASgkgSQDEKIKILKKLLKRATPEEAKYLIRI 155

                         170
                  ....*....|....*...
gi 2059423981 419 IKHDLKMNAGAKHVLDAL 436
Cdd:pfam04675 156 ILGDLRIGLGEKTVLDAL 173
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
 479-679 1.12e-39

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: 145.80  E-value: 1.12e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 479 SLMTPVQPMLAEACK-SIEYAMKKCPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLK-------PVLPHKVahFKDYIPQ 550
Cdd:cd07903     7 ELFSPFRPMLAERLNiGYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNdytylygASLTPGS--LTPYIHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 551 AF-PGGHSMILDAEVLLIDTKTSKPLPFGTLGVHKKAAFQDAN---VCLFVFDCIYFNGVSLM-----ERKFLHDNMV-E 620
Cdd:cd07903    85 AFnPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLREVEDSdlqPCFVVFDILYLNGKSLTnlplhERKKLLEKIItP 164

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2059423981 621 VHNRILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKKDYLN 679
Cdd:cd07903   165 IPGRLEVVKRTEASTKEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRggGWIKIKPEYLD 225
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
476-700 1.53e-39

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 151.23  E-value: 1.53e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 476 VEASLMtpVQPMLAEACKSIEYamkkcPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKdyipqAF 552
Cdd:COG1793   108 VSDWLL--VPPMLATLVDSPPD-----GGDWAYEPKWDGYRVQAHRDGGEVRLYSRNGEDItdrFPELVEALR-----AL 175

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 553 PGgHSMILDAEVLLIDtKTSKPlPFGTL------GVHKKAAFQDANVCLFVFDCIYFNGVSLME------RKFLHDNMVE 620
Cdd:COG1793   176 PA-DDAVLDGEIVALD-EDGRP-PFQALqqrlgrKRDVAKLAREVPVVFYAFDLLYLDGEDLRDlplserRALLEELLAG 252

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 621 VHNRILFSEmkHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKKdylnegamADTADLVVLGAFYGK 698
Cdd:COG1793   253 APPPLRLSP--HVIDWGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRsgDWLKVKC--------PRTQDLVVGGATPGK 322


                  ..
gi 2059423981 699 GS 700
Cdd:COG1793   323 GR 324
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
 97-182 2.95e-34

Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor.


Pssm-ID: 459887 [Multi-domain]  Cd Length: 87  Bit Score: 125.51  E-value: 2.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  97 EYAKRGTAGCKKCKDKIQKGIVRIGKIVPN-PFSESAGEMKEWYHVKCIFEKLERARATTKKIEDITDLEGWEELQDEDK 175
Cdd:pfam00645   1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80


                  ....*..
gi 2059423981 176 DLINKHV 182
Cdd:pfam00645  81 EKIRKAI 87
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
 364-707 2.13e-26

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 113.52  E-value: 2.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 364 SKAFPPAAKSLLTIQEVDASLTRLAQLTKEDEQQTELESIAK---KCTSNDLKCIIRLIKHDLKMNAGAKHVLDALdPNA 440
Cdd:PRK03180   62 RSLPAPAAEPTLTVADVDAALSEIAAVAGAGSQARRAALLAAlfaAATEDEQRFLRRLLTGELRQGALDGVMADAV-ARA 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 441 YD--------AFKASRNLGDVVERVLRNhqessngsGPRKLLTVEASLMTPVQPMLAEACKSIEYAMKKCPNGMYSEIKY 512
Cdd:PRK03180  141 AGvpaaavrrAAMLAGDLPAVAAAALTG--------GAAALARFRLEVGRPVRPMLAQTATSVAEALARLGGPAAVEAKL 212

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 513 DGERVQVHKNGDVFSYFSRSLKPV---LPHKVAhfkdyIPQAFPgGHSMILDAEVLLIDtKTSKPLPF----GTLGVHKK 585
Cdd:PRK03180  213 DGARVQVHRDGDDVRVYTRTLDDItarLPEVVE-----AVRALP-VRSLVLDGEAIALR-PDGRPRPFqvtaSRFGRRVD 285

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 586 AAFQDANVCL--FVFDCIYFNGVSLM-----ERKFLHDNMVEVHNRIlfseMKHVTRAGDLADMI-TRVIREGLEGLVLK 657
Cdd:PRK03180  286 VAAARATQPLspFFFDALHLDGRDLLdaplsERLAALDALVPAAHRV----PRLVTADPAAAAAFlAAALAAGHEGVMVK 361

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2059423981 658 DIKGTYEPGKR--HWLKVKKdylnegamADTADLVVLGAFYGKG------SN---GASCPA 707
Cdd:PRK03180  362 SLDAPYAAGRRgaGWLKVKP--------VHTLDLVVLAAEWGSGrrtgklSNlhlGARDPA 414
PLN03113 PLN03113
DNA ligase 1; Provisional
 483-708 1.02e-24

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 109.69  E-value: 1.02e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 483 PVQPMLAEACKSIEYAMKKCPNGMYS-EIKYDGERVQVH--KNGDVFSYfSRSLK------PVLPHKVAHFKDyipqafP 553
Cdd:PLN03113  369 PVGPMLAKPTKGVSEIVNKFQDMEFTcEYKYDGERAQIHflEDGSVEIY-SRNAErntgkyPDVVVAISRLKK------P 441

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 554 GGHSMILDAEVLLIDTKTSKPLPFGTLGVH--KKAAFQD--ANVCLFVFDCIYFNGVSLME------RKFLHDNMVEVHN 623
Cdd:PLN03113  442 SVKSFILDCELVAYDREKKKILPFQILSTRarKNVVMSDikVDVCIFAFDMLYLNGQPLIQeqlkirREHLYESFEEDPG 521

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 624 RILFSEMKHVTRAGDLADMITRVIREGLEGLVLKDIKG--TYEPGKR--HWLKVKKDYLNegAMADTADLVVLGAFYGKG 699
Cdd:PLN03113  522 FFQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKdaTYEPSKRsnNWLKLKKDYME--SIGDSLDLVPIAAFHGRG 599


                  ....*....
gi 2059423981 700 SNGASCPAF 708
Cdd:PLN03113  600 KRTGVYGAF 608
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
 484-674 2.09e-22

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: 95.30  E-value: 2.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 484 VQPMLAEACKSIeyamkkcPNG---MYsEIKYDGERVQVHKNGDVFSYFSRSLKPVLPHkvahfkdyipqaFP------- 553
Cdd:cd07906     1 IEPMLATLVDEP-------PDGedwLY-EIKWDGYRALARVDGGRVRLYSRNGLDWTAR------------FPelaeala 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 554 --GGHSMILDAE--VLLIDTKTSkplpFGTL----GVHKKAAfQDANVCLFVFDCIYFNGVSL-----MERK-FLHDNMV 619
Cdd:cd07906    61 alPVRDAVLDGEivVLDEGGRPD----FQALqnrlRLRRRLA-RTVPVVYYAFDLLYLDGEDLrglplLERKeLLEELLP 135

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2059423981 620 EVHNRILFSEmkHVTRAGdlADMITRVIREGLEGLVLKDIKGTYEPGKRH--WLKVK 674
Cdd:cd07906   136 AGSPRLRVSE--HFEGGG--AALFAAACELGLEGIVAKRADSPYRSGRRSrdWLKIK 188
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
 509-674 1.04e-11

DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.


Pssm-ID: 274295 [Multi-domain]  Cd Length: 298  Bit Score: 66.17  E-value: 1.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 509 EIKYDGERVQVHKNGDVFSYFSRSLKPvLPHKVAHFKDYipQAFPGGHSMILDAEVLLIDTKtskplpfgtlGVHKKAAF 588
Cdd:TIGR02779  17 EVKYDGYRCLARIEGGKVRLISRNGHD-WTEKFPILAAA--LAALPILPAVLDGEIVVLDES----------GRSDFSAL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 589 QDA-------NVCLFVFDCIYFNG-----VSLMERK-FLHDNMVEVH---NRILFSEmkHVTraGDLADMITRVIREGLE 652
Cdd:TIGR02779  84 QNRlragrdrPATYYAFDLLYLDGedlrdLPLSERKkLLEELLKAIKgplAPDRYSV--HFE--GDGQALLEAACRLGLE 159

                         170       180
                  ....*....|....*....|...
gi 2059423981 653 GLVLKDIKGTYEPGK-RHWLKVK 674
Cdd:TIGR02779 160 GVVAKRRDSPYRSGRsADWLKLK 182
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
 97-182 1.19e-11

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 68.28  E-value: 1.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  97 EYAKRGTAGCKKCKDKIQKGIVRIGKIVPNPfsESAGEMKEWYHVKCIFEKleraratTKKIEDITDLEGWEELQDEDKD 176
Cdd:PLN03123   11 EYAKSSRSSCKTCKSPIDKDELRLGKMVQST--QFDGFMPMWNHASCILKK-------KNQIKSIDDVEGIDSLRWEDQQ 81


                  ....*.
gi 2059423981 177 LINKHV 182
Cdd:PLN03123   82 KIRKYV 87
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
 480-700 6.31e-11

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 64.53  E-value: 6.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 480 LMTPVQPMLAEACKSIeyamkkcP--NGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKDYIPQAFpg 554
Cdd:PRK08224    5 VMPPVEPMLAKSVDAI-------PpgDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLtryFPELVAALRAELPERC-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 555 ghsmILDAEVLLIdtkTSKPLPFGTLG---------VHKKAAFQDAnvcLFV-FDCIYFNGVSLMERKFLH-----DNMV 619
Cdd:PRK08224   76 ----VLDGEIVVA---RDGGLDFEALQqrihpaasrVRKLAEETPA---SFVaFDLLALGDRDLTGRPFAErraalEAAA 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 620 EVHNRIlfsemkHVTRA-GDLADM---ITRVIREGLEGLVLKDIKGTYEPGKRHWLKVKKdylnegamADTADLVVLGAF 695
Cdd:PRK08224  146 AGSGPV------HLTPAtTDPATArrwFEEFEGAGLDGVIAKPLDGPYQPGKRAMFKVKH--------ERTADCVVAGYR 211


                  ....*
gi 2059423981 696 YGKGS 700
Cdd:PRK08224  212 YHKSG 216
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
 504-675 1.26e-10

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: 60.90  E-value: 1.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 504 NGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPVlPHKVAHFKDYIPQAFPGGhsMILDAEVLLIDTKTSKPLPfgtlgvh 583
Cdd:cd06846    19 DEYYVQEKYDGKRALIVALNGGVFAISRTGLEV-PLPSILIPGRELLTLKPG--FILDGELVVENREVANPKP------- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 584 kkaafqdanvCLFVFDCIYFNGVSLMERKF------LHDNmVEVHNRILFSEMKHVTRAG----DLADMITRVIREGLEG 653
Cdd:cd06846    89 ----------TYYAFDVVPLSGVGLRDLPYsdrfayLKSL-LKEFEGLDPVKLVPLENAPsydeTLDDLLEKLKKKGKEG 157

                         170       180
                  ....*....|....*....|....*
gi 2059423981 654 LVLKDIKGTYE--PGK-RHWLKVKK 675
Cdd:cd06846   158 LVFKHPDAPYKgrPGSsGNQLKLKP 182
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
 509-676 3.63e-10

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: 60.26  E-value: 3.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 509 EIKYDGERVQ-VHKNGDVFSYfSRSlkpvlphkvahfKDYIPQAFPGGHSMI--------LDAEVLLIdtKTSKPLPFGT 579
Cdd:cd07897    29 EWKWDGIRGQlIRRGGEVFLW-SRG------------EELITGSFPELLAAAealpdgtvLDGELLVW--RDGRPLPFND 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 580 L-------GVHKKaAFQDANVCLFVFDCIYFNGV-----SLMERKFLHDNMVEVH--NRILFSEMKHVTRAGDLADMITR 645
Cdd:cd07897    94 LqqrlgrkTVGKK-LLAEAPAAFRAYDLLELNGEdlralPLRERRARLEALLARLppPRLDLSPLIAFADWEELAALRAQ 172

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2059423981 646 VIREGLEGLVLKDIKGTYEPGKR--HWLKVKKD 676
Cdd:cd07897   173 SRERGAEGLMLKRRDSPYLVGRKkgDWWKWKID 205
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
 506-677 4.15e-10

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: 60.49  E-value: 4.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 506 MYSEIKYDGERVQVH----KNGDVFSYFSRSLKPVLPHKVA-HfkDYIPQAFPGG-------HSMILDAEVLLIDTKTSK 573
Cdd:cd08039    24 MWVETKYDGEYCQIHidlsKDSSPIRIFSKSGKDSTADRAGvH--SIIRKALRIGkpgckfsKNCILEGEMVVWSDRQGK 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 574 PLPFGTLGVHKK--AAF----QDA------NVCLFVFDCIYFNGVSLM-----ERKFLHDNMVEV-HNRILFSE-----M 630
Cdd:cd08039   102 IDPFHKIRKHVErsGSFigtdNDSppheyeHLMIVFFDVLLLDDESLLskpysERRDLLESLVHViPGYAGLSErfpidF 181

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2059423981 631 KHVTRAGDLADMITRVIREGLEGLVLK-------DIKGTYEPGKRHWLKVKKDY 677
Cdd:cd08039   182 SRSSGYERLRQIFARAIAERWEGLVLKgdeepyfDLFLEQGSFSGCWIKLKKDY 235
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
 484-674 6.95e-10

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: 59.18  E-value: 6.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 484 VQPMLAEACKSIEYamkkcPNGMYSEIKYDGERVQVHKNGDVFSYFSRSLKPV---LPHKVAHFKDYIPQAFpgghsmIL 560
Cdd:cd07905     1 VEPMLARAVDALPE-----PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLtryFPELVAAARALLPPGC------VL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 561 DAEVLLIDtktSKPLPFGTL---------GVHKKAAFQDANvcLFVFDCIYFNGVSLMERKF------LHDnmvevhnri 625
Cdd:cd07905    70 DGELVVWR---GGRLDFDALqqrihpaasRVRRLAEETPAS--FVAFDLLALGGRDLRGRPLrerraaLEA--------- 135

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2059423981 626 LFSEMK---HVTRA----GDLADMITRVIREGLEGLVLKDIKGTYEPGKRHWLKVK 674
Cdd:cd07905   136 LLAGWGpplHLSPAttdrAEAREWLEEFEGAGLEGVVAKRLDGPYRPGERAMLKVK 191
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
 478-700 6.81e-09

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 59.25  E-value: 6.81e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 478 ASLMTPVQPMLA-----EACKSIEYAMkkcpngmysEIKYDGERVQVHKNGDVFSYFSRSLKPVLPhkvahfkdyipqAF 552
Cdd:PRK09632  455 AEEADDLAPMLAtagtvAGLKASQWAF---------EGKWDGYRLLAEADHGALRLRSRSGRDVTA------------EY 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 553 P---------GGHSMILDAEVLLIDtKTSKPlPFGTLGVHKKaafqDANVCLFVFDCIYFNGVSLMERKFlHDNmvevhn 623
Cdd:PRK09632  514 PelaalaedlADHHVVLDGEIVALD-DSGVP-SFGLLQNRGR----DTRVEFWAFDLLYLDGRSLLRKPY-RDR------ 580

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 624 RILFSEMKHVTRA--------GDLADMITRVIREGLEGLVLKDIKGTYEPGKR--HWLKVKkdylnegaMADTADLVVLG 693
Cdd:PRK09632  581 RKLLEALAPSGGSltvppllpGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRssSWIKDK--------HWRTQEVVIGG 652


                  ....*..
gi 2059423981 694 AFYGKGS 700
Cdd:PRK09632  653 WRPGEGG 659
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
 84-220 8.57e-09

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 59.03  E-value: 8.57e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981  84 SNEPDMAEQRFLVEYAKRGTAGCKKCKDKIQKGIVRIGKIVPNPFSESAgemkEWYHVKCIFEKLERArattkkieDITD 163
Cdd:PLN03123   97 ASDAAASSFEYGIEVAKTSRATCRRCSEKILKGEVRISSKPEGQGYKGL----AWHHAKCFLEMSPST--------PVEK 164

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2059423981 164 LEGWEELQDEDK----DLINKHVSDLMAKVNA----SPKKKVQAKLNTTG--QLKAPPADPSVNAPR 220
Cdd:PLN03123  165 LSGWDTLSDSDQeavlPLVKKSPSEAKEEKAEerkqESKKGAKRKKDASGddKSKKAKTDRDVSTST 231
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
 509-676 2.07e-07

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 54.08  E-value: 2.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 509 EIKYDGERVQVHKNGDVFSYFSRSLKPVlphkVAHFKDYIP--QAFPGGHsmILDAEVLLIDTKTSKPLPFGTL------ 580
Cdd:PRK09247  230 EWKWDGIRVQLVRRGGEVRLWSRGEELI----TERFPELAEaaEALPDGT--VLDGELLVWRPEDGRPQPFADLqqrigr 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 581 -GVHKKaAFQDANVCLFVFDCIYFNGVSLMERKFLH-----DNMVE--VHNRILFSEMKHVTRAGDLADMITRVIREGLE 652
Cdd:PRK09247  304 kTVGKK-LLADYPAFLRAYDLLEDGGEDLRALPLAErrarlEALIArlPDPRLDLSPLVPFSDWDELAALRAAARERGVE 382

                         170       180
                  ....*....|....*....|....*.
gi 2059423981 653 GLVLKDIKGTYEPGKR--HWLKVKKD 676
Cdd:PRK09247  383 GLMLKRRDSPYLVGRKkgPWWKWKRD 408
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
 683-702 3.54e-07

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: 50.05  E-value: 3.54e-07
                          10        20
                  ....*....|....*....|
gi 2059423981 683 MADTADLVVLGAFYGKGSNG 702
Cdd:cd07967     1 MADTADLVVLGAYYGTGSKG 20
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
 509-673 7.68e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 51.30  E-value: 7.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 509 EIKYDGERVQVHKNGDVFSYFSRSLKPVlphkVAHFKDYIPQAFPggHSMILDAEVLLIDTkTSKPlPFGTL--GVHKKA 586
Cdd:PRK07636   23 EPKFDGIRLIASKNNGLIRLYTRHNNEV----TAKFPELLNLDIP--DGTVLDGELIVLGS-TGAP-DFEAVmeRFQSKK 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 587 AFQDANVCLFVFDCIYFNGVS-----LMERKflhdnmvEVHNRIL-----FSEMKHVTRAGDlaDMITRVIREGLEGLVL 656
Cdd:PRK07636   95 STKIHPVVFCVFDVLYINGVSltalpLSERK-------EILASLLlphpnVKIIEGIEGHGT--AYFELVEERELEGIVI 165

                         170
                  ....*....|....*....
gi 2059423981 657 KDIKGTYEPGKR--HWLKV 673
Cdd:PRK07636  166 KKANSPYEINKRsdNWLKV 184
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
 509-674 3.30e-05

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 47.21  E-value: 3.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 509 EIKYDGERVQVH-KNGDVfSYFSR-----SLKpvLPHKVAHFKD-YIPQAfpgghsmILDAEVLLIDtktSKPLP-FGTL 580
Cdd:PRK05972  254 EIKFDGYRILARiEGGEV-RLFTRngldwTAK--LPALAKAAAAlGLPDA-------WLDGEIVVLD---EDGVPdFQAL 320

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 581 gvhkKAAF---QDANVCLFVFDCIYFNG-----VSLMERKFLHDNMVEVHN--RILFSEmkHVTRAGDlaDMITRVIREG 650
Cdd:PRK05972  321 ----QNAFdegRTEDLVYFAFDLPFLGGedlreLPLEERRARLRALLEAARsdRIRFSE--HFDAGGD--AVLASACRLG 392

                         170       180
                  ....*....|....*....|....*
gi 2059423981 651 LEGLVLKDIKGTYEPGKRH-WLKVK 674
Cdd:PRK05972  393 LEGVIGKRADSPYVSGRSEdWIKLK 417
PHA00454 PHA00454
ATP-dependent DNA ligase
 493-698 6.91e-05

ATP-dependent DNA ligase


Pssm-ID: 222798 [Multi-domain]  Cd Length: 315  Bit Score: 45.41  E-value: 6.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 493 KSIEYAMKKcpNG-MYSEIKYDGERVQVHKNGDVFSYF-SRSLK--PVLPH------KVAHFKDYIPQAFPGGhsMILDA 562
Cdd:PHA00454   17 SAIEKALEK--AGyLIADVKYDGVRGNIVVDNTADHGWlSREGKtiPALEHlngfdrRWAKLLNDDRCIFPDG--FMLDG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 563 EVL-----------LIDTKTSKPLP----------FGTLGVHKKAAFQDANVclfvfdciyFNGVSLMERKFLHDNMVEV 621
Cdd:PHA00454   93 ELMvkgvdfntgsgLLRRKWKVLFElhlkklhvvvYDVTPLDVLESGEDYDV---------MSLLMYEHVRAMVPLLMEY 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059423981 622 HNRILF--SEMKHVTRAGDLADMITRVIREGLEGLVLKDIKGTYEPGKRH-WLKVKKDylnegamaDTADLVVLGAFYGK 698
Cdd:PHA00454  164 FPEIDWflSESYEVYDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSgWWKMKPE--------CEADGTIVGVVWGT 235
OBF_DNA_ligase cd07893
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
 685-708 5.98e-03

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: 37.33  E-value: 5.98e-03
                          10        20
                  ....*....|....*....|....
gi 2059423981 685 DTADLVVLGAFYGKGSNGASCPAF 708
Cdd:cd07893     1 DTLDLVIVGAYYGKGRRGGGIGAF 24
OBF_DNA_ligase_I cd07969
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ...
 684-699 9.61e-03

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: 37.07  E-value: 9.61e-03
                          10
                  ....*....|....*.
gi 2059423981 684 ADTADLVVLGAFYGKG 699
Cdd:cd07969     1 GDTLDLVPIGAYYGKG 16
 
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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