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Conserved domains on  [gi|568971912|ref|XP_006532411|]
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DNA ligase 3 isoform X2 [Mus musculus]

Protein Classification

PARP-type zinc finger-containing protein( domain architecture ID 12004034)

PARP-type zinc finger-containing protein similar to Schizosaccharomyces pombe PARP-type zinc finger-containing proteins C2A9.07c and C13F5.07c

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
373-885 0e+00

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: 669.79  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   373 VYNLNDKQIVKLFSRIFNCNPDDMARD-LEQGDVSETIRIFFEQSK--SFPPAAKSLLTIQEVDAFLLHLSKLTKEDEQQ 449
Cdd:TIGR00574    1 EYGIGEKLLIKAISEILGIPKDEIEEKvLEDGDLGEGIEGLFSKQKqtSFFPAPLTVKEVYEVLKFIARLSGEGSQDKKI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   450 QALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNA-------YEAFKASRNLQDVVERvLHNEqevekdPGR 522
Cdd:TIGR00574   81 KSLKSLLKRASPLEAKYLIRLILGDLRIGIAEKTILDALAKAFllsppdvERAFNLTNDLGKVAKI-LLEP------GLR 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   523 RRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPK 602
Cdd:TIGR00574  154 GLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKE 233
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   603 AFPGGQSMILDSEVLLIDNNTGKPLPFGTLGVHK-----KAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMV 677
Cdd:TIGR00574  234 AFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKrkydiKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILK 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   678 EIRNRIMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGQG 757
Cdd:TIGR00574  314 PIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEGMGDTLDLVVIGAYYGKG 393
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   758 SKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLkinkiyyPDFIVPDPKKAAVW 837
Cdd:TIGR00574  394 SRGGMYGSFLCACYDPESEEFKTITKVGTGFTDADLQELGKKLPPLWIDPPGSRVPSIL-------PDEPDIWPDPAIVW 466
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*...
gi 568971912   838 EITGAEFSRSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQ 885
Cdd:TIGR00574  467 EVTGAEITKSPAYKANGISLRFPRFSRIRDDKGPEDATTLEQIKELYE 514
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
151-236 2.39e-32

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: 120.50  E-value: 2.39e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   151 DYAKRGTAGCKKCKEKIVKGVCRIGKVVPN-PFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEK 229
Cdd:pfam00645    1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80

                   ....*..
gi 568971912   230 EQISQHI 236
Cdd:pfam00645   81 EKIRKAI 87
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
989-1059 2.63e-32

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


:

Pssm-ID: 465260  Cd Length: 77  Bit Score: 120.17  E-value: 2.63e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568971912   989 VLLDVFTGVRLYLPPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLG------NREKNTDAQLVSSEWIWACIRKR 1059
Cdd:pfam16759    1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVpkdsakEKEESSGAKHVTASWIWECIKKR 77
 
Name Accession Description Interval E-value
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
373-885 0e+00

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: 669.79  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   373 VYNLNDKQIVKLFSRIFNCNPDDMARD-LEQGDVSETIRIFFEQSK--SFPPAAKSLLTIQEVDAFLLHLSKLTKEDEQQ 449
Cdd:TIGR00574    1 EYGIGEKLLIKAISEILGIPKDEIEEKvLEDGDLGEGIEGLFSKQKqtSFFPAPLTVKEVYEVLKFIARLSGEGSQDKKI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   450 QALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNA-------YEAFKASRNLQDVVERvLHNEqevekdPGR 522
Cdd:TIGR00574   81 KSLKSLLKRASPLEAKYLIRLILGDLRIGIAEKTILDALAKAFllsppdvERAFNLTNDLGKVAKI-LLEP------GLR 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   523 RRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPK 602
Cdd:TIGR00574  154 GLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKE 233
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   603 AFPGGQSMILDSEVLLIDNNTGKPLPFGTLGVHK-----KAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMV 677
Cdd:TIGR00574  234 AFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKrkydiKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILK 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   678 EIRNRIMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGQG 757
Cdd:TIGR00574  314 PIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEGMGDTLDLVVIGAYYGKG 393
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   758 SKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLkinkiyyPDFIVPDPKKAAVW 837
Cdd:TIGR00574  394 SRGGMYGSFLCACYDPESEEFKTITKVGTGFTDADLQELGKKLPPLWIDPPGSRVPSIL-------PDEPDIWPDPAIVW 466
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*...
gi 568971912   838 EITGAEFSRSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQ 885
Cdd:TIGR00574  467 EVTGAEITKSPAYKANGISLRFPRFSRIRDDKGPEDATTLEQIKELYE 514
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
523-735 3.69e-160

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: 471.44  E-value: 3.69e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  523 RRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPK 602
Cdd:cd07902     1 KKKLSVRASLMTPVKPMLAEACKSVEDAMKKCPNGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  603 AFPGGQSMILDSEVLLIDNNTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNR 682
Cdd:cd07902    81 AFPHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNR 160
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568971912  683 IMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRHWLKVKKDY 735
Cdd:cd07902   161 IMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVKKDY 213
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
538-732 8.68e-87

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: 278.01  E-value: 8.68e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   538 PMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPKAFPGGQSMILDSEVL 617
Cdd:pfam01068    1 PMLAKSFKSIEEALKKFGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   618 LIDNNTGKPLPFGTLGVHKKAAFQD------ANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEMKQV 691
Cdd:pfam01068   81 AVDPETGEILPFQVLADRKKKKVDVeelaekVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVT 160
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 568971912   692 TKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVK 732
Cdd:pfam01068  161 KDVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRgkNWLKIK 203
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
336-891 6.35e-85

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 286.87  E-value: 6.35e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  336 TKTQIIHDFLQKgSTGDGFHGDVYLTVKLLLPGVIKSVYNLNDKQIVKLFSRIFNCNPDDMARDLEQ-GDVSETIRIFFE 414
Cdd:PRK01109   21 QLTKLLADLLKK-TPPEIIDKVVYLIQGKLWPDWLGLELGVGEKLLIKAISMATGISEKEVENLYKKtGDLGEVARRLKS 99
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  415 QSKSFPPAA---KSLLTIQEVDAFLLHLSKLTKE---DEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDAL 488
Cdd:PRK01109  100 KKKQKSLLAffsKEPLTVKEVYDTLVKIALATGEgsqDLKIKLLAGLLKDASPLEAKYIARFVEGRLRLGVGDATILDAL 179
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  489 DpnayEAFKASRNlQDVVERVLH------NEQEVEKDPGRRRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEI 562
Cdd:PRK01109  180 A----IAFGGAVA-RELVERAYNlradlgYIAKILAEGGIEALKKVKPQVGIPIRPMLAERLSSPKEILKKMGGEALVEY 254
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  563 KYDGERVQVHKKGDHFSYFSRSLKPV---LPHKVAHFKDYIpKAfpggQSMILDSEVLLIDNNTGKPLPFGTLgVHKK-- 637
Cdd:PRK01109  255 KYDGERAQIHKKGDKVKIFSRRLENIthqYPDVVEYAKEAI-KA----EEAIVEGEIVAVDPETGEMRPFQEL-MHRKrk 328
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  638 ----AAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNmVEIRNRIMFSEMKQVTKASDLADMINRVIREGLEGLV 713
Cdd:PRK01109  329 ydieEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEI-VKENDKVKLAERIITDDVEELEKFFHRAIEEGCEGLM 407
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  714 LKDVKGT--YEPGKRHWL--KVKKDYLNEgaMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHD 789
Cdd:PRK01109  408 AKSLGKDsiYQAGARGWLwiKYKRDYQSE--MADTVDLVVVGAFYGRGRRGGKYGSLLMAAYDPKTDTFETVCKVGSGFT 485
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  790 DATLARLQKELVMVKISKDPSKIPSWLKINKIYYPdfivpdpkkAAVWEITGAEFSRSEAHTAD--------GISIRFPR 861
Cdd:PRK01109  486 DEDLDELPKMLKPYKIDHKHPRVVSKMEPDVWVEP---------KLVAEIIGAEITLSPLHTCClgvvekgaGLAIRFPR 556
                         570       580       590
                  ....*....|....*....|....*....|
gi 568971912  862 CTRIRDDKDWKSATNLPQLKELYQLSKDKA 891
Cdd:PRK01109  557 FIRWRDDKSPEDATTTEEILEMYKRQKKKK 586
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
502-885 2.43e-64

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 224.41  E-value: 2.43e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  502 LQDVVERVLHNEQEVEKDPGRRRALRVQASLMtpVQPMLAEACKSIEYamkkcPNGMFSEIKYDGERVQVHKKGDHFSYF 581
Cdd:COG1793    82 LTKGTLFELAGEKLAGRWYLVRLGERVSDWLL--VPPMLATLVDSPPD-----GGDWAYEPKWDGYRVQAHRDGGEVRLY 154
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  582 SRSLKPV---LPHKVAHFKdyipkAFPGgQSMILDSEVLLIDNNtGKPlPFGTL------GVHKKAAFQDANVCLFVFDC 652
Cdd:COG1793   155 SRNGEDItdrFPELVEALR-----ALPA-DDAVLDGEIVALDED-GRP-PFQALqqrlgrKRDVAKLAREVPVVFYAFDL 226
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  653 IYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEmkQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLK 730
Cdd:COG1793   227 LYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSP--HVIDWGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRsgDWLK 304
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  731 VKKdylnegamADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDsQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPs 810
Cdd:COG1793   305 VKC--------PRTQDLVVGGATPGKGRRAGGFGSLLLGVYDPG-GELVYVGKVGTGFTDAELAELTERLRPLTRERSP- 374
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  811 kipswlkinkiyypdFIVPDPKKAAVW-------EITGAEFSRSEAhtadgisIRFPRCTRIRDDKDWKSATnLPQLKEL 883
Cdd:COG1793   375 ---------------FAVPSDGRPVRWvrpelvaEVAFDEITRSGA-------LRFPRFLRLREDKPPEEAT-LEELEAL 431

                  ..
gi 568971912  884 YQ 885
Cdd:COG1793   432 LA 433
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
151-236 2.39e-32

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: 120.50  E-value: 2.39e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   151 DYAKRGTAGCKKCKEKIVKGVCRIGKVVPN-PFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEK 229
Cdd:pfam00645    1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80

                   ....*..
gi 568971912   230 EQISQHI 236
Cdd:pfam00645   81 EKIRKAI 87
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
989-1059 2.63e-32

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


Pssm-ID: 465260  Cd Length: 77  Bit Score: 120.17  E-value: 2.63e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568971912   989 VLLDVFTGVRLYLPPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLG------NREKNTDAQLVSSEWIWACIRKR 1059
Cdd:pfam16759    1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVpkdsakEKEESSGAKHVTASWIWECIKKR 77
BRCT_DNA_ligase_III cd18431
BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ...
990-1061 1.82e-28

BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ligase III, or polydeoxyribonucleotide synthase [ATP] 3, functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.


Pssm-ID: 349384 [Multi-domain]  Cd Length: 78  Bit Score: 109.33  E-value: 1.82e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568971912  990 LLDVFTGVRLYLPPSTPD-FKRLKRYFVAFDGDLVQEFDMGSATHVLGNRE---KNTDAQLVSSEWIWACIRKRRL 1061
Cdd:cd18431     1 LPDIFTGVKVYLPGSVEDdYKKLKRYFIAYDGDVVEEYDEEDATHVVVDRDdklGNPSAKVVSPEWLWDCIKKQKL 76
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
150-232 4.14e-07

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 54.41  E-value: 4.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  150 VDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPfsesGGDMKEWYHIKCMFEKLERArattkkieDLTELEGWEELEDNEK 229
Cdd:PLN03123  109 IEVAKTSRATCRRCSEKILKGEVRISSKPEGQ----GYKGLAWHHAKCFLEMSPST--------PVEKLSGWDTLSDSDQ 176

                  ...
gi 568971912  230 EQI 232
Cdd:PLN03123  177 EAV 179
BRCT smart00292
breast cancer carboxy-terminal domain;
992-1056 1.67e-05

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 43.90  E-value: 1.67e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568971912    992 DVFTGVRLYL--PPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLGNRE----------KNTDAQLVSSEWIWACI 1056
Cdd:smart00292    2 KLFKGKTFYItgSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPeggklellkaIALGIPIVKEEWLLDCL 78
 
Name Accession Description Interval E-value
dnl1 TIGR00574
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ...
373-885 0e+00

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: 669.79  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   373 VYNLNDKQIVKLFSRIFNCNPDDMARD-LEQGDVSETIRIFFEQSK--SFPPAAKSLLTIQEVDAFLLHLSKLTKEDEQQ 449
Cdd:TIGR00574    1 EYGIGEKLLIKAISEILGIPKDEIEEKvLEDGDLGEGIEGLFSKQKqtSFFPAPLTVKEVYEVLKFIARLSGEGSQDKKI 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   450 QALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNA-------YEAFKASRNLQDVVERvLHNEqevekdPGR 522
Cdd:TIGR00574   81 KSLKSLLKRASPLEAKYLIRLILGDLRIGIAEKTILDALAKAFllsppdvERAFNLTNDLGKVAKI-LLEP------GLR 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   523 RRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPK 602
Cdd:TIGR00574  154 GLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYQYPEIFTEFIKE 233
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   603 AFPGGQSMILDSEVLLIDNNTGKPLPFGTLGVHK-----KAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMV 677
Cdd:TIGR00574  234 AFPGIKSCILDGEMVAIDPETGKPLPFGTLLRRKrkydiKAMDQKVPVCLFVFDILYLNGKSLIDEPLIERREILESILK 313
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   678 EIRNRIMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRHWLKVKKDYLNEGAMADTADLVVLGAFYGQG 757
Cdd:TIGR00574  314 PIPNRIEIAEMKIVSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKIKPEYLEGMGDTLDLVVIGAYYGKG 393
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   758 SKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLkinkiyyPDFIVPDPKKAAVW 837
Cdd:TIGR00574  394 SRGGMYGSFLCACYDPESEEFKTITKVGTGFTDADLQELGKKLPPLWIDPPGSRVPSIL-------PDEPDIWPDPAIVW 466
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*...
gi 568971912   838 EITGAEFSRSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQLKELYQ 885
Cdd:TIGR00574  467 EVTGAEITKSPAYKANGISLRFPRFSRIRDDKGPEDATTLEQIKELYE 514
Adenylation_DNA_ligase_III cd07902
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ...
523-735 3.69e-160

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: 471.44  E-value: 3.69e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  523 RRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPK 602
Cdd:cd07902     1 KKKLSVRASLMTPVKPMLAEACKSVEDAMKKCPNGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  603 AFPGGQSMILDSEVLLIDNNTGKPLPFGTLGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNR 682
Cdd:cd07902    81 AFPHGHSMILDSEVLLVDTKTGKPLPFGTLGIHKKSAFKDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNR 160
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568971912  683 IMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRHWLKVKKDY 735
Cdd:cd07902   161 IMLSEMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKRHWLKVKKDY 213
OBF_DNA_ligase_III cd07967
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ...
741-879 5.02e-105

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: 324.32  E-value: 5.02e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  741 MADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLKINK 820
Cdd:cd07967     1 MADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNSKKWCTVTKCGNGHDDATLARLQKELKMVKISKDPSKVPSWLKCNK 80
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568971912  821 IYYPDFIVPDPKKAAVWEITGAEFSRSEAHTADGISIRFPRCTRIRDDKDWKSATNLPQ 879
Cdd:cd07967    81 SLVPDFIVKDPKKAPVWEITGAEFSKSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139
DNA_ligase_A_M pfam01068
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ...
538-732 8.68e-87

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: 278.01  E-value: 8.68e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   538 PMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYIPKAFPGGQSMILDSEVL 617
Cdd:pfam01068    1 PMLAKSFKSIEEALKKFGGAFIAEYKYDGERAQIHKDGDEVKLFSRNLENITRHYPEIVEALKEAFKPDEKSFILDGEIV 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   618 LIDNNTGKPLPFGTLGVHKKAAFQD------ANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEMKQV 691
Cdd:pfam01068   81 AVDPETGEILPFQVLADRKKKKVDVeelaekVPVCLFVFDLLYLDGEDLTDLPLRERRKLLEEIFKEIPGRIQLAESIVT 160
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 568971912   692 TKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVK 732
Cdd:pfam01068  161 KDVEEAQEFLEEAISEGLEGLVVKDPDSTYEPGKRgkNWLKIK 203
PRK01109 PRK01109
ATP-dependent DNA ligase; Provisional
336-891 6.35e-85

ATP-dependent DNA ligase; Provisional


Pssm-ID: 234900 [Multi-domain]  Cd Length: 590  Bit Score: 286.87  E-value: 6.35e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  336 TKTQIIHDFLQKgSTGDGFHGDVYLTVKLLLPGVIKSVYNLNDKQIVKLFSRIFNCNPDDMARDLEQ-GDVSETIRIFFE 414
Cdd:PRK01109   21 QLTKLLADLLKK-TPPEIIDKVVYLIQGKLWPDWLGLELGVGEKLLIKAISMATGISEKEVENLYKKtGDLGEVARRLKS 99
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  415 QSKSFPPAA---KSLLTIQEVDAFLLHLSKLTKE---DEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDAL 488
Cdd:PRK01109  100 KKKQKSLLAffsKEPLTVKEVYDTLVKIALATGEgsqDLKIKLLAGLLKDASPLEAKYIARFVEGRLRLGVGDATILDAL 179
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  489 DpnayEAFKASRNlQDVVERVLH------NEQEVEKDPGRRRALRVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEI 562
Cdd:PRK01109  180 A----IAFGGAVA-RELVERAYNlradlgYIAKILAEGGIEALKKVKPQVGIPIRPMLAERLSSPKEILKKMGGEALVEY 254
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  563 KYDGERVQVHKKGDHFSYFSRSLKPV---LPHKVAHFKDYIpKAfpggQSMILDSEVLLIDNNTGKPLPFGTLgVHKK-- 637
Cdd:PRK01109  255 KYDGERAQIHKKGDKVKIFSRRLENIthqYPDVVEYAKEAI-KA----EEAIVEGEIVAVDPETGEMRPFQEL-MHRKrk 328
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  638 ----AAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNmVEIRNRIMFSEMKQVTKASDLADMINRVIREGLEGLV 713
Cdd:PRK01109  329 ydieEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEI-VKENDKVKLAERIITDDVEELEKFFHRAIEEGCEGLM 407
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  714 LKDVKGT--YEPGKRHWL--KVKKDYLNEgaMADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHD 789
Cdd:PRK01109  408 AKSLGKDsiYQAGARGWLwiKYKRDYQSE--MADTVDLVVVGAFYGRGRRGGKYGSLLMAAYDPKTDTFETVCKVGSGFT 485
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  790 DATLARLQKELVMVKISKDPSKIPSWLKINKIYYPdfivpdpkkAAVWEITGAEFSRSEAHTAD--------GISIRFPR 861
Cdd:PRK01109  486 DEDLDELPKMLKPYKIDHKHPRVVSKMEPDVWVEP---------KLVAEIIGAEITLSPLHTCClgvvekgaGLAIRFPR 556
                         570       580       590
                  ....*....|....*....|....*....|
gi 568971912  862 CTRIRDDKDWKSATNLPQLKELYQLSKDKA 891
Cdd:PRK01109  557 FIRWRDDKSPEDATTTEEILEMYKRQKKKK 586
Adenylation_DNA_ligase cd07898
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ...
536-734 5.87e-79

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: 256.49  E-value: 5.87e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  536 VQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHKVAHFKDYipKAFPggQSMILDSE 615
Cdd:cd07898     1 IKPMLAHPEESAEAAKAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAA--KALP--HEFILDGE 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  616 VLLIDNNTG--KPLPFGTLGVHKKAAF--QDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEMKQV 691
Cdd:cd07898    77 ILAWDDNRGlpFSELFKRLGRKFRDKFldEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPALPV 156
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 568971912  692 TKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVKKD 734
Cdd:cd07898   157 ESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRglAWLKLKKE 201
CDC9 COG1793
ATP-dependent DNA ligase [Replication, recombination and repair];
502-885 2.43e-64

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


Pssm-ID: 441398 [Multi-domain]  Cd Length: 435  Bit Score: 224.41  E-value: 2.43e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  502 LQDVVERVLHNEQEVEKDPGRRRALRVQASLMtpVQPMLAEACKSIEYamkkcPNGMFSEIKYDGERVQVHKKGDHFSYF 581
Cdd:COG1793    82 LTKGTLFELAGEKLAGRWYLVRLGERVSDWLL--VPPMLATLVDSPPD-----GGDWAYEPKWDGYRVQAHRDGGEVRLY 154
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  582 SRSLKPV---LPHKVAHFKdyipkAFPGgQSMILDSEVLLIDNNtGKPlPFGTL------GVHKKAAFQDANVCLFVFDC 652
Cdd:COG1793   155 SRNGEDItdrFPELVEALR-----ALPA-DDAVLDGEIVALDED-GRP-PFQALqqrlgrKRDVAKLAREVPVVFYAFDL 226
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  653 IYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEmkQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLK 730
Cdd:COG1793   227 LYLDGEDLRDLPLSERRALLEELLAGAPPPLRLSP--HVIDWGEGEALFAAAREAGLEGVMAKRLDSPYRPGRRsgDWLK 304
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  731 VKKdylnegamADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDsQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPs 810
Cdd:COG1793   305 VKC--------PRTQDLVVGGATPGKGRRAGGFGSLLLGVYDPG-GELVYVGKVGTGFTDAELAELTERLRPLTRERSP- 374
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  811 kipswlkinkiyypdFIVPDPKKAAVW-------EITGAEFSRSEAhtadgisIRFPRCTRIRDDKDWKSATnLPQLKEL 883
Cdd:COG1793   375 ---------------FAVPSDGRPVRWvrpelvaEVAFDEITRSGA-------LRFPRFLRLREDKPPEEAT-LEELEAL 431

                  ..
gi 568971912  884 YQ 885
Cdd:COG1793   432 LA 433
OBF_DNA_ligase cd07893
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
743-874 4.80e-53

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: 181.39  E-value: 4.80e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  743 DTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSkipswlKINKIY 822
Cdd:cd07893     1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPERDEFQTICKVGSGFTDEELEELRELLKELKTPEKPP------RVNSIE 74
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568971912  823 YPDFIVPdpkKAAVWEITGAEFSRSEAHTAD------GISIRFPRCTRIRDDKDWKSA 874
Cdd:cd07893    75 KPDFWVE---PKVVVEVLADEITRSPMHTAGrgeeeeGYALRFPRFVRIRDDKGPEDA 129
Adenylation_DNA_ligase_I_Euk cd07900
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ...
534-735 2.26e-51

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: 180.06  E-value: 2.26e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  534 TPVQPMLAEACKSIEYAMKKCPNGMFS-EIKYDGERVQVHK-KGDHFSYFSRSLKPV---LPHKVAHFKDYIPkafPGGQ 608
Cdd:cd07900     8 IPVKPMLAKPTKGVSEVLDRFEDKEFTcEYKYDGERAQIHLlEDGKVKIFSRNLENNtekYPDIVAVLPKSLK---PSVK 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  609 SMILDSEVLLIDNNTGKPLPFGTLGVHKK----AAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIM 684
Cdd:cd07900    85 SFILDSEIVAYDRETGKILPFQVLSTRKRkdvdANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQ 164
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568971912  685 FSEMKQVTKASDLADMINRVIREGLEGLVLK--DVKGTYEPGKR--HWLKVKKDY 735
Cdd:cd07900   165 FATSKDSEDTEEIQEFLEEAVKNNCEGLMVKtlDSDATYEPSKRshNWLKLKKDY 219
Adenylation_DNA_ligase_Arch_LigB cd07901
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ...
532-734 9.56e-49

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: 171.95  E-value: 9.56e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  532 LMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPV---LPHKVahfkDYIPKAFPGGq 608
Cdd:cd07901     1 VGRPVRPMLAQRAPSVEEALIKEGGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDItnaLPEVV----EAVRELVKAE- 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  609 SMILDSEVLLIDNnTGKPLPFGTL-----GVHKKAAFQDA-NVCLFVFDCIYFNDVSLMDRPLCERRKFLhDNMVEIRNR 682
Cdd:cd07901    76 DAILDGEAVAYDP-DGRPLPFQETlrrfrRKYDVEEAAEEiPLTLFLFDILYLDGEDLLDLPLSERRKIL-EEIVPETEA 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568971912  683 IMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVKKD 734
Cdd:cd07901   154 ILLAPRIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRgkNWLKVKPD 207
Adenylation_DNA_ligase_IV cd07903
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ...
531-737 1.29e-48

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: 172.38  E-value: 1.29e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  531 SLMTPVQPMLAEACK-SIEYAMKKCPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLK-------PVLPHKVahFKDYIPK 602
Cdd:cd07903     7 ELFSPFRPMLAERLNiGYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNdytylygASLTPGS--LTPYIHL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  603 AF-PGGQSMILDSEVLLIDNNTGKPLPFGTLGVHKKAAFQDAN---VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVE 678
Cdd:cd07903    85 AFnPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLREVEDSdlqPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITP 164
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568971912  679 IRNRIMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLN 737
Cdd:cd07903   165 IPGRLEVVKRTEASTKEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRggGWIKIKPEYLD 225
PLN03113 PLN03113
DNA ligase 1; Provisional
535-888 4.27e-48

DNA ligase 1; Provisional


Pssm-ID: 215584 [Multi-domain]  Cd Length: 744  Bit Score: 184.42  E-value: 4.27e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  535 PVQPMLAEACKSIEYAMKKCPNGMFS-EIKYDGERVQVHKKGD-HFSYFSRSLK------PVLPHKVAHFKDyipkafPG 606
Cdd:PLN03113  369 PVGPMLAKPTKGVSEIVNKFQDMEFTcEYKYDGERAQIHFLEDgSVEIYSRNAErntgkyPDVVVAISRLKK------PS 442
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  607 GQSMILDSEVLLIDNNTGKPLPFGTLGVH--KKAAFQD--ANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNR 682
Cdd:PLN03113  443 VKSFILDCELVAYDREKKKILPFQILSTRarKNVVMSDikVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGF 522
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  683 IMFSEMKQVTKASDLADMINRVIREGLEGLVLKDVKG--TYEPGKR--HWLKVKKDYLNegAMADTADLVVLGAFYGQGS 758
Cdd:PLN03113  523 FQFATAITSNDLEEIQKFLDAAVDASCEGLIIKTLNKdaTYEPSKRsnNWLKLKKDYME--SIGDSLDLVPIAAFHGRGK 600
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  759 KGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDpskipswlkinKIYY--PDFIVPD----PK 832
Cdd:PLN03113  601 RTGVYGAFLLACYDSNKEEFQSICKIGTGFSEAVLEERSASLRSQVIPTP-----------KSYYryGDSIKPDvwfePT 669
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568971912  833 KaaVWEITGAEFSRSEAHTA--------DGISIRFPRCTRIRDDKDWKSATNLPQLKELYQLSK 888
Cdd:PLN03113  670 E--VWEVKAADLTISPVHRAavgivdpdKGISLRFPRLVRVREDKSPEQATSSEQVADMYNAQK 731
OBF_DNA_ligase_I cd07969
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ...
742-885 3.91e-38

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: 139.15  E-value: 3.91e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  742 ADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLKinki 821
Cdd:cd07969     1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPETEEFQTVCKIGTGFSDEFLEELYESLKEHVIPKKPYRVDSSLE---- 76
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568971912  822 yyPDFIVpDPKKaaVWEITGAEFSRSEAHTA--------DGISIRFPRCTRIRDDKDWKSATNLPQLKELYQ 885
Cdd:cd07969    77 --PDVWF-EPKE--VWEVKAADLTLSPVHTAaiglvdeeKGISLRFPRFIRVRDDKKPEDATTSEQIAEMYK 143
DNA_ligase_A_N pfam04675
DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase ...
319-488 9.42e-38

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: 139.25  E-value: 9.42e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   319 REFRKLCAMVAEN-PSYNTKTQIIHDFLQkgSTGDGFHGDVYLTVKLLLPGVIKSVYNLNDKQIVKLFSRIFNCNPDDM- 396
Cdd:pfam04675    3 SLLAELFEKIEATtSSRLEKTAILANFFR--SVIGAGPEDLYPALRLLLPDYDGREYGIGEKLLAKAIAEALGLSKDSIk 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   397 ARDLEQGDVSETIRIFFEQSKSfpPAAKSLLTIQEVDAFLLHLSKLT---KEDEQQQALQDIASRCTANDLKCIIRLIKH 473
Cdd:pfam04675   81 DAYRKAGDLGEVAEEVLSKRST--LFKPSPLTIDEVNELLDKLAAASgkgSQDEKIKILKKLLKRATPEEAKYLIRIILG 158
                          170
                   ....*....|....*
gi 568971912   474 DLKMNSGAKHVLDAL 488
Cdd:pfam04675  159 DLRIGLGEKTVLDAL 173
ligB PRK03180
ATP-dependent DNA ligase; Reviewed
420-885 4.30e-35

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235108 [Multi-domain]  Cd Length: 508  Bit Score: 141.26  E-value: 4.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  420 PPAAKSLLTIQEVDAFLLHLSKLT---KEDEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNA---- 492
Cdd:PRK03180   66 APAAEPTLTVADVDAALSEIAAVAgagSQARRAALLAALFAAATEDEQRFLRRLLTGELRQGALDGVMADAVARAAgvpa 145
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  493 ---YEAFKASRNLQDVVERVLhneqevekdPGRRRAL-RVQASLMTPVQPMLAEACKSIEYAMKKCPNGMFSEIKYDGER 568
Cdd:PRK03180  146 aavRRAAMLAGDLPAVAAAAL---------TGGAAALaRFRLEVGRPVRPMLAQTATSVAEALARLGGPAAVEAKLDGAR 216
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  569 VQVHKKGDHFSYFSRSLKPV---LPHKVAhfkdyIPKAFPgGQSMILDSEVLLIDNNtGKPLPF----GTLGVHKKAAFQ 641
Cdd:PRK03180  217 VQVHRDGDDVRVYTRTLDDItarLPEVVE-----AVRALP-VRSLVLDGEAIALRPD-GRPRPFqvtaSRFGRRVDVAAA 289
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  642 DANVCL--FVFDCIYFNDVSLMDRPLCERRKFLhDNMVEIRNRImfseMKQVTKASDLADMI-NRVIREGLEGLVLKDVK 718
Cdd:PRK03180  290 RATQPLspFFFDALHLDGRDLLDAPLSERLAAL-DALVPAAHRV----PRLVTADPAAAAAFlAAALAAGHEGVMVKSLD 364
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  719 GTYEPGKR--HWLKVKKdylnegamADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARL 796
Cdd:PRK03180  365 APYAAGRRgaGWLKVKP--------VHTLDLVVLAAEWGSGRRTGKLSNLHLGARDPATGGFVMLGKTFKGMTDAMLAWQ 436
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  797 QKELVMVKISKDPSKIPSWlkinkiyyPDFIVpdpkkaavwEITGAEFSRSEAHTAdGISIRFPRCTRIRDDKDWKSATN 876
Cdd:PRK03180  437 TERFLELAVGRDGWTVYVR--------PELVV---------EIAFDGVQRSTRYPG-GVALRFARVLRYRPDKTPAEADT 498

                  ....*....
gi 568971912  877 LPQLKELYQ 885
Cdd:PRK03180  499 IDTVRALLP 507
zf-PARP pfam00645
Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; Poly(ADP-ribose) polymerase is an ...
151-236 2.39e-32

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: 120.50  E-value: 2.39e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   151 DYAKRGTAGCKKCKEKIVKGVCRIGKVVPN-PFSESGGDMKEWYHIKCMFEKLERARATTKKIEDLTELEGWEELEDNEK 229
Cdd:pfam00645    1 EYAKSGRAKCKGCKKKIEKGELRIGKVVDFvPSPFFDGGSKRWYHWGCFTKKQLKNRKETKEIDDADDLDGFDELKDEDQ 80

                   ....*..
gi 568971912   230 EQISQHI 236
Cdd:pfam00645   81 EKIRKAI 87
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
989-1059 2.63e-32

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


Pssm-ID: 465260  Cd Length: 77  Bit Score: 120.17  E-value: 2.63e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568971912   989 VLLDVFTGVRLYLPPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLG------NREKNTDAQLVSSEWIWACIRKR 1059
Cdd:pfam16759    1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVpkdsakEKEESSGAKHVTASWIWECIKKR 77
BRCT_DNA_ligase_III cd18431
BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ...
990-1061 1.82e-28

BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ligase III, or polydeoxyribonucleotide synthase [ATP] 3, functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.


Pssm-ID: 349384 [Multi-domain]  Cd Length: 78  Bit Score: 109.33  E-value: 1.82e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568971912  990 LLDVFTGVRLYLPPSTPD-FKRLKRYFVAFDGDLVQEFDMGSATHVLGNRE---KNTDAQLVSSEWIWACIRKRRL 1061
Cdd:cd18431     1 LPDIFTGVKVYLPGSVEDdYKKLKRYFIAYDGDVVEEYDEEDATHVVVDRDdklGNPSAKVVSPEWLWDCIKKQKL 76
Adenylation_DNA_ligase_LigD_LigC cd07906
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ...
536-732 9.21e-26

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: 105.31  E-value: 9.21e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  536 VQPMLAEACKSIeyamkkcPNG---MFsEIKYDGERVQVHKKGDHFSYFSRSLKPVLPHkvahfkdyipkaFP------- 605
Cdd:cd07906     1 IEPMLATLVDEP-------PDGedwLY-EIKWDGYRALARVDGGRVRLYSRNGLDWTAR------------FPelaeala 60
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  606 --GGQSMILDSEVLLIDNNtGKPlPFGTL----GVHKKAAfQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEI 679
Cdd:cd07906    61 alPVRDAVLDGEIVVLDEG-GRP-DFQALqnrlRLRRRLA-RTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAG 137
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568971912  680 RNRIMFSEmkqvTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRH--WLKVK 732
Cdd:cd07906   138 SPRLRVSE----HFEGGGAALFAAACELGLEGIVAKRADSPYRSGRRSrdWLKIK 188
OBF_DNA_ligase_IV cd07968
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is ...
743-874 1.41e-20

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: 88.77  E-value: 1.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  743 DTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKC------AGGHDDATLARLQKELVMVKISKDPSKIPSWL 816
Cdd:cd07968     2 EDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFysfckvGSGFSDEELDEIRRKLKPHWKPFDKKAPPSSL 81
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568971912  817 KINKIYYPDFIVpDPKKAAVWEITGAEFSRSEAHTAdGISIRFPRCTRIRDDKDWKSA 874
Cdd:cd07968    82 LKFGKEKPDVWI-EPKDSVVLEVKAAEIVPSDSYKT-GYTLRFPRCEKIRYDKDWHDC 137
NHEJ_ligase_lig TIGR02779
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ...
561-875 2.43e-20

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: 92.75  E-value: 2.43e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   561 EIKYDGERVQVHKKGDHFSYFSRSLKPvLPHKVAHfkdyIPKAFP--GGQSMILDSEVLLIDNNtGKPlPFgtlgvhkkA 638
Cdd:TIGR02779   17 EVKYDGYRCLARIEGGKVRLISRNGHD-WTEKFPI----LAAALAalPILPAVLDGEIVVLDES-GRS-DF--------S 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   639 AFQDA-------NVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRiMFSEMKQVTKASDLADMINRVIREGLEG 711
Cdd:TIGR02779   82 ALQNRlragrdrPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGP-LAPDRYSVHFEGDGQALLEAACRLGLEG 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   712 LVLKDVKGTYEPGK-RHWLKVKKDYLNEgamadtadlVVLGAFY-GQGSKGGMMSiFLMGCYDPDsqKWCTVTKCAGGHD 789
Cdd:TIGR02779  161 VVAKRRDSPYRSGRsADWLKLKCRRRQE---------FVIGGYTpPNGSRSGFGA-LLLGVYEGG--GLRYVGRVGTGFS 228
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   790 DATLARLQKEL--VMVKISKDPSKIPS---WLKinkiyyPDFIVpdpkkaavwEITGAEFsrseahTADGIsIRFPRCTR 864
Cdd:TIGR02779  229 EAELATIKERLkpLESKPDKPGAREKRgvhWVK------PELVA---------EVEFAGW------TRDGR-LRQASFVG 286
                          330
                   ....*....|.
gi 568971912   865 IRDDKDWKSAT 875
Cdd:TIGR02779  287 LREDKPASEVT 297
DNA_ligase_A_C pfam04679
ATP dependent DNA ligase C terminal region; This region is found in many but not all ...
759-869 3.35e-17

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: 77.63  E-value: 3.35e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   759 KGGMMSIFLMGCYDPDsqKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLKINKIY-YPDFivpdpkkaaVW 837
Cdd:pfam04679    1 RRGGFGSLLLGVYDDG--RLVYVGKVGTGFTDADLEELRERLKPLERKKPPFAEPPPEARGAVWvEPEL---------VA 69
                           90       100       110
                   ....*....|....*....|....*....|..
gi 568971912   838 EITGAEFSRSEahtadgiSIRFPRCTRIRDDK 869
Cdd:pfam04679   70 EVEFAEWTRSG-------RLRFPRFKGLREDK 94
OBF_DNA_ligase_Arch_LigB cd07972
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ...
743-882 1.20e-16

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: 77.20  E-value: 1.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  743 DTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWCTVTKCAGGHDDATLARLQKELVMVKISKDPSKIpsWLKinkiy 822
Cdd:cd07972     1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEETGELVPVGKVATGLTDEELEELTERLRELIIEKFGPVV--SVK----- 73
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  823 ypdfivpdPKkaAVWEITGAEFSRSEAHTAdGISIRFPRCTRIRDDKDWKSATNLPQLKE 882
Cdd:cd07972    74 --------PE--LVFEVAFEEIQRSPRYKS-GYALRFPRIVRIRDDKDPDEADTLERVEA 122
ligC PRK08224
ATP-dependent DNA ligase; Reviewed
532-776 9.05e-16

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236191 [Multi-domain]  Cd Length: 350  Bit Score: 79.94  E-value: 9.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  532 LMTPVQPMLAEACKSIeyamkkcP--NGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPV---LPHKVAHFKDYIPKAFpg 606
Cdd:PRK08224    5 VMPPVEPMLAKSVDAI-------PpgDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLtryFPELVAALRAELPERC-- 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  607 gqsmILDSEVLLIdnnTGKPLPFGTLG---------VHKKAAFQDAnvcLFV-FDCIYFNDVSLMDRPLCERRKFLHDNM 676
Cdd:PRK08224   76 ----VLDGEIVVA---RDGGLDFEALQqrihpaasrVRKLAEETPA---SFVaFDLLALGDRDLTGRPFAERRAALEAAA 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  677 VEirnrimfSEMKQVTKASDLADMINRVIRE----GLEGLVLKDVKGTYEPGKRHWLKVKKdylnegamADTADLVVLGA 752
Cdd:PRK08224  146 AG-------SGPVHLTPATTDPATARRWFEEfegaGLDGVIAKPLDGPYQPGKRAMFKVKH--------ERTADCVVAGY 210
                         250       260
                  ....*....|....*....|....*
gi 568971912  753 FYGQGSKG-GMMsifLMGCYDPDSQ 776
Cdd:PRK08224  211 RYHKSGPVvGSL---LLGLYDDDGQ 232
Adenylation_DNA_ligase_like cd06846
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ...
556-733 8.59e-15

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: 73.61  E-value: 8.59e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  556 NGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPVlPHKVAHFKDYIP-KAFPGGqsmILDSEvLLIDNNTgkplpfgtlgv 634
Cdd:cd06846    19 DEYYVQEKYDGKRALIVALNGGVFAISRTGLEV-PLPSILIPGRELlTLKPGF---ILDGE-LVVENRE----------- 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  635 hkkaaFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFsEMKQVTKA----SDLADMINRVIREGLE 710
Cdd:cd06846    83 -----VANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPV-KLVPLENApsydETLDDLLEKLKKKGKE 156
                         170       180
                  ....*....|....*....|....*.
gi 568971912  711 GLVLKDVKGTYE--PGK-RHWLKVKK 733
Cdd:cd06846   157 GLVFKHPDAPYKgrPGSsGNQLKLKP 182
Adenylation_DNA_ligase_LigC cd07905
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ...
536-732 4.85e-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: 71.89  E-value: 4.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  536 VQPMLAEACKSIEYamkkcPNGMFSEIKYDGERVQVHKKGDHFSYFSRSLKPV---LPHKVAHFKDYIPKAFpggqsmIL 612
Cdd:cd07905     1 VEPMLARAVDALPE-----PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLtryFPELVAAARALLPPGC------VL 69
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  613 DSEVLLIDnntGKPLPFGTL---------GVHKKAAFQDANvcLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRI 683
Cdd:cd07905    70 DGELVVWR---GGRLDFDALqqrihpaasRVRRLAEETPAS--FVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPL 144
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568971912  684 mfsemkQVTKA-SDLAdminrVIRE--------GLEGLVLKDVKGTYEPGKRHWLKVK 732
Cdd:cd07905   145 ------HLSPAtTDRA-----EAREwleefegaGLEGVVAKRLDGPYRPGERAMLKVK 191
Adenylation_DNA_ligase_Fungal cd08039
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ...
558-735 2.09e-13

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: 70.89  E-value: 2.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  558 MFSEIKYDGERVQVH----KKGDHFSYFSRSLKPVLPHKVA-HfkDYIPKAFPGGQS-------MILDSEVLLIDNNTGK 625
Cdd:cd08039    24 MWVETKYDGEYCQIHidlsKDSSPIRIFSKSGKDSTADRAGvH--SIIRKALRIGKPgckfsknCILEGEMVVWSDRQGK 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  626 PLPFGTLGVHKK--AAF----QDA------NVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRNRIMFSEMKQV-- 691
Cdd:cd08039   102 IDPFHKIRKHVErsGSFigtdNDSppheyeHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGYAGLSERFPIdf 181
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568971912  692 ---TKASDLADMINRVIREGLEGLVLKDVKGTYEP-------GKRHWLKVKKDY 735
Cdd:cd08039   182 srsSGYERLRQIFARAIAERWEGLVLKGDEEPYFDlfleqgsFSGCWIKLKKDY 235
PRK09632 PRK09632
ATP-dependent DNA ligase; Reviewed
518-870 2.26e-13

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236599 [Multi-domain]  Cd Length: 764  Bit Score: 74.65  E-value: 2.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  518 KD-PGRRRAlrvQASLMTPVQPMLA-----EACKSIEYAMkkcpngmfsEIKYDGERVQVHKKGDHFSYFSRSLKPVLPh 591
Cdd:PRK09632  445 KDqAPGASP---KAEEADDLAPMLAtagtvAGLKASQWAF---------EGKWDGYRLLAEADHGALRLRSRSGRDVTA- 511
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  592 kvahfkdyipkAFP---------GGQSMILDSEVLLIDNnTGKPlPFGTLGVHKKaafqDANVCLFVFDCIYFNDVSLMD 662
Cdd:PRK09632  512 -----------EYPelaalaedlADHHVVLDGEIVALDD-SGVP-SFGLLQNRGR----DTRVEFWAFDLLYLDGRSLLR 574
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  663 RPLCERRKFLHDnMVEIRNRIMFSEMkqvtKASDLADMINRVIREGLEGLVLKDVKGTYEPGKR--HWLKVKkdylnega 740
Cdd:PRK09632  575 KPYRDRRKLLEA-LAPSGGSLTVPPL----LPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRssSWIKDK-------- 641
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  741 MADTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKWctVTKCAGGHDDATLARLQKELVMVKISKDPSKIPswlkink 820
Cdd:PRK09632  642 HWRTQEVVIGGWRPGEGGRSSGIGSLLLGIPDPGGLRY--VGRVGTGFTERELASLKETLAPLHRDTSPFDAD------- 712
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568971912  821 iyypdfiVPDP-KKAAVW---EITGaEFSRSEaHTADGIsIRFPRCTRIRDDKD 870
Cdd:PRK09632  713 -------LPAAdAKGATWvrpELVG-EVRYSE-WTPDGR-LRQPSWRGLRPDKK 756
PRK09247 PRK09247
ATP-dependent DNA ligase; Validated
561-883 8.06e-13

ATP-dependent DNA ligase; Validated


Pssm-ID: 236428 [Multi-domain]  Cd Length: 539  Bit Score: 72.18  E-value: 8.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  561 EIKYDGERVQVHKKGDHFSYFSRSLKPVlphkVAHFKDYIPKA--FPGGqsMILDSEVLLIDNNTGKPLPFGTL------ 632
Cdd:PRK09247  230 EWKWDGIRVQLVRRGGEVRLWSRGEELI----TERFPELAEAAeaLPDG--TVLDGELLVWRPEDGRPQPFADLqqrigr 303
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  633 -GVHKKaAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLhDNMVEI--RNRIMFSEMKQVTKASDLADMINRVIREGL 709
Cdd:PRK09247  304 kTVGKK-LLADYPAFLRAYDLLEDGGEDLRALPLAERRARL-EALIARlpDPRLDLSPLVPFSDWDELAALRAAARERGV 381
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  710 EGLVLKDVKGTYEPGKR--HWLKVKKDYLnegamadTADLVVLGAFYGQGSKGGMMSIFLMGCYD--PDSQKWCTVTKCA 785
Cdd:PRK09247  382 EGLMLKRRDSPYLVGRKkgPWWKWKRDPL-------TIDAVLMYAQRGHGRRASLYTDYTFGVWDgpEGGRQLVPFAKAY 454
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  786 GGHDDATLARLQKelvmvkiskdpskipsWLKINKI--YYPdfiVPDPKKAAVWEItGAE-FSRSEAHTAdGISIRFPRC 862
Cdd:PRK09247  455 SGLTDEEIKQLDR----------------WVRKNTVerFGP---VRSVRPELVFEI-AFEgIQRSKRHKS-GIAVRFPRI 513
                         330       340
                  ....*....|....*....|.
gi 568971912  863 TRIRDDKDWKSATNLPQLKEL 883
Cdd:PRK09247  514 LRWRWDKPAREADTLETLQAL 534
Adenylation_DNA_ligase_Bac1 cd07897
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ...
555-734 5.60e-12

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: 66.04  E-value: 5.60e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  555 PNGMFSEIKYDGERVQVHKKGDHFSYFSRS--LkpvlphkVAH-FKDYIPKA--FPGGqsMILDSEVLLIDNntGKPLPF 629
Cdd:cd07897    23 PSDWQAEWKWDGIRGQLIRRGGEVFLWSRGeeL-------ITGsFPELLAAAeaLPDG--TVLDGELLVWRD--GRPLPF 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  630 GTL-------GVHKKaAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLhDNMVEI--RNRIMFSEMKQVTKASDLADM 700
Cdd:cd07897    92 NDLqqrlgrkTVGKK-LLAEAPAAFRAYDLLELNGEDLRALPLRERRARL-EALLARlpPPRLDLSPLIAFADWEELAAL 169
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 568971912  701 INRVIREGLEGLVLKDVKGTYEPGKR--HWLKVKKD 734
Cdd:cd07897   170 RAQSRERGAEGLMLKRRDSPYLVGRKkgDWWKWKID 205
NHEJ_ligase_prk TIGR02776
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ...
600-898 3.71e-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: 66.96  E-value: 3.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   600 IPKAFPG--GQSMILDSEVLLIDNNtgkplpfgtlGVHKKAAFQDA-------NVCLFVFDCIYFNDVSLMDRPLCERRK 670
Cdd:TIGR02776   14 IVKALALlkLLPAWIDGEIVVLDER----------GRADFAALQNAlsagasrPLTYYAFDLLFLSGEDLRDLPLEERKK 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   671 FLHDNMVEIRNR-IMFSEmkQVtkASDLADMINRVIREGLEGLVLKDVKGTYEPGkRH--WLKVKKDYLNEgamadtadl 747
Cdd:TIGR02776   84 RLKQLLKAQDEPaIRYSD--HF--ESDGDALLESACRLGLEGVVSKRLDSPYRSG-RSkdWLKLKCRRRQE--------- 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912   748 VVLGAFYGQGSKGGMmsiFLMGCYDPDSQKWctVTKCAGGHDDATLARLQKELVMVKISKDPSKIPSWLKINKIYY--PD 825
Cdd:TIGR02776  150 FVITGYTPPNRRFGA---LLVGVYEGGQLVY--AGKVGTGFGADTLKTLLARLKALGAKASPFSGPAGAKTRGVHWvrPS 224
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568971912   826 FivpdpkkaaVWEITGAEFsrseahTADGIsIRFPRCTRIRDDKDWKSAT-NLPQLKelyQLSKDKADFAVVAG 898
Cdd:TIGR02776  225 L---------VAEVEYAGI------TRDGI-LREASFKGLREDKPAEEVTlETPQRH---AAAKRKRSAALVAG 279
ligD PRK05972
ATP-dependent DNA ligase; Reviewed
561-869 9.95e-10

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 235658 [Multi-domain]  Cd Length: 860  Bit Score: 62.62  E-value: 9.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  561 EIKYDGERVQVHKKGDHFSYFSR-----SLKpvLPHKVAHFKDYipkafpGGQSMILDSEVLLIDNNtGKPlPFGTLgvh 635
Cdd:PRK05972  254 EIKFDGYRILARIEGGEVRLFTRngldwTAK--LPALAKAAAAL------GLPDAWLDGEIVVLDED-GVP-DFQAL--- 320
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  636 kKAAF---QDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIRN-RIMFSEmkqvTKASDLADMINRVIREGLEG 711
Cdd:PRK05972  321 -QNAFdegRTEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSdRIRFSE----HFDAGGDAVLASACRLGLEG 395
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  712 LVLKDVKGTYEPGKRH-WLKVKKDYLNEgamadtadlVVLGAFYG-QGSKGGMMSIfLMGCYDPDSQKWctVTKCAGGHD 789
Cdd:PRK05972  396 VIGKRADSPYVSGRSEdWIKLKCRARQE---------FVIGGYTDpKGSRSGFGSL-LLGVHDDDHLRY--AGRVGTGFG 463
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  790 DATLARLQKELVMVKISKDP-SKIPS--------WLKinkiyypdfivpdPKKAAvwEITGAEFsrseahTADGIsIRFP 860
Cdd:PRK05972  464 AATLKTLLPRLKALATDKSPfAGKPAprkargvhWVK-------------PELVA--EVEFAGW------TRDGI-VRQA 521

                  ....*....
gi 568971912  861 RCTRIRDDK 869
Cdd:PRK05972  522 VFKGLREDK 530
OBF_DNA_ligase_family cd08040
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ...
743-866 3.64e-08

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


Pssm-ID: 153442  Cd Length: 108  Bit Score: 52.64  E-value: 3.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  743 DTADLVVLGAFYGQGSKGGMMSIFLMGCYDPDSQKwcTVTKCAGGHDDATLARLQKELVMVKISKDPskiPSWLKINKIY 822
Cdd:cd08040     1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGEDGLQ--AVFSVGTGFSADERRDLWQNLEPLVTSFDD---HPVWNVGKDL 75
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 568971912  823 YPDFIVPdpkkAAVWEITGAEFSrseahtaDGISIRFPRCTRIR 866
Cdd:cd08040    76 SFVPLYP----GKVVEVKYFEMG-------SKDCLRFPVFIGIR 108
ligB PRK07636
ATP-dependent DNA ligase; Reviewed
561-731 1.41e-07

ATP-dependent DNA ligase; Reviewed


Pssm-ID: 236070 [Multi-domain]  Cd Length: 275  Bit Score: 53.99  E-value: 1.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  561 EIKYDGERVQVHKKGDHFSYFSRSLKPVlphkVAHFKDYIPKAFPGGqsMILDSEVLLIdNNTGKPlPFGTL--GVHKKA 638
Cdd:PRK07636   23 EPKFDGIRLIASKNNGLIRLYTRHNNEV----TAKFPELLNLDIPDG--TVLDGELIVL-GSTGAP-DFEAVmeRFQSKK 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  639 AFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFL------HDNMVEirnrIMFSEMKqvtkasdlADMINRVIRE-GLEG 711
Cdd:PRK07636   95 STKIHPVVFCVFDVLYINGVSLTALPLSERKEILaslllpHPNVKI----IEGIEGH--------GTAYFELVEErELEG 162
                         170       180
                  ....*....|....*....|..
gi 568971912  712 LVLKDVKGTYEPGKR--HWLKV 731
Cdd:PRK07636  163 IVIKKANSPYEINKRsdNWLKV 184
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
150-232 4.14e-07

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 54.41  E-value: 4.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  150 VDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPfsesGGDMKEWYHIKCMFEKLERArattkkieDLTELEGWEELEDNEK 229
Cdd:PLN03123  109 IEVAKTSRATCRRCSEKILKGEVRISSKPEGQ----GYKGLAWHHAKCFLEMSPST--------PVEKLSGWDTLSDSDQ 176

                  ...
gi 568971912  230 EQI 232
Cdd:PLN03123  177 EAV 179
PLN03123 PLN03123
poly [ADP-ribose] polymerase; Provisional
151-236 4.98e-07

poly [ADP-ribose] polymerase; Provisional


Pssm-ID: 215590 [Multi-domain]  Cd Length: 981  Bit Score: 54.03  E-value: 4.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  151 DYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPfsESGGDMKEWYHIKCMFEKleraratTKKIEDLTELEGWEELEDNEKE 230
Cdd:PLN03123   11 EYAKSSRSSCKTCKSPIDKDELRLGKMVQST--QFDGFMPMWNHASCILKK-------KNQIKSIDDVEGIDSLRWEDQQ 81

                  ....*.
gi 568971912  231 QISQHI 236
Cdd:PLN03123   82 KIRKYV 87
ligD PRK09633
DNA ligase D;
533-732 1.07e-06

DNA ligase D;


Pssm-ID: 182006 [Multi-domain]  Cd Length: 610  Bit Score: 52.73  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  533 MTPVQPMLAEACksieyamkkcPNGM--FSEIKYDGERVQV--HKKGDHF-SYFSRSLKPVLPHKV-------AHFKDYI 600
Cdd:PRK09633    1 MKPMQPTLTTSI----------PIGDewRYEVKYDGFRCLLiiDETGITLiSRNGRELTNTFPEIIefcesnfEHLKEEL 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  601 PkafpggqsMILDSE-VLLIDNNTGKPLPFGTLGVHKK--AAFQDAN---VCLFVFDCIYFNDVSLMDRPLCERRKFLHD 674
Cdd:PRK09633   71 P--------LTLDGElVCLVNPYRSDFEHVQQRGRLKNteVIAKSANarpCQLLAFDLLELKGESLTSLPYLERKKQLDK 142
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568971912  675 NMVEIR----NRIMFSEMKQVTKA-SDLADMINRVIREGLEGLVLKDVKGTYEPGKRH--WLKVK 732
Cdd:PRK09633  143 LMKAAKlpasPDPYAKARIQYIPStTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSkdWLKIK 207
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
992-1062 2.88e-06

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 46.20  E-value: 2.88e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568971912   992 DVFTGVRLYL-PPSTPDFKRLKRYFVAFDGDLVQEFDMGsATHVLGNREK------NTDAQLVSSEWIWACIRKRRLI 1062
Cdd:pfam16589    3 NLFEPLRFYInAIPSPSRSKLKRLIEANGGTVVDNINPA-VYIVIAPYNKtdklaeNTKLGVVSPQWIFDCVKKGKLL 79
BRCT_XRCC1_rpt2 cd17707
Second (C-terminal) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and ...
990-1065 5.81e-06

Second (C-terminal) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar proteins; XRCC1 is a DNA repair protein that corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. It forms homodimers and interacts with polynucleotide kinase (PNK), DNA polymerase-beta (POLB), DNA ligase III (LIG3), APTX, APLF, and APEX1. XRCC1 contains an N-terminal XRCC1-specific domain and two BRCT domains. This model corresponds to the second BRCT domain.


Pssm-ID: 349340  Cd Length: 94  Bit Score: 45.72  E-value: 5.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  990 LLDVFTGVRLYLPPSTPD--FKRLKRYFVAFDGdLVQEFDMGSATHVLGN----------REKNTDAQLVSSEWIWACIR 1057
Cdd:cd17707     2 LPDFFSGKHFFLYGDFPAdeRRLLKRYITAFNG-EVEDYMSDKVTFVVTNqewddnfdeaLAENPSLAFVRPRWIYACHE 80

                  ....*...
gi 568971912 1058 KRRLIaPC 1065
Cdd:cd17707    81 KQKLL-PC 87
BRCT smart00292
breast cancer carboxy-terminal domain;
992-1056 1.67e-05

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 43.90  E-value: 1.67e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568971912    992 DVFTGVRLYL--PPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLGNRE----------KNTDAQLVSSEWIWACI 1056
Cdd:smart00292    2 KLFKGKTFYItgSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPeggklellkaIALGIPIVKEEWLLDCL 78
PHA00454 PHA00454
ATP-dependent DNA ligase
545-755 1.87e-05

ATP-dependent DNA ligase


Pssm-ID: 222798 [Multi-domain]  Cd Length: 315  Bit Score: 48.11  E-value: 1.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  545 KSIEYAMKKcpNG-MFSEIKYDGER--VQVHKKGDHFsYFSRSLK--PVLPH------KVAHFKDYIPKAFPGGqsMILD 613
Cdd:PHA00454   17 SAIEKALEK--AGyLIADVKYDGVRgnIVVDNTADHG-WLSREGKtiPALEHlngfdrRWAKLLNDDRCIFPDG--FMLD 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  614 SEVLL--IDNNTGKplpfGTLGVHKKAAFQDANVCL--FVFDCIYFNDV---SLMDRPLC---ERRKFLHDNMVEIRNRI 683
Cdd:PHA00454   92 GELMVkgVDFNTGS----GLLRRKWKVLFELHLKKLhvVVYDVTPLDVLesgEDYDVMSLlmyEHVRAMVPLLMEYFPEI 167
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568971912  684 MF--SEMKQVTKASDLADMINRVIREGLEGLVLKDVKGTYEPGKRH-WLKVKKDylnegamaDTADLVVLGAFYG 755
Cdd:PHA00454  168 DWflSESYEVYDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSgWWKMKPE--------CEADGTIVGVVWG 234
Adenylation_kDNA_ligase_like cd07896
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ...
538-733 2.86e-05

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: 45.63  E-value: 2.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  538 PMLAEacksiEYAMKKCPNGMF-SEiKYDGERVQVHKKgdhfSYFSRSLKPVlphkvaHFKDYIPKAFPggqSMILDSEv 616
Cdd:cd07896     3 LLLAK-----TYDEGEDISGYLvSE-KLDGVRAYWDGK----QLLSRSGKPI------AAPAWFTAGLP---PFPLDGE- 62
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  617 LLIDNNTgkplpF----GTLGVHKKAAFQDANVCLFVFDCIYfndvslMDRPLCERRKFLHDNMVEIRN-RIMFSEMKQV 691
Cdd:cd07896    63 LWIGRGQ-----FeqtsSIVRSKKPDDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNpHIKIVPQIPV 131
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 568971912  692 TKASDLADMINRVIREGLEGLVLKDVKGTYEPGK-RHWLKVKK 733
Cdd:cd07896   132 KSNEALDQYLDEVVAAGGEGLMLRRPDAPYETGRsDNLLKLKP 174
BRCT_polymerase_lambda cd17715
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
994-1062 9.73e-04

BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.


Pssm-ID: 349347  Cd Length: 80  Bit Score: 39.01  E-value: 9.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568971912  994 FTGVRLYLPPS---TPDFKRLKRYFVAFDGDLVQEFDMGsATHVL---GNREK------NTDAQLVSSEWIWACIRKRRL 1061
Cdd:cd17715     1 FEGLTIHLVRTgigRARAELFQRYIVQYGGQIVEDFGEG-VTHVVvddGMDAErkvdrdPPGAQLVKSGWLSACIQEKRL 79

                  .
gi 568971912 1062 I 1062
Cdd:cd17715    80 V 80
 
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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