|
Name |
Accession |
Description |
Interval |
E-value |
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
1-660 |
0e+00 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 1122.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPML 80
Cdd:COG0272 3 PEEAKERIEELREELRRHNYRYYVLDAPEISDAEYDALLRELQALEAEHPELITPDSPTQRVGGAPLEGFAKVRHAVPML 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 81 SLGNAFNEDDLRKFDQRIREQIGN--VEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE 158
Cdd:COG0272 83 SLDNAFSEEELRDFDRRVRKFLGDepVEYVCELKIDGLAISLRYENGRLVRAATRGDGTVGEDVTANVRTIRSIPLRLKG 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 159 ---PLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEA 235
Cdd:COG0272 163 ddvPEVLEVRGEVYMPKADFEALNEEREEAGEKPFANPRNAAAGSLRQLDPKITAKRPLDFFAYGLGEVEGLLPDTQSEA 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 236 LDELDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVT 315
Cdd:COG0272 243 LELLKEWGFPVNPERRVCKSIEEVLAYIEEWEEKRHSLPYEIDGVVIKVNDLALQERLGFTSRAPRWAIAYKFPAEEATT 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 316 KLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTY 395
Cdd:COG0272 323 KLLDIEVQVGRTGALTPVARLEPVFVAGVTVSRATLHNEDEIERKDVRIGDTVVVRKAGDVIPEVVGVVLEKRPGDEKPF 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 396 HMPTHCPSCGHELVRIEGEVALRCINPK-CQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDL 474
Cdd:COG0272 403 VMPTHCPVCGSPLVREEGEAALRCTNGLsCPAQLKERLKHFASRKAMDIEGLGEKLIEQLVDAGLVKDPADLYRLTKEDL 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 475 LPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVT 554
Cdd:COG0272 483 LGLERMGEKSAQNLLAAIEKSKKTPLARFLFALGIRHVGETTAKLLARHFGSLDALMAASEEELAAVDGIGPVVAESIVE 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 555 YLENEDIRALIQKLKYKHVNMIYKGIKTSdiEGHPeFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIA 634
Cdd:COG0272 563 FFAEPHNRELIERLRAAGVNMEEEEAEAA--ADSP-LAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVA 639
|
650 660
....*....|....*....|....*.
gi 612673055 635 GEDAGSKLTKAQSLGIEIWTEQQFVD 660
Cdd:COG0272 640 GENAGSKLDKAEELGVPILDEAEFLE 665
|
|
| ligA |
PRK07956 |
NAD-dependent DNA ligase LigA; Validated |
1-658 |
0e+00 |
|
NAD-dependent DNA ligase LigA; Validated
Pssm-ID: 236137 [Multi-domain] Cd Length: 665 Bit Score: 1084.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPML 80
Cdd:PRK07956 2 MEEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAPLDGFEKVRHLVPML 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 81 SLGNAFNEDDLRKFDQRIREQIG--NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKM-- 156
Cdd:PRK07956 82 SLDNAFSEEELRAFDKRVRKRLPdpPLTYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLhg 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 157 KEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTD-FNARSQSEA 235
Cdd:PRK07956 162 NEPERLEVRGEVFMPKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGgELPDSQSEA 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 236 LDELDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVT 315
Cdd:PRK07956 242 LEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAEEATT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 316 KLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTY 395
Cdd:PRK07956 322 KLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 396 HMPTHCPSCGHELVRIEGEVALRCINPK-CQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDL 474
Cdd:PRK07956 402 VMPTHCPVCGSELVRVEGEAVLRCTNGLsCPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDL 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 475 LPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVT 554
Cdd:PRK07956 482 LGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVE 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 555 YLENEDIRALIQKLKYKHVNMIYKGIKTSdieghpeFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIA 634
Cdd:PRK07956 562 FFAVEENRELIDELLEAGVNMEYKGEEVD-------LAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVA 634
|
650 660
....*....|....*....|....
gi 612673055 635 GEDAGSKLTKAQSLGIEIWTEQQF 658
Cdd:PRK07956 635 GEAAGSKLAKAQELGIEVLDEEEF 658
|
|
| dnlj |
TIGR00575 |
DNA ligase, NAD-dependent; All proteins in this family with known functions are NAD-dependent ... |
11-658 |
0e+00 |
|
DNA ligase, NAD-dependent; All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273148 [Multi-domain] Cd Length: 652 Bit Score: 910.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 11 LHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDD 90
Cdd:TIGR00575 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRFPKVRHSTPMLSLDNAFDEDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 91 LRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE---PLNVEVRG 166
Cdd:TIGR00575 81 LAAFIKRIRRQLGlKVEYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGdnpPERLEVRG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 167 EAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTT 246
Cdd:TIGR00575 161 EVFMPKEDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELPDATQYEALAWLKKWGFPV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 247 NKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIELSIGR 326
Cdd:TIGR00575 241 SPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEEAQTKLLDVVVQVGR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 327 TGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCPSCGH 406
Cdd:TIGR00575 321 TGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGS 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 407 ELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKKVD 486
Cdd:TIGR00575 401 PLVKIEEEAVIRCPNLNCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQ 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 487 NLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRALIQ 566
Cdd:TIGR00575 481 NLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNNRQLIK 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 567 KLKYKHVNMIYKGIKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAGSKLTKAQ 646
Cdd:TIGR00575 561 KLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQ 640
|
650
....*....|..
gi 612673055 647 SLGIEIWTEQQF 658
Cdd:TIGR00575 641 ELGIPIINEEEL 652
|
|
| LIGANc |
smart00532 |
Ligase N family; |
7-440 |
0e+00 |
|
Ligase N family;
Pssm-ID: 214709 [Multi-domain] Cd Length: 441 Bit Score: 686.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAF 86
Cdd:smart00532 4 EISELRKLLNQHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKPLEGFNKVRHPVPMLSLDNAF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 87 NEDDLRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPL--NVE 163
Cdd:smart00532 84 DEDELRAFDERIEKALGsPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVpeRLE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 164 VRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTD-FNARSQSEALDELDKL 242
Cdd:smart00532 164 VRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEElFLPKTQSEALKWLKEL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 243 GFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIEL 322
Cdd:smart00532 244 GFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEEAETKLLDIIV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 323 SIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCP 402
Cdd:smart00532 324 QVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHCP 403
|
410 420 430
....*....|....*....|....*....|....*...
gi 612673055 403 SCGHELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQA 440
Cdd:smart00532 404 SCGSELVREEGEVDIRCPNPLCPAQLIERIIHFASRKA 441
|
|
| LIGANc |
cd00114 |
NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining ... |
6-310 |
6.29e-170 |
|
NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Pssm-ID: 238062 [Multi-domain] Cd Length: 307 Bit Score: 487.48 E-value: 6.29e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 6 SRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNA 85
Cdd:cd00114 1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTPLSGFKKVRHPVPMLSLDNA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 86 FNEDDLRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE-PLNVE 163
Cdd:cd00114 81 FDEEELRAFDERIKRFLGeEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLAGaPETLE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 164 VRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLG 243
Cdd:cd00114 161 VRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEALAFLKEWG 240
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 612673055 244 FTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPA 310
Cdd:cd00114 241 FPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA 307
|
|
| DNA_ligase_aden |
pfam01653 |
NAD-dependent DNA ligase adenylation domain; DNA ligases catalyze the crucial step of joining ... |
7-311 |
3.19e-163 |
|
NAD-dependent DNA ligase adenylation domain; DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism.
Pssm-ID: 396292 [Multi-domain] Cd Length: 318 Bit Score: 471.06 E-value: 3.19e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAF 86
Cdd:pfam01653 6 QLEELRELIRKYDYEYYVLDNPSVPDAEYDRLYRELKALEEKHPELITPDSPTQRVGAVPLADFNKVRHLTPMLSLDNAF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 87 NEDDLRKFDQRIREQIGN---VEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE---PL 160
Cdd:pfam01653 86 NLDELQAFIERIRRALGNkekVEYVVEPKIDGLSISLLYENGLLVRAATRGDGTTGEDVTANVKTIRNIPLKLKGdnpPE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 161 NVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSV--NDFTDFNARSQSEALDE 238
Cdd:pfam01653 166 RLEVRGEVFMPKEDFEALNEERLEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLglLEGHELGFDTQYQALAF 245
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612673055 239 LDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAE 311
Cdd:pfam01653 246 LKSLGFPVSPLLALCDGIEEVLAYYADWEKKRDSLPYEIDGVVVKVDELALQRELGFTAKAPRWAIAYKFPAE 318
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
1-660 |
0e+00 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 1122.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPML 80
Cdd:COG0272 3 PEEAKERIEELREELRRHNYRYYVLDAPEISDAEYDALLRELQALEAEHPELITPDSPTQRVGGAPLEGFAKVRHAVPML 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 81 SLGNAFNEDDLRKFDQRIREQIGN--VEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE 158
Cdd:COG0272 83 SLDNAFSEEELRDFDRRVRKFLGDepVEYVCELKIDGLAISLRYENGRLVRAATRGDGTVGEDVTANVRTIRSIPLRLKG 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 159 ---PLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEA 235
Cdd:COG0272 163 ddvPEVLEVRGEVYMPKADFEALNEEREEAGEKPFANPRNAAAGSLRQLDPKITAKRPLDFFAYGLGEVEGLLPDTQSEA 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 236 LDELDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVT 315
Cdd:COG0272 243 LELLKEWGFPVNPERRVCKSIEEVLAYIEEWEEKRHSLPYEIDGVVIKVNDLALQERLGFTSRAPRWAIAYKFPAEEATT 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 316 KLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTY 395
Cdd:COG0272 323 KLLDIEVQVGRTGALTPVARLEPVFVAGVTVSRATLHNEDEIERKDVRIGDTVVVRKAGDVIPEVVGVVLEKRPGDEKPF 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 396 HMPTHCPSCGHELVRIEGEVALRCINPK-CQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDL 474
Cdd:COG0272 403 VMPTHCPVCGSPLVREEGEAALRCTNGLsCPAQLKERLKHFASRKAMDIEGLGEKLIEQLVDAGLVKDPADLYRLTKEDL 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 475 LPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVT 554
Cdd:COG0272 483 LGLERMGEKSAQNLLAAIEKSKKTPLARFLFALGIRHVGETTAKLLARHFGSLDALMAASEEELAAVDGIGPVVAESIVE 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 555 YLENEDIRALIQKLKYKHVNMIYKGIKTSdiEGHPeFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIA 634
Cdd:COG0272 563 FFAEPHNRELIERLRAAGVNMEEEEAEAA--ADSP-LAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVA 639
|
650 660
....*....|....*....|....*.
gi 612673055 635 GEDAGSKLTKAQSLGIEIWTEQQFVD 660
Cdd:COG0272 640 GENAGSKLDKAEELGVPILDEAEFLE 665
|
|
| ligA |
PRK07956 |
NAD-dependent DNA ligase LigA; Validated |
1-658 |
0e+00 |
|
NAD-dependent DNA ligase LigA; Validated
Pssm-ID: 236137 [Multi-domain] Cd Length: 665 Bit Score: 1084.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 1 MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPML 80
Cdd:PRK07956 2 MEEAKKRIEELREELNHHAYAYYVLDAPSISDAEYDRLYRELVALEAEHPELITPDSPTQRVGGAPLDGFEKVRHLVPML 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 81 SLGNAFNEDDLRKFDQRIREQIG--NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKM-- 156
Cdd:PRK07956 82 SLDNAFSEEELRAFDKRVRKRLPdpPLTYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLhg 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 157 KEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTD-FNARSQSEA 235
Cdd:PRK07956 162 NEPERLEVRGEVFMPKADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEGgELPDSQSEA 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 236 LDELDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVT 315
Cdd:PRK07956 242 LEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAEEATT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 316 KLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTY 395
Cdd:PRK07956 322 KLLDIEVQVGRTGAVTPVARLEPVEVAGVTVSRATLHNADEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 396 HMPTHCPSCGHELVRIEGEVALRCINPK-CQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDL 474
Cdd:PRK07956 402 VMPTHCPVCGSELVRVEGEAVLRCTNGLsCPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDL 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 475 LPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVT 554
Cdd:PRK07956 482 LGLEGFGEKSAQNLLDAIEKSKETSLARFLYALGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVE 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 555 YLENEDIRALIQKLKYKHVNMIYKGIKTSdieghpeFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIA 634
Cdd:PRK07956 562 FFAVEENRELIDELLEAGVNMEYKGEEVD-------LAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVA 634
|
650 660
....*....|....*....|....
gi 612673055 635 GEDAGSKLTKAQSLGIEIWTEQQF 658
Cdd:PRK07956 635 GEAAGSKLAKAQELGIEVLDEEEF 658
|
|
| dnlj |
TIGR00575 |
DNA ligase, NAD-dependent; All proteins in this family with known functions are NAD-dependent ... |
11-658 |
0e+00 |
|
DNA ligase, NAD-dependent; All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273148 [Multi-domain] Cd Length: 652 Bit Score: 910.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 11 LHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDD 90
Cdd:TIGR00575 1 LRKLIRHHDYRYYVLDEPSISDAEYDRLYRELQELEEKHPELITPDSPTQRVGAAPLSRFPKVRHSTPMLSLDNAFDEDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 91 LRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE---PLNVEVRG 166
Cdd:TIGR00575 81 LAAFIKRIRRQLGlKVEYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGdnpPERLEVRG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 167 EAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTT 246
Cdd:TIGR00575 161 EVFMPKEDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGEGLELPDATQYEALAWLKKWGFPV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 247 NKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIELSIGR 326
Cdd:TIGR00575 241 SPHIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAEEAQTKLLDVVVQVGR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 327 TGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCPSCGH 406
Cdd:TIGR00575 321 TGAITPVAKLEPVFVAGTTVSRATLHNEDEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRFPTHCPSCGS 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 407 ELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKKVD 486
Cdd:TIGR00575 401 PLVKIEEEAVIRCPNLNCPAQRVERIKHFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQ 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 487 NLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRALIQ 566
Cdd:TIGR00575 481 NLLNAIEKSKEKPLARLLFALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNNRQLIK 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 567 KLKYKHVNMIYKGIKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAGSKLTKAQ 646
Cdd:TIGR00575 561 KLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQ 640
|
650
....*....|..
gi 612673055 647 SLGIEIWTEQQF 658
Cdd:TIGR00575 641 ELGIPIINEEEL 652
|
|
| LIGANc |
smart00532 |
Ligase N family; |
7-440 |
0e+00 |
|
Ligase N family;
Pssm-ID: 214709 [Multi-domain] Cd Length: 441 Bit Score: 686.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAF 86
Cdd:smart00532 4 EISELRKLLNQHDYRYYVLDAPIISDAEYDRLMRELKELEEKHPELKTPDSPTQRVGGKPLEGFNKVRHPVPMLSLDNAF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 87 NEDDLRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPL--NVE 163
Cdd:smart00532 84 DEDELRAFDERIEKALGsPFAYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLSGDVpeRLE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 164 VRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTD-FNARSQSEALDELDKL 242
Cdd:smart00532 164 VRGEVFMPKEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEElFLPKTQSEALKWLKEL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 243 GFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIEL 322
Cdd:smart00532 244 GFPVSPHTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAEEAETKLLDIIV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 323 SIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCP 402
Cdd:smart00532 324 QVGRTGKITPVAELEPVFLAGSTVSRATLHNEDEIEEKDIRIGDTVVVRKAGDVIPKVVGVVKEKRPGDEREIEMPTHCP 403
|
410 420 430
....*....|....*....|....*....|....*...
gi 612673055 403 SCGHELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQA 440
Cdd:smart00532 404 SCGSELVREEGEVDIRCPNPLCPAQLIERIIHFASRKA 441
|
|
| ligA |
PRK14351 |
NAD-dependent DNA ligase LigA; Provisional |
7-658 |
0e+00 |
|
NAD-dependent DNA ligase LigA; Provisional
Pssm-ID: 184640 [Multi-domain] Cd Length: 689 Bit Score: 576.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHpEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAF 86
Cdd:PRK14351 35 QAEQLREAIREHDHRYYVEADPVIADRAYDALFARLQALEDAF-DLDTENSPTRRVGGEPLDELETVEHVAPMLSIDQSG 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 87 NEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMK--EPLNVEV 164
Cdd:PRK14351 114 EADDVREFDERVRREVGAVEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLRgdYPDFLAV 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 165 RGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNArSQSEALDELDKLGF 244
Cdd:PRK14351 194 RGEVYMPKDAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASELFD-SHWEELERFPEWGL 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 245 TTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIELSI 324
Cdd:PRK14351 273 RVTDRTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFPARAEETTIRDIVVQV 352
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 325 GRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIpERRPEDavTYHMPTHCPSC 404
Cdd:PRK14351 353 GRTGRLTPVALLDPVDVGGVTVSRASLHNPAEIEELGVNVGDRVRVKRAGDVIPYVEEVV-EKDSEG--TFEFPDTCPVC 429
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 405 GHELVRiEGEVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKK 484
Cdd:PRK14351 430 DSAVER-DGPLAFCTGGLACPAQLERSIEHYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETS 508
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 485 VDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRAL 564
Cdd:PRK14351 509 AENLLAELEASREPPLADFLVALGIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSERNRAV 588
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 565 IQKLKYKHVNMiykgiKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAG-SKLT 643
Cdd:PRK14351 589 IDDLLDHGVDP-----QPAESEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGqSKRD 663
|
650
....*....|....*
gi 612673055 644 KAQSLGIEIWTEQQF 658
Cdd:PRK14351 664 DAEANDVPTLDEEEF 678
|
|
| LIGANc |
cd00114 |
NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining ... |
6-310 |
6.29e-170 |
|
NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Pssm-ID: 238062 [Multi-domain] Cd Length: 307 Bit Score: 487.48 E-value: 6.29e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 6 SRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNA 85
Cdd:cd00114 1 ERIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVGGTPLSGFKKVRHPVPMLSLDNA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 86 FNEDDLRKFDQRIREQIG-NVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE-PLNVE 163
Cdd:cd00114 81 FDEEELRAFDERIKRFLGeEPAYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLAGaPETLE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 164 VRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLG 243
Cdd:cd00114 161 VRGEVFMPKADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLGPKTQSEALAFLKEWG 240
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 612673055 244 FTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPA 310
Cdd:cd00114 241 FPVSPETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPA 307
|
|
| DNA_ligase_aden |
pfam01653 |
NAD-dependent DNA ligase adenylation domain; DNA ligases catalyze the crucial step of joining ... |
7-311 |
3.19e-163 |
|
NAD-dependent DNA ligase adenylation domain; DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism.
Pssm-ID: 396292 [Multi-domain] Cd Length: 318 Bit Score: 471.06 E-value: 3.19e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 7 RVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAF 86
Cdd:pfam01653 6 QLEELRELIRKYDYEYYVLDNPSVPDAEYDRLYRELKALEEKHPELITPDSPTQRVGAVPLADFNKVRHLTPMLSLDNAF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 87 NEDDLRKFDQRIREQIGN---VEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE---PL 160
Cdd:pfam01653 86 NLDELQAFIERIRRALGNkekVEYVVEPKIDGLSISLLYENGLLVRAATRGDGTTGEDVTANVKTIRNIPLKLKGdnpPE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 161 NVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSV--NDFTDFNARSQSEALDE 238
Cdd:pfam01653 166 RLEVRGEVFMPKEDFEALNEERLEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLglLEGHELGFDTQYQALAF 245
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612673055 239 LDKLGFTTNKNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAE 311
Cdd:pfam01653 246 LKSLGFPVSPLLALCDGIEEVLAYYADWEKKRDSLPYEIDGVVVKVDELALQRELGFTAKAPRWAIAYKFPAE 318
|
|
| ligA |
PRK14350 |
NAD-dependent DNA ligase LigA; Provisional |
3-666 |
1.64e-119 |
|
NAD-dependent DNA ligase LigA; Provisional
Pssm-ID: 172826 [Multi-domain] Cd Length: 669 Bit Score: 371.47 E-value: 1.64e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 3 DLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSL 82
Cdd:PRK14350 4 DIQDEILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQELESKYPEYKTLDSPTLKFGSDLLNDFKEVEHSFPILSL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 83 GNAFNEDDLRKFDQRIREQIGNVEYM----CELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKE 158
Cdd:PRK14350 84 DKVYDLKLLKLWIEKMDLENSNLGFDfgisVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRNVPLFIDE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 159 PLNVEVRGEAYMPRRSFLRLNEEKEKNdeqlFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNdFTDFNARSQSEALDE 238
Cdd:PRK14350 164 KVELVLRGEIYITKENFLKINKTLEKP----YTNARNLASGILRRIDSREVANFPLDIFVYDIL-YSSLELKTNHDAFDK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 239 LDKLGFTTN---KNRARVSDIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVT 315
Cdd:PRK14350 239 LKKFGFKVNpfcRFFDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESLSGFS 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 316 KLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERrpeDAVTY 395
Cdd:PRK14350 319 KVNDIVVQVGRSGKITPVANIEKVFVAGAFITNASLHNQDYIDSIGLNVGDVVKISRRGDVIPAVELVIEKL---SVGFF 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 396 HMPTHCPSCGHELVRiEGeVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLL 475
Cdd:PRK14350 396 KIPDNCPSCKTALIK-EG-AHLFCVNNHCPSVIVERIKYFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLI 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 476 PLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVL----AEKYETIDRLLTVTE---AELVEIHDIGDKV 548
Cdd:PRK14350 474 NLKGFKDKRINNLKRSIEASKKRPFSKLLLSMGIKDLGENTILLLinnnLNSFDKISTLCQDREfalSKLLKIKGIGEKI 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 549 AQSVVTYLENEDIralIQKLK-YKHVNMIYKGIKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTK 627
Cdd:PRK14350 554 ALNIIEAFNDKII---LDKFNfFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTK 630
|
650 660 670
....*....|....*....|....*....|....*....
gi 612673055 628 NTDVVIAGEDAGSKLTKAQSLGIEIWTeqqFVDKQNELN 666
Cdd:PRK14350 631 YLDFLLVGEKAGLKLKKANNLGIKIMS---LFDIKSYVD 666
|
|
| ligB |
PRK08097 |
NAD-dependent DNA ligase LigB; |
112-568 |
2.65e-50 |
|
NAD-dependent DNA ligase LigB;
Pssm-ID: 236150 [Multi-domain] Cd Length: 562 Bit Score: 183.97 E-value: 2.65e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 112 KIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEV-RGEAYmprrsfLRLNEEKEKNDEQlf 190
Cdd:PRK08097 125 KVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLPGALANLVlQGELF------LRREGHIQQQMGG-- 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 191 ANPRNAAAGSLR--QLDSKLtakRKLSVFIYSVNDftdfNARSQSEALDELDKLGFT-TNKNRARVSDIDGVleyiEKWT 267
Cdd:PRK08097 197 INARAKVAGLMMrkDPSPTL---NQIGVFVWAWPD----GPASMPERLAQLATAGFPlTQRYTHPVKNAEEV----ARWR 265
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 268 SQ--RESLPYDIDGIVIKvndldQQDEMGFTQ---KSPRWAIAYKFPAEEVVTKLLDIELSIGRTGVVTPTAILEPVKVA 342
Cdd:PRK08097 266 ERwyRAPLPFVTDGVVVR-----QAKEPPGRYwqpGQGEWAVAWKYPPVQQVAEVRAVQFAVGRTGKITVVLELEPVMLD 340
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 343 GTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIP---EVVRSIPERR---PEDAVTYHmpthcpscghelvriegevA 416
Cdd:PRK08097 341 DKRVSRVNIGSVRRWQQWDIAPGDQVLVSLAGQGIPrldKVVWRGAERTkptPPDADRFH-------------------S 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 417 LRCI--NPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKKVDNLLAAIQQ 494
Cdd:PRK08097 402 LSCFraSPGCQEQFLARLVWLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNL 481
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 612673055 495 AKDNSLENLLFGLGIRhLGVKASQVLAEkyETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRALIQKL 568
Cdd:PRK08097 482 ARQQPFSRWLKALGIP-LPQAALNALDD--RSWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEVKALADWL 552
|
|
| DNA_ligase_OB |
pfam03120 |
NAD-dependent DNA ligase OB-fold domain; DNA ligases catalyze the crucial step of joining the ... |
314-392 |
9.03e-43 |
|
NAD-dependent DNA ligase OB-fold domain; DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding.
Pssm-ID: 460813 [Multi-domain] Cd Length: 79 Bit Score: 148.67 E-value: 9.03e-43
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 612673055 314 VTKLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDA 392
Cdd:pfam03120 1 ETKLLDIEFQVGRTGAITPVAVLEPVELAGTTVSRATLHNEDEIKRKDIRIGDTVIVRKAGDVIPEVVGVVLEKRPGDE 79
|
|
| BRCT_DNA_ligase_like |
cd17748 |
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ... |
591-660 |
5.72e-26 |
|
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349379 [Multi-domain] Cd Length: 76 Bit Score: 101.40 E-value: 5.72e-26
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 612673055 591 FSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAGSKLT-----KAQSLGIEIWTEQQFVD 660
Cdd:cd17748 1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKkgeelKAKGLGIKIISEEEFLD 75
|
|
| HHH_2 |
pfam12826 |
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ... |
503-565 |
3.05e-22 |
|
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Pssm-ID: 432812 [Multi-domain] Cd Length: 64 Bit Score: 90.28 E-value: 3.05e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612673055 503 LLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRALI 565
Cdd:pfam12826 2 LLFALGIRHVGETTAKLLARRFGSLDALAEASLEELLEVDDIGPEIAQSIVEFFADPANRELI 64
|
|
| BRCT_RFC1 |
cd17752 |
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ... |
587-660 |
9.14e-17 |
|
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349383 [Multi-domain] Cd Length: 79 Bit Score: 75.33 E-value: 9.14e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 612673055 587 GHPE-FSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAG-SKLTKAQSLGIEIWTEQQFVD 660
Cdd:cd17752 1 GAPNcLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGpSKLEKAKELGTKIIDEDGLFD 76
|
|
| BRCT |
pfam00533 |
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ... |
591-660 |
1.91e-13 |
|
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.
Pssm-ID: 425736 [Multi-domain] Cd Length: 75 Bit Score: 65.78 E-value: 1.91e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 591 FSGKTIVLTGKLhQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAgSKLTKAQSLGIEIWTEQQFVD 660
Cdd:pfam00533 6 FSGKTFVITGLD-GLERDELKELIEKLGGKVTDSLSKKTTHVIVEART-KKYLKAKELGIPIVTEEWLLD 73
|
|
| DNA_ligase_ZBD |
pfam03119 |
NAD-dependent DNA ligase C4 zinc finger domain; DNA ligases catalyze the crucial step of ... |
400-424 |
8.00e-12 |
|
NAD-dependent DNA ligase C4 zinc finger domain; DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases.
Pssm-ID: 460812 [Multi-domain] Cd Length: 26 Bit Score: 59.75 E-value: 8.00e-12
|
| BRCT |
smart00292 |
breast cancer carboxy-terminal domain; |
591-660 |
2.76e-10 |
|
breast cancer carboxy-terminal domain;
Pssm-ID: 214602 [Multi-domain] Cd Length: 78 Bit Score: 57.00 E-value: 2.76e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 612673055 591 FSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVT-KNTDVVIAGEDAGSKLT--KAQSLGIEIWTEQQFVD 660
Cdd:smart00292 4 FKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSsKTTTHVIVGSPEGGKLEllKAIALGIPIVKEEWLLD 76
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
581-664 |
1.17e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 54.02 E-value: 1.17e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612673055 581 KTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAG---------EDAGSKLTKAQSL--- 648
Cdd:PRK06195 211 KIIESFGFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNtkdiedlnrEEMSNKLKKAIDLkkk 290
|
90
....*....|....*...
gi 612673055 649 --GIEIWTEQQFVDKQNE 664
Cdd:PRK06195 291 gqNIKFLNEEEFLQKCKE 308
|
|
| BRCT_PARP1 |
cd17747 |
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ... |
591-655 |
1.31e-05 |
|
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2.30), also termed ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1), or NAD(+) ADP-ribosyltransferase 1 (ADPRT 1), or poly[ADP-ribose] synthase 1, is involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism.
Pssm-ID: 349378 [Multi-domain] Cd Length: 76 Bit Score: 43.67 E-value: 1.31e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 612673055 591 FSGKTIVLTGKLhQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDA----GSKLTKAQSLGIEIWTE 655
Cdd:cd17747 1 LTGMKFALIGKL-SKSKDELKKLIEKLGGKVASKVTKKVTLCISTKAEvekmSKKMKEAKEAGVPVVSE 68
|
|
| BRCT |
cd00027 |
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ... |
595-652 |
7.30e-04 |
|
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.
Pssm-ID: 349339 [Multi-domain] Cd Length: 68 Bit Score: 38.50 E-value: 7.30e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 612673055 595 TIVLTGkLHQMTRNEASKWLTSQGAKVTSSVTKNTDVVIAGEDAGSK-LTKAQSLGIEI 652
Cdd:cd00027 2 VICFSG-LDDEEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEKyYLAALAWGIPI 59
|
|
| |
