|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
1-609 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 916.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 1 MFNSKKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHN 80
Cdd:PRK00558 1 KEFLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 81 FIKLYQPRYNVLLRDDKSYPFILL-TKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNR 159
Cdd:PRK00558 81 LIKKYKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 160 SRPCLQYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEK 239
Cdd:PRK00558 161 KRPCLLYQIGRCLAPCV-GLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 240 QFVSNERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANtDLSELTETFVGQFYLQGhqgrSIPNSIIVDR 319
Cdd:PRK00558 240 QKVSLKDGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSET-ELEEILEAFLGQFYLQK----SIPKEILVPH 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 320 QLAEKsELEQLLseQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQSSRMSERYQALCELLNLPE-IKRMECFDI 398
Cdd:PRK00558 315 ELDDE-ELAEAL--LAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEpPYRIECFDI 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 399 SHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEE-DKIPDIIFIDGGKGQLNRALNVF 477
Cdd:PRK00558 392 SHIQGTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEfGPLPDLILIDGGKGQLNAAKEVL 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 478 QHLQVKwdknrPHLIGVAKGVDRRAGQEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLE 557
Cdd:PRK00558 472 EELGLD-----IPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALD 546
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 1497429894 558 TIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLKND 609
Cdd:PRK00558 547 DIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
1-609 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 882.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 1 MFNSKKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHN 80
Cdd:COG0322 3 PFDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 81 FIKLYQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNRS 160
Cdd:COG0322 83 LIKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRS 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 161 RPCLQYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQ 240
Cdd:COG0322 163 RPCLLYQIGRCSAPCV-GLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQ 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 241 FVSNERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANTDLSELTETFVGQFYLQGHqgrSIPNSIIVDRQ 320
Cdd:COG0322 242 KVVLPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRP---SIPKEILVPEE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 321 LAEKSELEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQS----SRMSERYQALCELLNLPEI-KRMEC 395
Cdd:COG0322 319 LEDAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERerdeARQERALEELAEALGLPELpRRIEC 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 396 FDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEED-KIPDIIFIDGGKGQLNRAL 474
Cdd:COG0322 399 FDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDePLPDLILIDGGKGQLNAAR 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 475 NVFQHLQVKwdknRPHLIGVAKgvdRRagqEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQS 554
Cdd:COG0322 479 EVLEELGLD----DIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLKS 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 1497429894 555 GLETIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLKND 609
Cdd:COG0322 549 VLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLHKE 603
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
5-587 |
0e+00 |
|
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 272953 [Multi-domain] Cd Length: 574 Bit Score: 846.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 5 KKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSsKKTEALVASIHHIDTTLTSSETEALLLEHNFIKL 84
Cdd:TIGR00194 2 KEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFRENNS-AKTQALVKQIADIEYILTKNENEALILEANLIKQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 85 YQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSvysNRSRPCL 164
Cdd:TIGR00194 81 YQPRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAKH---NRNRPCL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 165 QYQIGRCSAPCVQGYvSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSN 244
Cdd:TIGR00194 158 YYQIGRCLGPCVKEI-TEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 245 ERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPAnTDLSELTETFVGQFYLQGHQGRSIPNSIIVDRQLAEK 324
Cdd:TIGR00194 237 TDLIDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPG-TDLDELVETFLIQFYQQGYQNRLIPSEILVSLSLEDL 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 325 SELEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQSSRMSERYQALCELLNLPEIKRMECFDISHTMGN 404
Cdd:TIGR00194 316 KLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPKIKRIEIFDISHIDGS 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 405 QTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEEDKIP--DIIFIDGGKGQLNRALNVFQHLQV 482
Cdd:TIGR00194 396 QTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQKKNNLPlpDLILIDGGKGQLNAALEVLKSLGV 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 483 kwdKNRPHLIGVAKgVDRRAGQEVLIISKQDREIHLpdDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLETIEGV 562
Cdd:TIGR00194 476 ---VNKPIVIGLAK-AKRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPGV 549
|
570 580
....*....|....*....|....*
gi 1497429894 563 GAKRRQALLKYLGGLQGVKKATLDE 587
Cdd:TIGR00194 550 GEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
383-539 |
1.23e-65 |
|
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyzes nucleotide excision repair in a multi-step process. UvrC catalyzes the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteriztic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates.
Pssm-ID: 462484 [Multi-domain] Cd Length: 150 Bit Score: 211.54 E-value: 1.23e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 383 ELLNLPE-IKRMECFDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEED-KIPDI 460
Cdd:pfam08459 2 EALGLPKlPRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFgPLPDL 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1497429894 461 IFIDGGKGQLNRALNVFQHLQVKWDknrphLIGVAKGVDRRagqevLIISKQDREIHLPDDSLALHLIQHIRDESHNHA 539
Cdd:pfam08459 82 ILIDGGKGQLNAALEVLEELGLDIP-----VIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRFA 150
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
13-91 |
6.39e-37 |
|
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.
Pssm-ID: 198381 [Multi-domain] Cd Length: 81 Bit Score: 132.22 E-value: 6.39e-37
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1497429894 13 HEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPRYNV 91
Cdd:cd10434 3 DSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
14-95 |
1.14e-18 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 80.93 E-value: 1.14e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 14 EPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKK-TEALVASIHHIDTTLTSSETE-ALLLEHNFIKLYQPRYNV 91
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLlIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 1497429894 92 LLRD 95
Cdd:smart00465 81 LLKG 84
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
1-609 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 916.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 1 MFNSKKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHN 80
Cdd:PRK00558 1 KEFLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 81 FIKLYQPRYNVLLRDDKSYPFILL-TKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNR 159
Cdd:PRK00558 81 LIKKYKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 160 SRPCLQYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEK 239
Cdd:PRK00558 161 KRPCLLYQIGRCLAPCV-GLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 240 QFVSNERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANtDLSELTETFVGQFYLQGhqgrSIPNSIIVDR 319
Cdd:PRK00558 240 QKVSLKDGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSET-ELEEILEAFLGQFYLQK----SIPKEILVPH 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 320 QLAEKsELEQLLseQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQSSRMSERYQALCELLNLPE-IKRMECFDI 398
Cdd:PRK00558 315 ELDDE-ELAEAL--LAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEpPYRIECFDI 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 399 SHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEE-DKIPDIIFIDGGKGQLNRALNVF 477
Cdd:PRK00558 392 SHIQGTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEfGPLPDLILIDGGKGQLNAAKEVL 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 478 QHLQVKwdknrPHLIGVAKGVDRRAGQEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLE 557
Cdd:PRK00558 472 EELGLD-----IPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALD 546
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 1497429894 558 TIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLKND 609
Cdd:PRK00558 547 DIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
1-609 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 882.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 1 MFNSKKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHN 80
Cdd:COG0322 3 PFDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 81 FIKLYQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNRS 160
Cdd:COG0322 83 LIKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRS 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 161 RPCLQYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQ 240
Cdd:COG0322 163 RPCLLYQIGRCSAPCV-GLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQ 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 241 FVSNERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANTDLSELTETFVGQFYLQGHqgrSIPNSIIVDRQ 320
Cdd:COG0322 242 KVVLPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRP---SIPKEILVPEE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 321 LAEKSELEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQS----SRMSERYQALCELLNLPEI-KRMEC 395
Cdd:COG0322 319 LEDAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERerdeARQERALEELAEALGLPELpRRIEC 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 396 FDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEED-KIPDIIFIDGGKGQLNRAL 474
Cdd:COG0322 399 FDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDePLPDLILIDGGKGQLNAAR 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 475 NVFQHLQVKwdknRPHLIGVAKgvdRRagqEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQS 554
Cdd:COG0322 479 EVLEELGLD----DIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLKS 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 1497429894 555 GLETIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLKND 609
Cdd:COG0322 549 VLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLHKE 603
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
5-587 |
0e+00 |
|
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 272953 [Multi-domain] Cd Length: 574 Bit Score: 846.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 5 KKFLADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSsKKTEALVASIHHIDTTLTSSETEALLLEHNFIKL 84
Cdd:TIGR00194 2 KEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFRENNS-AKTQALVKQIADIEYILTKNENEALILEANLIKQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 85 YQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSvysNRSRPCL 164
Cdd:TIGR00194 81 YQPRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAKH---NRNRPCL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 165 QYQIGRCSAPCVQGYvSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSN 244
Cdd:TIGR00194 158 YYQIGRCLGPCVKEI-TEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 245 ERLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPAnTDLSELTETFVGQFYLQGHQGRSIPNSIIVDRQLAEK 324
Cdd:TIGR00194 237 TDLIDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPG-TDLDELVETFLIQFYQQGYQNRLIPSEILVSLSLEDL 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 325 SELEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQLKQSSRMSERYQALCELLNLPEIKRMECFDISHTMGN 404
Cdd:TIGR00194 316 KLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPKIKRIEIFDISHIDGS 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 405 QTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEEDKIP--DIIFIDGGKGQLNRALNVFQHLQV 482
Cdd:TIGR00194 396 QTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQKKNNLPlpDLILIDGGKGQLNAALEVLKSLGV 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 483 kwdKNRPHLIGVAKgVDRRAGQEVLIISKQDREIHLpdDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLETIEGV 562
Cdd:TIGR00194 476 ---VNKPIVIGLAK-AKRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPGV 549
|
570 580
....*....|....*....|....*
gi 1497429894 563 GAKRRQALLKYLGGLQGVKKATLDE 587
Cdd:TIGR00194 550 GEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| uvrC |
PRK14669 |
excinuclease ABC subunit C; Provisional |
15-602 |
1.56e-132 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237784 [Multi-domain] Cd Length: 624 Bit Score: 401.59 E-value: 1.56e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 15 PGVYRMYDDKDQVIYVGKAKDLKKRLSSYF-RKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPRYNVLL 93
Cdd:PRK14669 14 PGVYLYKNAGGEVIYVGKAKNLRSRVRSYFsEDKLGNIKTGSLIREAVDIDYILVDNEKEALALENNLIKQYKPRFNILL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 94 RDDKSYPFILLTK-ERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNRSRPCLQYQIGRCS 172
Cdd:PRK14669 94 RDDKTYPYVKLTLgEKYPRVYVTRRLRKDGAQYYGPFFPANLAYRLVDLIHRHFLVPSCKVDLTRYHPRPCLQFYIHRCL 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 173 APCVQGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSNERLDDMDI 252
Cdd:PRK14669 174 GPCVQGLTTDEAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVEELEEKQRMAAAKGDDADV 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 253 MSIAYQHGLACVQVMFIRQGKVLGNRSYF------PKVPANTDLSELTETFVGQFYLqghQGRSIPNSIIVDRQLAEKSE 326
Cdd:PRK14669 254 FGYHYENPMVAVNLFHMRGGKIVDRREFFwedlgeVQVEFEYDEGLFFSSLLKQIYL---DQQYVPREIYVPVEFEDREA 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 327 LEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAALNVQ---LKQSSRMSEryQALCELLNLPEI-KRMECFDISHTM 402
Cdd:PRK14669 331 LEELLTEQRHRRIEIRVPQRGDKRSLLDLVEQNAKQSYDQRfrvMKPSSRAIQ--EALQDALNLPELpSRIECFDISHIQ 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 403 GNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEEDK-IPDIIFIDGGKGQLNRALNVFQHLQ 481
Cdd:PRK14669 409 GAETVASMVVWEDGKMKKSDYRKFIIKTVVGVDDFASMREVVTRRYSRLQEEKQpMPGLVLIDGGLGQLHAAAEALEAIG 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 482 VkwdKNRPhLIGVAKgvdrraGQEVL-IISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLETIE 560
Cdd:PRK14669 489 I---TDQP-LASIAK------REEIIyVFGQEDEPIVLDRFSPVLHLVQSIRDEAHRFAITFHRKRRETRDRTSELLEIP 558
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 1497429894 561 GVGAKRRQALLKYLGGLQGVKKATLDEIASVpgISPKLAERI 602
Cdd:PRK14669 559 GVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAI 598
|
|
| uvrC |
PRK14666 |
excinuclease ABC subunit C; Provisional |
8-607 |
1.59e-108 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237782 [Multi-domain] Cd Length: 694 Bit Score: 341.48 E-value: 1.59e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 8 LADVSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRK-NLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQ 86
Cdd:PRK14666 6 LSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDvSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKHR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 87 PRYNVLLRDDKSYPFILLTKERH-PRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNRSRPCLQ 165
Cdd:PRK14666 86 PRYNIVLRDDKQYVLFRLGAKHPyPRLEIVRKARRDGARYFGPFTSASAARETWKTIHRAFPLRRCSDRAFGNRVRACLY 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 166 YQIGRCSAPCVQGyVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSNE 245
Cdd:PRK14666 166 HFMGQCLGPCVND-VPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAVERTVERQAAVLP 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 246 RLDDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANTDLSELTETFVGQFYlqgHQGRSIPNSIIV-------D 318
Cdd:PRK14666 245 GGGDLDVVGLVEAEGGLALGVLFVRQGVLLDGRAFFWPGLGFEEAPELLWSFLGQFY---GPQSTIPPRIVVpwlpdteG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 319 RQLAEKSE------------------------------------------------------------------------ 326
Cdd:PRK14666 322 REGDDLAPtavctdagllpdtpllpdapegssdpvvpvaaatpvdaslpdvrtgtaptslanvshadpavaqptqaatla 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 327 -----------LEQLLSEQAGRKVTIQESVKGDKSKYLQLAQVNAKAalNVQLKQSSRMSERYQALCELLNLPeiKRMEC 395
Cdd:PRK14666 402 gaapkgathlmLEETLADLRGGPVRIVPPRNPAENRLVDMAMSNARE--EARRKAETPLQDLLARALHLSGPP--HRIEA 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 396 FDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGiTGGDDYAAMEQALQKRYERDleeDKIPDIIFIDGGKGQLNRALN 475
Cdd:PRK14666 478 VDVSHTGGRNTRVGMVVFEDGKPARDAYRTYAFED-GEGDDYGTLAAWAGRRVESG---PPWPDLLLVDGGRGQLAAVVR 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 476 VFQhlqvkwDKNRPHLIGVAK---------GVDRRAGqevliiSKQDReIHLPDDSLALHL---------IQHIRDESHN 537
Cdd:PRK14666 554 ALE------EAGMGGLFAVASiakarteegRADRRAG------NVADR-IFLPGRANPLPLragapellfLQHVRDTVHD 620
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 538 HAISGHRKKRQKAFTQSGLETIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLK 607
Cdd:PRK14666 621 YAIGRHRRARAGAALTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690
|
|
| uvrC |
PRK14667 |
excinuclease ABC subunit C; Provisional |
5-607 |
2.86e-108 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237783 [Multi-domain] Cd Length: 567 Bit Score: 337.09 E-value: 2.86e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 5 KKFLADVSHEPGVYrMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKL 84
Cdd:PRK14667 7 LELIEKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQ 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 85 YQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKfTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENsvYSNRSRPCL 164
Cdd:PRK14667 86 YKPKYNVLLKSGSGYPMLLITDDEYPTVKIVRGTGE-KGEYFGPFLPARKARKVKKLIHKLFKLRTCDP--MPKRKEPCM 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 165 QYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSN 244
Cdd:PRK14667 163 DYHLGLCSGPCC-GKISKEDYELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALENLIKGQEVSG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 245 ERLDDMDIMsiaYQHGlACVQVMFIRQGKVLGNRSYFPKvpantDLSELTETFVGQFYlqghQGRSIPNSIIVDRQLAEk 324
Cdd:PRK14667 242 LPIEEADIF---YFMG-SRLGLFLVRSSKLVGKEEFRLE-----SEEQEEEEVILGYY----YSNYIPQKIITNFELSD- 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 325 sELEQLLSEQAGRKVTIQESVKGDKSKYLQlAQVNAKAALNVqLKqssrmSERYqalcELLNLPEIKRMECFDISHTMGN 404
Cdd:PRK14667 308 -NLKQWLSKRKGGDVEFLTLIPKELEKFIE-ENIGIKVDLEV-LK-----EEFK----KTFGFPLPERIEGFDISHFYGE 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 405 QTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLE-EDKIPDIIFIDGGKGQLNRALNVFQhlqvK 483
Cdd:PRK14667 376 FTVGSCVVWEDGSMNKKEYRRYKIKTVDGIDDYASLREVLTRRARRYKEgENPMPDLWLIDGGKGQLSVGIEVRD----R 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 484 WDKNRpHLIGVAKgvdrragQEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLETIEGVG 563
Cdd:PRK14667 452 LGLNI-KVFSLAK-------KEEILYTEDGKEIPLKENPILYKVFGLIRDEAHRFALSYNRKLREKEGLKDILDKIKGIG 523
|
570 580 590 600
....*....|....*....|....*....|....*....|....
gi 1497429894 564 AKRRQALLKYLGGLQGVKKATLDEIASVpGISPKLAERIFETLK 607
Cdd:PRK14667 524 EVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566
|
|
| uvrC |
PRK14668 |
excinuclease ABC subunit C; Provisional |
9-606 |
5.12e-108 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 184785 [Multi-domain] Cd Length: 577 Bit Score: 336.74 E-value: 5.12e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 9 ADVSHEPGVYRMYDDKDqVIYVGKAKDLKKRLSSYfrKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPR 88
Cdd:PRK14668 11 AELPREPGVYQFVAGGT-VLYVGKAVDLRDRVRSY--ADPRSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQPR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 89 YNVLLRDDKSYPFILLTKERHPRITSYRGSKKfTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENSVYSNRSRPCLQYQI 168
Cdd:PRK14668 88 YNVRLKDDKSYPLVQLTDHPVPRIEVTRDPDE-GATVFGPYTDKGRVETVVKALRETYGLRGCSDHKYSNRDRPCLDYEM 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 169 GRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEK-----QFVS 243
Cdd:PRK14668 167 GLCTAPCT-GEIDEEAYAEDVESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHGGggeavSSTG 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 244 NERldDMDIMSIAYQHGLACVQVMFIRQGKVLGNRSYFPKVPANTD-LSELTETFVGQFYLQghqgRSIPNSIIVDRQLA 322
Cdd:PRK14668 246 DER--AVDVLGVAIEGDRATVARLHAEGGQLVDRDRHRLEAPDGEDrGAAVLAAFIVQYYAE----RELPDALLLSERPG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 323 EKSELEQLLSEqagrKVTIQESVKGDKSKYLQLAQVNAkaalnvqlKQSSRMSERYQALCELLNLPEIKRMECFDISHTM 402
Cdd:PRK14668 320 DDDVRAWLEAE----GVDVRVPGAGREATLVDLALKNA--------RRRGGRDDEVGALADALGIDRPERIEGFDVSHAQ 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 403 GNQTVASCVVFNQEGPLKSDYRRFNIEgiTGGDDYAAMEQALQKRYERDLE--EDKI-PDIIFIDGGKGQLNRALNVFQh 479
Cdd:PRK14668 388 GRAVVGSNVCFVDGSAETADYRRKKLT--ERNDDYANMRELVRWRAERAVEgrDDRPdPDLLLIDGGDGQLGAARDALA- 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 480 lQVKWDKNrphLIGVAKgvdrraGQEVLIISkqDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQsgLETI 559
Cdd:PRK14668 465 -ETGWDVP---AIALAK------AEELVVTP--DRTYDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLRDDVSTV--LDDV 530
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1497429894 560 EGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETL 606
Cdd:PRK14668 531 PGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRERL 577
|
|
| uvrC |
PRK14670 |
excinuclease ABC subunit C; Provisional |
20-602 |
5.74e-90 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173133 [Multi-domain] Cd Length: 574 Bit Score: 289.50 E-value: 5.74e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 20 MYDDKDQVIYVGKAKDLKKRLSSYFRKNLSsKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPRYNVLLRDDKSY 99
Cdd:PRK14670 1 MYSENNKILYIGKAKNLRSRVKNYFLEKIS-HKTKILMKNVKNIEVITTNSEYEALLLECNLIKTHKPDYNIKLKDDKGY 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 100 PFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCENsvysNRSRPCLQYQIGRCSAPCVQGY 179
Cdd:PRK14670 80 PMIRITCEKYPRIFKTRKIINDGSEYFGPYVNVKKLDLVLDLINKTFKTRKCKK----KSKNPCLYFHMGQCLGVCYRED 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 180 VsDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSNERLDDMDIMSIAYQH 259
Cdd:PRK14670 156 L-EKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLIEISQTQIITKINKLSIDYVYIHPTE 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 260 GLACVQVMFIRQGKVLGNRSYFPKVPANTDlsELTETFVGQFYLQGHQgrSIPNSIIVDRQLaEKSELEQLLSEQAGRKV 339
Cdd:PRK14670 235 NLNTIVILKYKDGKLVEKDINFDESIYEED--ELILQFITQYYTSINM--IVPDKIHIFKKI-DTKNITKLINELKNTKT 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 340 TIQESVKGDKSKYLQLAQVNAKAALNVQLKQSSRMSERYQALCELLNLPeiKRMECFDISHTMGNQTVASCVVFNQEGPL 419
Cdd:PRK14670 310 EIIYKETKEIIKIMEMAISNAKLALREYENEKNKALESLKIILEMDKLP--KTIEGFDIAHLNGQKTVASLVTFKMGKPF 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 420 KSDYRRFNIEGITGG--DDYAAMEQALQKRYERDLEED-KIPDIIFIDGGKGQLNRALNVFQHLQVkwdKNRPHLIGVAK 496
Cdd:PRK14670 388 KDGYRVYKINSLLKGeiDDFKAIKEVISRRYSKLINEQlELPNLILIDGGKGQLNAAYSILKGLKI---ENKVKVCALAK 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 497 gvdrraGQEVLIISKQDREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKafTQSGLETIEGVGAKRRQALLKYLGG 576
Cdd:PRK14670 465 ------KEETIFLPNKKQGIKLPKGNPALRILQNVRDEAHRKANGFNKKLREN--IKLNYTKIKGIGEKKAKKILKSLGT 536
|
570 580
....*....|....*....|....*.
gi 1497429894 577 LQGVKKATLDEIASVPGISPKLAERI 602
Cdd:PRK14670 537 YKDILLLNEDEIAEKMKINIKMAKKI 562
|
|
| uvrC |
PRK14672 |
excinuclease ABC subunit C; Provisional |
16-590 |
2.48e-73 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173135 [Multi-domain] Cd Length: 691 Bit Score: 248.49 E-value: 2.48e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 16 GVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNlSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPRYNVLLRD 95
Cdd:PRK14672 23 GVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHTPRYNICLKD 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 96 DKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCenSVYSNRSRPCLQYQIGRCSAPC 175
Cdd:PRK14672 102 GKTYPLLKLTCEPFPRIFRTRQFCQDGARYFGPFPDVQILDSFLKLILRTYKIRTC--TTLRKRKNPCLYYHLKRCDAPC 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 176 VqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQFVSNERLDDMDIMSI 255
Cdd:PRK14672 180 C-GWVSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITHKSLVQDMDERARDYIAW 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 256 AYQHGLACVQVMFIRQGKVLGNRSYFPKVPANTD--LSELTETF-----------------VGQFYLQGHQGR------- 309
Cdd:PRK14672 259 SSTGAIVTFAVLRMRGGKLNGRELFRTRSLKNEEeiLSEFLITYysdhtipphlfvhssagLAEHWLSHKAGTqctvtli 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 310 --------SIPNSIIVD-------------------RQLAEKSELEQL-------LSEQAGRKVTIQESVKGDKSK-YLQ 354
Cdd:PRK14672 339 plhtfptpQTPSSTVTTnaptlaasqnsnavqdsglRSCSETSTMHTLqkahdacTASEGTRENTPHESAHTPHHRaILA 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 355 LAQVNAKAALNVQLKQSSrMSERYQALCELLNLPEIKRM-ECFDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEG-IT 432
Cdd:PRK14672 419 MAQLNAHEDITRYLKNRG-ADDALKELQKQLHLARIPTLiEGFDISHLGGKYTVASLICFKNGAPDTKNYRLFNLRAhDT 497
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 433 GGDDYAAMEQALQKRYERDLEEDKIPDIIFIDGGKGQLNRALNVFQHLQVKWDknrphLIGVAKgvdrRAgqEVLIISKQ 512
Cdd:PRK14672 498 RIDDFASMREAIARRYTHTPEGYTLPDLILVDGGIGHVSAAQHVLDALGLSIP-----LVGLAK----RA--EELFIPNS 566
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1497429894 513 DREIHLPDDSLALHLIQHIRDESHNHAISGHRKKRQKAFTQSGLETIEGVGAKRRQALLKYLGGLQGVKKATLDEIAS 590
Cdd:PRK14672 567 PTPLVLDRRNPALHMLQRIRDEAHRFAITRNRHLRTKKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIAT 644
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
383-539 |
1.23e-65 |
|
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyzes nucleotide excision repair in a multi-step process. UvrC catalyzes the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteriztic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates.
Pssm-ID: 462484 [Multi-domain] Cd Length: 150 Bit Score: 211.54 E-value: 1.23e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 383 ELLNLPE-IKRMECFDISHTMGNQTVASCVVFNQEGPLKSDYRRFNIEGITGGDDYAAMEQALQKRYERDLEED-KIPDI 460
Cdd:pfam08459 2 EALGLPKlPRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFgPLPDL 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1497429894 461 IFIDGGKGQLNRALNVFQHLQVKWDknrphLIGVAKGVDRRagqevLIISKQDREIHLPDDSLALHLIQHIRDESHNHA 539
Cdd:pfam08459 82 ILIDGGKGQLNAALEVLEELGLDIP-----VIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRFA 150
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
5-240 |
1.87e-55 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 197.06 E-value: 1.87e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 5 KKFLAD-VSHEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIK 83
Cdd:PRK07883 207 KRHLADgLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIA 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 84 LYQPRYNVLLRDDKSYPFILLTKERHPRITSYRGSKKFTGEYFGPYPHAGAVRETLSLLQKLFPVRQCEN--SVYSNRSR 161
Cdd:PRK07883 287 AHKPPYNRRSKFPERRWWVRLTDEAFPRLSVVRAVEDDGAAYLGPFRSRRAAEEAAEALARAFPLRQCTDrlSRRARHGP 366
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1497429894 162 PCLQYQIGRCSAPCVqGYVSDEEYNQQVELARLFLQGKDQQVLDYLIGKMEQASKNLDFEQAARYRDQIQAVRSVIEKQ 240
Cdd:PRK07883 367 ACALAELGRCPAPCD-GRESAAEYAEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLAALLRALARA 444
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
13-91 |
6.39e-37 |
|
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.
Pssm-ID: 198381 [Multi-domain] Cd Length: 81 Bit Score: 132.22 E-value: 6.39e-37
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1497429894 13 HEPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQPRYNV 91
Cdd:cd10434 3 DSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
14-95 |
1.14e-18 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 80.93 E-value: 1.14e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 14 EPGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKK-TEALVASIHHIDTTLTSSETE-ALLLEHNFIKLYQPRYNV 91
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLlIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 1497429894 92 LLRD 95
Cdd:smart00465 81 LLKG 84
|
|
| PRK10545 |
PRK10545 |
excinuclease Cho; |
7-175 |
2.97e-10 |
|
excinuclease Cho;
Pssm-ID: 182535 Cd Length: 286 Bit Score: 61.61 E-value: 2.97e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 7 FLADVSHEPGVYRMYDDKDQV-IYVGKAKDLKKRLSSYFRknlsSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLY 85
Cdd:PRK10545 27 FLEDLPKLPGVYLFHGESDTMpLYIGKSVNIRSRVLSHLR----TPDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQ 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 86 QPRYNVLLRDDKSYPFILLTKERhPRITsYRGSKKFTGE--YFGPYPHAGAVRETLSLL---QKL-FPVRQCENsvySNR 159
Cdd:PRK10545 103 QPLFNKRLRRNRQLCSLQLNEGR-VDVV-YAKEVDFSRApnLFGLFANRRAALQALQSIadeQKLcYGLLGLEP---LSR 177
|
170
....*....|....*.
gi 1497429894 160 SRPCLQYQIGRCSAPC 175
Cdd:PRK10545 178 GRACFRSALKRCAGAC 193
|
|
| GIY-YIG_SF |
cd00719 |
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ... |
16-85 |
8.24e-10 |
|
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.
Pssm-ID: 198380 [Multi-domain] Cd Length: 69 Bit Score: 55.06 E-value: 8.24e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1497429894 16 GVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKteaLVASIHHIDT--TLTSSETEALLLEHNFIKLY 85
Cdd:cd00719 1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWT---KGLKPFEILYleVAPEAESELLDLEAALIKKL 69
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
556-608 |
4.74e-08 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 49.79 E-value: 4.74e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1497429894 556 LETIEGVGAKRRQALLKYLGG-LQGVKKATLDEIASVPGISPKLAERIFETLKN 608
Cdd:pfam14520 4 LLSISGIGPKTALALLSAGIGtVEDLAEADVDELAEIPGIGEKTAQRIILELRD 57
|
|
| GIY-YIG |
pfam01541 |
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ... |
15-90 |
5.73e-08 |
|
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.
Pssm-ID: 426314 [Multi-domain] Cd Length: 78 Bit Score: 50.03 E-value: 5.73e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497429894 15 PGVYRMYDDKDQVIYVGKAKDLKKRLSSYFRKNLSSKKTEALVASIHHIDTTLTSSETEALLLEHNFIKLYQP-RYN 90
Cdd:pfam01541 2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPnKYN 78
|
|
| MUS81 |
COG1948 |
ERCC4-type crossover junction endonuclease [Replication, recombination and repair]; |
556-606 |
3.99e-07 |
|
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
Pssm-ID: 441551 [Multi-domain] Cd Length: 214 Bit Score: 50.95 E-value: 3.99e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1497429894 556 LETIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETL 606
Cdd:COG1948 157 VESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVEGIGEKTAERIREVL 207
|
|
| UVR |
pfam02151 |
UvrB/uvrC motif; |
210-234 |
1.39e-06 |
|
UvrB/uvrC motif;
Pssm-ID: 308001 [Multi-domain] Cd Length: 36 Bit Score: 45.08 E-value: 1.39e-06
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
177-235 |
2.58e-06 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 50.39 E-value: 2.58e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497429894 177 QGYVSDEEYNQQVELARLFLQGKDQqvLDYLIGK----MEQASKNLDFEQAARYRDQIQAVRS 235
Cdd:COG0556 596 GTYEADEETEELVAEADAAKLSKEE--LEKLIKElekeMKEAAKNLEFEEAARLRDEIKELKK 656
|
|
| GIY-YIG_bI1_like |
cd10445 |
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The ... |
15-93 |
6.19e-06 |
|
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The prototype of this family is a putative intron-encoded mitochondrial DNA endonuclease bI1 found in mitochondrion Ustilago maydis. This protein may arise from proteolytic cleavage of an in-frame translation of COB exon 1 plus intron 1, containing the bI1 open reading frame. It contains an N-terminal truncated non-functional cytochrome b region and a C-terminal intron-encoded endonuclease bI1 region. The bI1 region shows high sequence similarity to endonucleases of group I introns of fungi and phage and might be involved in intron homing. Many uncharacterized bI1 homologs existing in fungi and chlorophyta in this family do not contain the cytochrome b region, but have a standalone bI1-like region, which contains a GIY-YIG domain and a minor-groove binding alpha-helix nuclease-associated modular domain (NUMOD). This family also includes a Yarrowia lipolytica mobile group-II intron COX1-i1, also called intron alpha, encoding protein with reverse transcriptase activity. The group-II intron COX1-i1 may be involv ed both in the generation of the circular multimeric DNA molecules (senDNA alpha) which amplify during the senescence syndrome and in the generation of the site-specific deletion which accumulates in the premature-death syndrome.
Pssm-ID: 198392 [Multi-domain] Cd Length: 88 Bit Score: 44.91 E-value: 6.19e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 15 PGVYRMYDDKDQVIYVGKAKDLKKRLSSYFrkNLSSKKTEALVA-SIH---HIDTTLT-------SSETEALLLEHNFIK 83
Cdd:cd10445 1 SGIYIWINKINGKIYVGSSINLYKRLRSYL--NPSYLKKNSPILrALLkygLSNFTLTileyyngENKEELLELEQYYID 78
|
90
....*....|
gi 1497429894 84 LYQPRYNVLL 93
Cdd:cd10445 79 LLKPEYNILK 88
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
210-234 |
1.89e-05 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 47.73 E-value: 1.89e-05
10 20
....*....|....*....|....*
gi 1497429894 210 KMEQASKNLDFEQAARYRDQIQAVR 234
Cdd:PRK05298 621 QMKEAAKNLEFEEAARLRDEIKELK 645
|
|
| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
552-602 |
8.50e-05 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 41.00 E-value: 8.50e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1497429894 552 TQSGLETIEGVGAKRRQALLKY---LGGLQgvkkaTLDEIASVPGISPKLAERI 602
Cdd:COG1555 19 TAEELQTLPGIGPKLAQRIVEYrekNGPFK-----SVEDLLEVKGIGPKTLEKL 67
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
556-606 |
1.39e-04 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 44.86 E-value: 1.39e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1497429894 556 LETIEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETL 606
Cdd:PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
|
|
| GIY-YIG_EndoII_Hpy188I_like |
cd10436 |
Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction ... |
15-91 |
4.24e-04 |
|
Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins; This family includes two different GIY-YIG enzymes, coliphage T4 non-specific endonuclease II (EndoII), and type II restriction endonuclease R.Hpy188I. They display high sequence similarity to each other, and both of them contain an extra N-terminal hairpin that lacks counterparts in other GIY-YIG enzymes. EndoII encoded by gene denA catalyzes the initial step in degradation of host DNA, which permits scavenging of host-derived nucleotides for phage DNA synthesis. R.Hpy188I recognizes the unique sequence, 5'-TCNGA-3', and cleaves the DNA between nucleotides N and G in its recognition sequence to generate a single nucleotide 3'-overhang. EndoII binds to two DNA substrates as an X-shaped tetrameric structure composed as a dimer of dimers. In contrast, two subunits of R.Hpy188I form a dimer to embrace one bound DNA. Divalent metal-ion cofactors are required for their catalytic events, but not for the substrates binding.
Pssm-ID: 198383 [Multi-domain] Cd Length: 97 Bit Score: 39.64 E-value: 4.24e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497429894 15 PGVYRMYDDkDQVIYVGKAKDLKKRLSSY-------------FRKN------LSSKKT-EALVASIHHIDTTLTSSETEA 74
Cdd:cd10436 1 NGVYAFVVD-GEIVYIGETQDLRKRFNSYrggisprngqttnCRINklilkaLKKGKVvELYVKQPEELVITLGDPVNTA 79
|
90
....*....|....*..
gi 1497429894 75 LLLEHNFIKLYQPRYNV 91
Cdd:cd10436 80 KGLEDELIEKIKPEWNS 96
|
|
| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
582-602 |
2.35e-03 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 36.76 E-value: 2.35e-03
|
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
559-609 |
3.05e-03 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 40.39 E-value: 3.05e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1497429894 559 IEGVGAKRRQALLKYLGGLQGVKKATLDEIASVPGISPKLAERIFETLKND 609
Cdd:COG0272 517 IRHVGETTAKLLARHFGSLDALMAASEEELAAVDGIGPVVAESIVEFFAEP 567
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| GIY-YIG_NifU |
cd10458 |
GIY-YIG domain found in iron-sulfur cluster assembly proteins; This family includes a group of ... |
16-46 |
4.86e-03 |
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GIY-YIG domain found in iron-sulfur cluster assembly proteins; This family includes a group of uncharacterized iron-sulfur cluster assembly proteins that transiently bind the iron-sulfur cluster before transfer to target apoproteins. These iron-sulfur cluster assembly proteins contains a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. They also contain a C-terminal NifU-like domain that corresponds to a common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Pssm-ID: 198405 Cd Length: 76 Bit Score: 36.37 E-value: 4.86e-03
10 20 30
....*....|....*....|....*....|.
gi 1497429894 16 GVYRMYDDKDQVIYVGKAKDLKKRLSSYFRK 46
Cdd:cd10458 1 GVYAMYDPSDNMQYVGYARNVVLAVKTHLAR 31
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