|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
8-610 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 963.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 8 KAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKL 87
Cdd:PRK00558 5 KEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKK 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 88 YQPRYNVLLRDDKSYPFIFL-SGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPC 166
Cdd:PRK00558 85 YKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRKRPC 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 167 LQYQIGRCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVS 246
Cdd:PRK00558 165 LLYQIGRCLAPCV-GLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQKVS 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 247 NT-GDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTElSEVVETFVGQFYLQGSqmrtLPGEILLDFNLSD 325
Cdd:PRK00558 244 LKdGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSETEL-EEILEAFLGQFYLQKS----IPKEILVPHELDD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 326 KTLLADslsELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQSTVHQRLTALASVLKLPEV-KRMECFDISHTM 404
Cdd:PRK00558 319 EELAEA---LLAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPpYRIECFDISHIQ 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 405 GEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDD-SKIPDVILIDGGKGQLAQAKNVFAELD 483
Cdd:PRK00558 396 GTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEfGPLPDLILIDGGKGQLNAAKEVLEELG 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 484 VswdknHPLLLGVAKGADRKAGLETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSLETIEG 563
Cdd:PRK00558 476 L-----DIPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDDIPG 550
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 90111354 564 VGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 610
Cdd:PRK00558 551 IGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
3-605 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 915.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 3 DQFDAKAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEH 82
Cdd:COG0322 2 DPFDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLEN 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 83 NYIKLYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNR 162
Cdd:COG0322 82 NLIKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 163 SRPCLQYQIGRCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEK 242
Cdd:COG0322 162 SRPCLLYQIGRCSAPCV-GLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 243 QFV-SNTGDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTELSEVVETFVGQFYLQGSQmrtLPGEILLDF 321
Cdd:COG0322 241 QKVvLPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRPS---IPKEILVPE 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 322 NLSDKTLLADSLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQ----STVHQRLTALASVLKLPEV-KRME 396
Cdd:COG0322 318 ELEDAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERerdeARQERALEELAEALGLPELpRRIE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 397 CFDISHTMGEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAID-DSKIPDVILIDGGKGQLAQA 475
Cdd:COG0322 398 CFDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEeDEPLPDLILIDGGKGQLNAA 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 476 KNVFAELDVSwdknHPLLLGVAKgadRKaglETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNT 555
Cdd:COG0322 478 REVLEELGLD----DIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLK 547
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 90111354 556 SSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIF 605
Cdd:COG0322 548 SVLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIY 597
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
7-589 |
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: 875.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 7 AKAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLaSRKTEALVAQIQQIDVTVTHTETEALLLEHNYIK 86
Cdd:TIGR00194 1 LKEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFRENN-SAKTQALVKQIADIEYILTKNENEALILEANLIK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 87 LYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENsvyRNRSRPC 166
Cdd:TIGR00194 80 QYQPRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAK---HNRNRPC 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 167 LQYQIGRCLGPCVEGLvSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVS 246
Cdd:TIGR00194 157 LYYQIGRCLGPCVKEI-TEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVS 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 247 NT-GDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGgTELSEVVETFVGQFYLQGSQMRTLPGEILLDFNLSD 325
Cdd:TIGR00194 236 LTdLIDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPG-TDLDELVETFLIQFYQQGYQNRLIPSEILVSLSLED 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 326 KTLLADSLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQSTVHQRLTALASVLKLPEVKRMECFDISHTMG 405
Cdd:TIGR00194 315 LKLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPKIKRIEIFDISHIDG 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 406 EQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDDSKIP--DVILIDGGKGQLAQAKNVFAELD 483
Cdd:TIGR00194 395 SQTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQKKNNLPlpDLILIDGGKGQLNAALEVLKSLG 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 484 VswdKNHPLLLGVAKgADRKAGLETLFFEPEGEGFSLppDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSLETIEG 563
Cdd:TIGR00194 475 V---VNKPIVIGLAK-AKRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPG 548
|
570 580
....*....|....*....|....*.
gi 90111354 564 VGPKRRQMLLKYMGGLQGLRNASVEE 589
Cdd:TIGR00194 549 VGEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
384-541 |
4.85e-64 |
|
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: 207.30 E-value: 4.85e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 384 ASVLKLPEV-KRMECFDISHTMGEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAID-DSKIPD 461
Cdd:pfam08459 1 QEALGLPKLpRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEeFGPLPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 462 VILIDGGKGQLAQAKNVFAELDVswdknHPLLLGVAKGADRKagletLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHA 541
Cdd:pfam08459 81 LILIDGGKGQLNAALEVLEELGL-----DIPVIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRFA 150
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
17-94 |
1.55e-38 |
|
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: 136.46 E-value: 1.55e-38
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 90111354 17 QPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQPRYNV 94
Cdd:cd10434 4 SPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
17-98 |
8.80e-18 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 78.23 E-value: 8.80e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 17 QPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFR-SNLASRKTEALVAQIQQIDVTVTHTETE-ALLLEHNYIKLYQPRYNV 94
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSgSRKGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 90111354 95 LLRD 98
Cdd:smart00465 81 LLKG 84
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
8-610 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 963.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 8 KAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKL 87
Cdd:PRK00558 5 KEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKK 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 88 YQPRYNVLLRDDKSYPFIFL-SGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPC 166
Cdd:PRK00558 85 YKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRKRPC 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 167 LQYQIGRCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVS 246
Cdd:PRK00558 165 LLYQIGRCLAPCV-GLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQKVS 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 247 NT-GDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTElSEVVETFVGQFYLQGSqmrtLPGEILLDFNLSD 325
Cdd:PRK00558 244 LKdGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSETEL-EEILEAFLGQFYLQKS----IPKEILVPHELDD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 326 KTLLADslsELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQSTVHQRLTALASVLKLPEV-KRMECFDISHTM 404
Cdd:PRK00558 319 EELAEA---LLAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPpYRIECFDISHIQ 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 405 GEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDD-SKIPDVILIDGGKGQLAQAKNVFAELD 483
Cdd:PRK00558 396 GTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEfGPLPDLILIDGGKGQLNAAKEVLEELG 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 484 VswdknHPLLLGVAKGADRKAGLETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSLETIEG 563
Cdd:PRK00558 476 L-----DIPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDDIPG 550
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 90111354 564 VGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 610
Cdd:PRK00558 551 IGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
3-605 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 915.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 3 DQFDAKAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEH 82
Cdd:COG0322 2 DPFDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLEN 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 83 NYIKLYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNR 162
Cdd:COG0322 82 NLIKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 163 SRPCLQYQIGRCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEK 242
Cdd:COG0322 162 SRPCLLYQIGRCSAPCV-GLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 243 QFV-SNTGDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTELSEVVETFVGQFYLQGSQmrtLPGEILLDF 321
Cdd:COG0322 241 QKVvLPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRPS---IPKEILVPE 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 322 NLSDKTLLADSLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQ----STVHQRLTALASVLKLPEV-KRME 396
Cdd:COG0322 318 ELEDAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERerdeARQERALEELAEALGLPELpRRIE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 397 CFDISHTMGEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAID-DSKIPDVILIDGGKGQLAQA 475
Cdd:COG0322 398 CFDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEeDEPLPDLILIDGGKGQLNAA 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 476 KNVFAELDVSwdknHPLLLGVAKgadRKaglETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNT 555
Cdd:COG0322 478 REVLEELGLD----DIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLK 547
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 90111354 556 SSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIF 605
Cdd:COG0322 548 SVLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIY 597
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
7-589 |
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: 875.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 7 AKAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLaSRKTEALVAQIQQIDVTVTHTETEALLLEHNYIK 86
Cdd:TIGR00194 1 LKEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFRENN-SAKTQALVKQIADIEYILTKNENEALILEANLIK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 87 LYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENsvyRNRSRPC 166
Cdd:TIGR00194 80 QYQPRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAK---HNRNRPC 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 167 LQYQIGRCLGPCVEGLvSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVS 246
Cdd:TIGR00194 157 LYYQIGRCLGPCVKEI-TEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVS 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 247 NT-GDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGgTELSEVVETFVGQFYLQGSQMRTLPGEILLDFNLSD 325
Cdd:TIGR00194 236 LTdLIDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPG-TDLDELVETFLIQFYQQGYQNRLIPSEILVSLSLED 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 326 KTLLADSLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQSTVHQRLTALASVLKLPEVKRMECFDISHTMG 405
Cdd:TIGR00194 315 LKLLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPKIKRIEIFDISHIDG 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 406 EQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDDSKIP--DVILIDGGKGQLAQAKNVFAELD 483
Cdd:TIGR00194 395 SQTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQKKNNLPlpDLILIDGGKGQLNAALEVLKSLG 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 484 VswdKNHPLLLGVAKgADRKAGLETLFFEPEGEGFSLppDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSLETIEG 563
Cdd:TIGR00194 475 V---VNKPIVIGLAK-AKRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPG 548
|
570 580
....*....|....*....|....*.
gi 90111354 564 VGPKRRQMLLKYMGGLQGLRNASVEE 589
Cdd:TIGR00194 549 VGEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| uvrC |
PRK14669 |
excinuclease ABC subunit C; Provisional |
11-604 |
1.63e-139 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237784 [Multi-domain] Cd Length: 624 Bit Score: 419.70 E-value: 1.63e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 11 LKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYF-RSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQ 89
Cdd:PRK14669 7 IRTLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFsEDKLGNIKTGSLIREAVDIDYILVDNEKEALALENNLIKQYK 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 90 PRYNVLLRDDKSYPFIFLS-GDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPCLQ 168
Cdd:PRK14669 87 PRFNILLRDDKTYPYVKLTlGEKYPRVYVTRRLRKDGAQYYGPFFPANLAYRLVDLIHRHFLVPSCKVDLTRYHPRPCLQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 169 YQIGRCLGPCVEGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFV-SN 247
Cdd:PRK14669 167 FYIHRCLGPCVQGLTTDEAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVEELEEKQRMaAA 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 248 TGDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYF------PKVPGGTELSEVVETFVGQFYLqgsQMRTLPGEILLDF 321
Cdd:PRK14669 247 KGDDADVFGYHYENPMVAVNLFHMRGGKIVDRREFFwedlgeVQVEFEYDEGLFFSSLLKQIYL---DQQYVPREIYVPV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 322 NLSDKTLLADSLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSK---LSQQSTVHQrlTALASVLKLPEV-KRMEC 397
Cdd:PRK14669 324 EFEDREALEELLTEQRHRRIEIRVPQRGDKRSLLDLVEQNAKQSYDQRfrvMKPSSRAIQ--EALQDALNLPELpSRIEC 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 398 FDISHTMGEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDDSK-IPDVILIDGGKGQLAQAK 476
Cdd:PRK14669 402 FDISHIQGAETVASMVVWEDGKMKKSDYRKFIIKTVVGVDDFASMREVVTRRYSRLQEEKQpMPGLVLIDGGLGQLHAAA 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 477 NVFAELDVSwdkNHPLllgvAKGADRKaglETLF-FEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNT 555
Cdd:PRK14669 482 EALEAIGIT---DQPL----ASIAKRE---EIIYvFGQEDEPIVLDRFSPVLHLVQSIRDEAHRFAITFHRKRRETRDRT 551
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 90111354 556 SSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQglAEKI 604
Cdd:PRK14669 552 SELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAVVGRAA--AEAI 598
|
|
| uvrC |
PRK14666 |
excinuclease ABC subunit C; Provisional |
11-609 |
1.12e-127 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237782 [Multi-domain] Cd Length: 694 Bit Score: 391.17 E-value: 1.12e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 11 LKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLA-SRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQ 89
Cdd:PRK14666 6 LSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSAlTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKHR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 90 PRYNVLLRDDKSYpFIFLSGDTH--PRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPCL 167
Cdd:PRK14666 86 PRYNIVLRDDKQY-VLFRLGAKHpyPRLEIVRKARRDGARYFGPFTSASAARETWKTIHRAFPLRRCSDRAFGNRVRACL 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 168 QYQIGRCLGPCVEgLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQ-FVS 246
Cdd:PRK14666 165 YHFMGQCLGPCVN-DVPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAVERTVERQaAVL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 247 NTGDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTELSEVVETFVGQFYLQGSqmrTLPGEILL------- 319
Cdd:PRK14666 244 PGGGDLDVVGLVEAEGGLALGVLFVRQGVLLDGRAFFWPGLGFEEAPELLWSFLGQFYGPQS---TIPPRIVVpwlpdte 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 320 --------------DFNLSDKTLLADSLSELAGRKI--------------NVQTKPRGDR-------------------- 351
Cdd:PRK14666 321 gregddlaptavctDAGLLPDTPLLPDAPEGSSDPVvpvaaatpvdaslpDVRTGTAPTSlanvshadpavaqptqaatl 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 352 -------ARYLKLARTNAA------------TALTSKLSQQSTVHQRLTA-----------LASVLKLP-EVKRMECFDI 400
Cdd:PRK14666 401 agaapkgATHLMLEETLADlrggpvrivpprNPAENRLVDMAMSNAREEArrkaetplqdlLARALHLSgPPHRIEAVDV 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 401 SHTMGEQTVASCVVFDANGPLRAEYRRYNITGiTPGDDYAAMNQVLRRRYGKAiddSKIPDVILIDGGKGQLAQAKNVFA 480
Cdd:PRK14666 481 SHTGGRNTRVGMVVFEDGKPARDAYRTYAFED-GEGDDYGTLAAWAGRRVESG---PPWPDLLLVDGGRGQLAAVVRALE 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 481 EldvswdKNHPLLLGVAK---------GADRKAG--LETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKR 549
Cdd:PRK14666 557 E------AGMGGLFAVASiakarteegRADRRAGnvADRIFLPGRANPLPLRAGAPELLFLQHVRDTVHDYAIGRHRRAR 630
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 550 AKVKNTSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 609
Cdd:PRK14666 631 AGAALTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690
|
|
| uvrC |
PRK14668 |
excinuclease ABC subunit C; Provisional |
16-604 |
4.72e-118 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 184785 [Multi-domain] Cd Length: 577 Bit Score: 362.55 E-value: 4.72e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 16 SQPGVYRmYDAGGTVIYVGKAKDLKKRLSSYfrSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQPRYNVL 95
Cdd:PRK14668 15 REPGVYQ-FVAGGTVLYVGKAVDLRDRVRSY--ADPRSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQPRYNVR 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 96 LRDDKSYPFIFLSGDTHPRLAMHRGAKHAkGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPCLQYQIGRCL 175
Cdd:PRK14668 92 LKDDKSYPLVQLTDHPVPRIEVTRDPDEG-ATVFGPYTDKGRVETVVKALRETYGLRGCSDHKYSNRDRPCLDYEMGLCT 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 176 GPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEK--QFVSNTGDD-- 251
Cdd:PRK14668 171 APCT-GEIDEEAYAEDVESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHGGggEAVSSTGDEra 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 252 LDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTE-LSEVVETFVGQFYLQgsqmRTLPGEILLDFNLSDktllA 330
Cdd:PRK14668 250 VDVLGVAIEGDRATVARLHAEGGQLVDRDRHRLEAPDGEDrGAAVLAAFIVQYYAE----RELPDALLLSERPGD----D 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 331 DSLSELAGRKINVQTKPRGDRARYLKLARTNAataltsklsQQSTVHQ-RLTALASVLKLPEVKRMECFDISHTMGEQTV 409
Cdd:PRK14668 322 DVRAWLEAEGVDVRVPGAGREATLVDLALKNA---------RRRGGRDdEVGALADALGIDRPERIEGFDVSHAQGRAVV 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 410 ASCVVFDANGPLRAEYRRYNITgiTPGDDYAAMNQVLRRRYGKAI---DDSKIPDVILIDGGKGQLAQAKNVFAEldVSW 486
Cdd:PRK14668 393 GSNVCFVDGSAETADYRRKKLT--ERNDDYANMRELVRWRAERAVegrDDRPDPDLLLIDGGDGQLGAARDALAE--TGW 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 487 DKNhplLLGVAKGadrkaglETLFFEPEGEgFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTssLETIEGVGP 566
Cdd:PRK14668 469 DVP---AIALAKA-------EELVVTPDRT-YDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLRDDVSTV--LDDVPGVGP 535
|
570 580 590
....*....|....*....|....*....|....*...
gi 90111354 567 KRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKI 604
Cdd:PRK14668 536 ETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETI 573
|
|
| uvrC |
PRK14667 |
excinuclease ABC subunit C; Provisional |
6-604 |
1.75e-98 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237783 [Multi-domain] Cd Length: 567 Bit Score: 311.67 E-value: 1.75e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 6 DAKAFLKTVTSQPGVYrMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYI 85
Cdd:PRK14667 5 DALELIEKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 86 KLYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHaKGEYFGPFPNGYAVRETLALLQKIFPIRQCENsvYRNRSRP 165
Cdd:PRK14667 84 QQYKPKYNVLLKSGSGYPMLLITDDEYPTVKIVRGTGE-KGEYFGPFLPARKARKVKKLIHKLFKLRTCDP--MPKRKEP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 166 CLQYQIGRCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFV 245
Cdd:PRK14667 161 CMDYHLGLCSGPCC-GKISKEDYELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALENLIKGQEV 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 246 SNTG-DDLDVigvafdagmacvhvlFIRQGKVLG---SRSYfpKVPGGTELSEVVETFVGQFYLQGSQMRT-LPGEILLD 320
Cdd:PRK14667 240 SGLPiEEADI---------------FYFMGSRLGlflVRSS--KLVGKEEFRLESEEQEEEEVILGYYYSNyIPQKIITN 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 321 FNLSDKtlLADSLSELAGRKINVQT-KPRgdraRYLKLARTNAATALTSKLSQQStvhqrltaLASVLKLPEVKRMECFD 399
Cdd:PRK14667 303 FELSDN--LKQWLSKRKGGDVEFLTlIPK----ELEKFIEENIGIKVDLEVLKEE--------FKKTFGFPLPERIEGFD 368
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 400 ISHTMGEQTVASCVVFDaNGPL-RAEYRRYNITGITPGDDYAAMNQVLRRRYGKAID-DSKIPDVILIDGGKGQLAQAKN 477
Cdd:PRK14667 369 ISHFYGEFTVGSCVVWE-DGSMnKKEYRRYKIKTVDGIDDYASLREVLTRRARRYKEgENPMPDLWLIDGGKGQLSVGIE 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 478 VFAELDVSWdknhpLLLGVAKGadrkaglETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSS 557
Cdd:PRK14667 448 VRDRLGLNI-----KVFSLAKK-------EEILYTEDGKEIPLKENPILYKVFGLIRDEAHRFALSYNRKLREKEGLKDI 515
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 90111354 558 LETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVpGISQGLAEKI 604
Cdd:PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEV 561
|
|
| uvrC |
PRK14670 |
excinuclease ABC subunit C; Provisional |
23-604 |
6.06e-95 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173133 [Multi-domain] Cd Length: 574 Bit Score: 302.60 E-value: 6.06e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 23 MYDAGGTVIYVGKAKDLKKRLSSYFrSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQPRYNVLLRDDKSY 102
Cdd:PRK14670 1 MYSENNKILYIGKAKNLRSRVKNYF-LEKISHKTKILMKNVKNIEVITTNSEYEALLLECNLIKTHKPDYNIKLKDDKGY 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 103 PFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCEnsvyRNRSRPCLQYQIGRCLGPCV-EG 181
Cdd:PRK14670 80 PMIRITCEKYPRIFKTRKIINDGSEYFGPYVNVKKLDLVLDLINKTFKTRKCK----KKSKNPCLYFHMGQCLGVCYrED 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 182 LvsEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVSNTGD-DLDVIGVAFD 260
Cdd:PRK14670 156 L--EKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLIEISQTQIITKINKlSIDYVYIHPT 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 261 AGMACVHVLFIRQGKVLGSRSYFPKvpGGTELSEVVETFVGQFYLQGSQMRTLPGEILLDFNLSDKTLLadsLSELAGRK 340
Cdd:PRK14670 234 ENLNTIVILKYKDGKLVEKDINFDE--SIYEEDELILQFITQYYTSINMIVPDKIHIFKKIDTKNITKL---INELKNTK 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 341 INVQTKPRGDRARYLKLARTNAATALTSKLSQQSTVHQRLTALASVLKLPevKRMECFDISHTMGEQTVASCVVFDANGP 420
Cdd:PRK14670 309 TEIIYKETKEIIKIMEMAISNAKLALREYENEKNKALESLKIILEMDKLP--KTIEGFDIAHLNGQKTVASLVTFKMGKP 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 421 LRAEYRRYNITGITPG--DDYAAMNQVLRRRYGKAIDDS-KIPDVILIDGGKGQLAQAKNVFAELDVswdKNHPLLLGVA 497
Cdd:PRK14670 387 FKDGYRVYKINSLLKGeiDDFKAIKEVISRRYSKLINEQlELPNLILIDGGKGQLNAAYSILKGLKI---ENKVKVCALA 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 498 KGAdrkaglETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSleTIEGVGPKRRQMLLKYMG 577
Cdd:PRK14670 464 KKE------ETIFLPNKKQGIKLPKGNPALRILQNVRDEAHRKANGFNKKLRENIKLNYT--KIKGIGEKKAKKILKSLG 535
|
570 580
....*....|....*....|....*..
gi 90111354 578 GLQGLRNASVEEIAKVPGISQGLAEKI 604
Cdd:PRK14670 536 TYKDILLLNEDEIAEKMKINIKMAKKI 562
|
|
| uvrC |
PRK14672 |
excinuclease ABC subunit C; Provisional |
13-591 |
3.62e-77 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173135 [Multi-domain] Cd Length: 691 Bit Score: 258.89 E-value: 3.62e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 13 TVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNlASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQPRY 92
Cdd:PRK14672 17 SAPSTSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHTPRY 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 93 NVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCenSVYRNRSRPCLQYQIG 172
Cdd:PRK14672 96 NICLKDGKTYPLLKLTCEPFPRIFRTRQFCQDGARYFGPFPDVQILDSFLKLILRTYKIRTC--TTLRKRKNPCLYYHLK 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 173 RCLGPCVeGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARIRDQIQAVRRVTEKQFVSNTGDDL 252
Cdd:PRK14672 174 RCDAPCC-GWVSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITHKSLVQDMDERA 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 253 -DVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTElsEVVETFVGQFYLQgsqmRTLPGEIlldFNLSDKTLLAD 331
Cdd:PRK14672 253 rDYIAWSSTGAIVTFAVLRMRGGKLNGRELFRTRSLKNEE--EILSEFLITYYSD----HTIPPHL---FVHSSAGLAEH 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 332 SLSELAGRKINVQTKPRGDRARYLKLARTNAATALTSKLSQQSTV----------------------------------- 376
Cdd:PRK14672 324 WLSHKAGTQCTVTLIPLHTFPTPQTPSSTVTTNAPTLAASQNSNAvqdsglrscsetstmhtlqkahdactasegtrent 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 377 ---------HQRLTALASVLKLPEVKR--------------------------MECFDISHTMGEQTVASCVVFDANGPL 421
Cdd:PRK14672 404 phesahtphHRAILAMAQLNAHEDITRylknrgaddalkelqkqlhlariptlIEGFDISHLGGKYTVASLICFKNGAPD 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 422 RAEYRRYNITG-ITPGDDYAAMNQVLRRRYGKAIDDSKIPDVILIDGGKGQLAQAKNVFAELDVSWDknhplLLGVAKGA 500
Cdd:PRK14672 484 TKNYRLFNLRAhDTRIDDFASMREAIARRYTHTPEGYTLPDLILVDGGIGHVSAAQHVLDALGLSIP-----LVGLAKRA 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 501 drkaglETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAIGGHRKKRAKVKNTSSLETIEGVGPKRRQMLLKYMGGLQ 580
Cdd:PRK14672 559 ------EELFIPNSPTPLVLDRRNPALHMLQRIRDEAHRFAITRNRHLRTKKELVLSFERLPHVGKVRAHRLLAHFGSFR 632
|
650
....*....|.
gi 90111354 581 GLRNASVEEIA 591
Cdd:PRK14672 633 SLQSATPQDIA 643
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
384-541 |
4.85e-64 |
|
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: 207.30 E-value: 4.85e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 384 ASVLKLPEV-KRMECFDISHTMGEQTVASCVVFDANGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAID-DSKIPD 461
Cdd:pfam08459 1 QEALGLPKLpRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEeFGPLPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 462 VILIDGGKGQLAQAKNVFAELDVswdknHPLLLGVAKGADRKagletLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHA 541
Cdd:pfam08459 81 LILIDGGKGQLNAALEVLEELGL-----DIPVIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRFA 150
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
6-300 |
2.15e-62 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 215.94 E-value: 2.15e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 6 DAKAFLKTVTSQ--------------PGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVT 71
Cdd:PRK07883 192 ELLTYLPRVTPAqrrkrhladglphaPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRGRMREMVALAERVDHVEC 271
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 72 HTETEALLLEHNYIKLYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPI 151
Cdd:PRK07883 272 AHALEAEVRELRLIAAHKPPYNRRSKFPERRWWVRLTDEAFPRLSVVRAVEDDGAAYLGPFRSRRAAEEAAEALARAFPL 351
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 152 RQCEN--SVYRNRSRPCLQYQIGRCLGPCvEGLVSEEEYAQQVEYVRLFLSGKDDQVLTQLISRMETASQNLEFEEAARI 229
Cdd:PRK07883 352 RQCTDrlSRRARHGPACALAELGRCPAPC-DGRESAAEYAEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARL 430
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 90111354 230 RDQIQAVRRVTEKQ--FVSNTGddLDVIGVAFDAGMACVHVLFIRQGKVLGSRsyfpKVPGGTELSEVVETFV 300
Cdd:PRK07883 431 RDRLAALLRALARAqrLAALAA--VPELVAARPDGEGGWELAVVRHGRLAAAG----VAPRGVPPMPVVDALV 497
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
17-94 |
1.55e-38 |
|
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: 136.46 E-value: 1.55e-38
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 90111354 17 QPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQPRYNV 94
Cdd:cd10434 4 SPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
17-98 |
8.80e-18 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 78.23 E-value: 8.80e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 17 QPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFR-SNLASRKTEALVAQIQQIDVTVTHTETE-ALLLEHNYIKLYQPRYNV 94
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSgSRKGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 90111354 95 LLRD 98
Cdd:smart00465 81 LLKG 84
|
|
| PRK10545 |
PRK10545 |
excinuclease Cho; |
8-198 |
5.66e-11 |
|
excinuclease Cho;
Pssm-ID: 182535 Cd Length: 286 Bit Score: 63.54 E-value: 5.66e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 8 KAFLKTVTSQPGVYRMYDAGGTV-IYVGKAKDLKKRLSSYFRSnlasrKTEA-LVAQIQQIDVTVTHTETEALLLEHNYI 85
Cdd:PRK10545 25 RPFLEDLPKLPGVYLFHGESDTMpLYIGKSVNIRSRVLSHLRT-----PDEAaMLRQSRRISWICTAGEIGALLLEARLI 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 86 KLYQPRYNVLLRDDKSYPFIFLSGDThPRL--AMHRGAKHAKGEYfGPFPNGYAVRETLALL---QKI-FPIRQCENSvy 159
Cdd:PRK10545 100 KEQQPLFNKRLRRNRQLCSLQLNEGR-VDVvyAKEVDFSRAPNLF-GLFANRRAALQALQSIadeQKLcYGLLGLEPL-- 175
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 90111354 160 rNRSRPCLQYQIGRCLGPCVeGLVSEEEYAQ----QVEYVRLF 198
Cdd:PRK10545 176 -SRGRACFRSALKRCAGACC-GKESHEAHALrlraSLERLRVV 216
|
|
| GIY-YIG |
pfam01541 |
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ... |
17-93 |
3.20e-10 |
|
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: 56.58 E-value: 3.20e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 90111354 17 QPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIDVTVTHTETEALLLEHNYIKLYQP-RYN 93
Cdd:pfam01541 1 KGGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPnKYN 78
|
|
| GIY-YIG_SF |
cd00719 |
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ... |
19-88 |
2.30e-09 |
|
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: 53.91 E-value: 2.30e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 19 GVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVAQIQQIdVTVTHTETEALLLEHNYIKLY 88
Cdd:cd00719 1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYL-EVAPEAESELLDLEAALIKKL 69
|
|
| UVR |
pfam02151 |
UvrB/uvrC motif; |
204-238 |
5.72e-08 |
|
UvrB/uvrC motif;
Pssm-ID: 308001 [Multi-domain] Cd Length: 36 Bit Score: 48.93 E-value: 5.72e-08
10 20 30
....*....|....*....|....*....|....*
gi 90111354 204 DQVLTQLISRMETASQNLEFEEAARIRDQIQAVRR 238
Cdd:pfam02151 1 KKLIKELEEEMEEAAENEDFEKAAKLRDQINALKK 35
|
|
| MUS81 |
COG1948 |
ERCC4-type crossover junction endonuclease [Replication, recombination and repair]; |
545-606 |
8.82e-07 |
|
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
Pssm-ID: 441551 [Multi-domain] Cd Length: 214 Bit Score: 50.17 E-value: 8.82e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 90111354 545 HRKKRAKVKNT---SSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFW 606
Cdd:COG1948 141 HGKKKPKTLREqqlYVVESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVEGIGEKTAERIRE 205
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
558-609 |
1.28e-06 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 45.56 E-value: 1.28e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 90111354 558 LETIEGVGPKRRQMLLKYMGG-LQGLRNASVEEIAKVPGISQGLAEKIFWSLK 609
Cdd:pfam14520 4 LLSISGIGPKTALALLSAGIGtVEDLAEADVDELAEIPGIGEKTAQRIILELR 56
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
199-238 |
2.72e-06 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 50.39 E-value: 2.72e-06
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 90111354 199 LSGKD-DQVLTQLISRMETASQNLEFEEAARIRDQIQAVRR 238
Cdd:COG0556 616 LSKEElEKLIKELEKEMKEAAKNLEFEEAARLRDEIKELKK 656
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
193-238 |
1.31e-05 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 48.12 E-value: 1.31e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 90111354 193 EYVRLFLSGKD-DQVLTQLISRMETASQNLEFEEAARIRDQIQAVRR 238
Cdd:PRK05298 600 VYKKDKLSKKElEKLIKELEKQMKEAAKNLEFEEAARLRDEIKELKE 646
|
|
| HHH |
pfam00633 |
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated ... |
579-606 |
6.18e-05 |
|
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Pssm-ID: 425789 [Multi-domain] Cd Length: 30 Bit Score: 40.09 E-value: 6.18e-05
10 20
....*....|....*....|....*...
gi 90111354 579 LQGLRNASVEEIAKVPGISQGLAEKIFW 606
Cdd:pfam00633 2 LEGLIPASVEELLALPGVGPKTAEAILS 29
|
|
| GIY-YIG_bI1_like |
cd10445 |
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The ... |
18-96 |
7.65e-05 |
|
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: 41.44 E-value: 7.65e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 18 PGVYRMYDAGGTVIYVGKAKDLKKRLSSYFrsNLASRKTEALVAQ------IQQIDVTV-----THTETEALLLEHNYIK 86
Cdd:cd10445 1 SGIYIWINKINGKIYVGSSINLYKRLRSYL--NPSYLKKNSPILRallkygLSNFTLTIleyynGENKEELLELEQYYID 78
|
90
....*....|
gi 90111354 87 LYQPRYNVLL 96
Cdd:cd10445 79 LLKPEYNILK 88
|
|
| GIY-YIG_EndoII_Hpy188I_like |
cd10436 |
Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction ... |
18-94 |
8.58e-05 |
|
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: 41.95 E-value: 8.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 18 PGVYrMYDAGGTVIYVGKAKDLKKRLSSY---------FRSNlaSRKTEAL---VAQIQQIDVTVTHTETE--------- 76
Cdd:cd10436 1 NGVY-AFVVDGEIVYIGETQDLRKRFNSYrggisprngQTTN--CRINKLIlkaLKKGKVVELYVKQPEELvitlgdpvn 77
|
90
....*....|....*....
gi 90111354 77 -ALLLEHNYIKLYQPRYNV 94
Cdd:cd10436 78 tAKGLEDELIEKIKPEWNS 96
|
|
| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
554-604 |
2.74e-04 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 39.46 E-value: 2.74e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 90111354 554 NTSS---LETIEGVGPKRRQMLLKY---MGGLQglrnaSVEEIAKVPGISQGLAEKI 604
Cdd:COG1555 16 NTATaeeLQTLPGIGPKLAQRIVEYrekNGPFK-----SVEDLLEVKGIGPKTLEKL 67
|
|
| denA |
PHA02598 |
endonuclease II; Provisional |
27-98 |
2.07e-03 |
|
endonuclease II; Provisional
Pssm-ID: 222902 [Multi-domain] Cd Length: 138 Bit Score: 38.97 E-value: 2.07e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111354 27 GGTVIYVGKAKDLKKRLSSY---------FRSN----------LASRKT-EALVAQIQQIDVTVTH---TETEALLLEHN 83
Cdd:PHA02598 42 DDELVYIGKTKNLRKRIDYYrnsknwrntNTSDitksalleeaLKKGKKvEFYARQCFNLSITNPLgsmTIATMDLEEPK 121
|
90
....*....|....*
gi 90111354 84 YIKLYQPRYNVLLRD 98
Cdd:PHA02598 122 FIKKFNPEWNKQHKK 136
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
558-604 |
3.71e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 40.24 E-value: 3.71e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 90111354 558 LETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKI 604
Cdd:PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRI 763
|
|
| HHH_2 |
pfam12826 |
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ... |
561-604 |
6.51e-03 |
|
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: 35.58 E-value: 6.51e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 90111354 561 IEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKI 604
Cdd:pfam12826 8 IRHVGETTAKLLARRFGSLDALAEASLEELLEVDDIGPEIAQSI 51
|
|
| |
