|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
22-628 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 902.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 22 FDIPLFLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNF 101
Cdd:PRK00558 2 EFLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 102 IKALSPKYNILFRDDKSYPYLML-SGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRD 180
Cdd:PRK00558 82 IKKYKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 181 RPCLLYQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQF 260
Cdd:PRK00558 162 RPCLLYQIGRCLAPCVGLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQK 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 261 IDsknPNNPNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEpngQDYAEAFVAQHYLGKSKPDIIISNFS 340
Cdd:PRK00558 242 VS---LKDGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSETEL---EEILEAFLGQFYLQKSIPKEILVPHE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 341 VPD-ALKEALEgeHGKQMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQQHRIDELAKILGMDSDGlNRLECFDIS 419
Cdd:PRK00558 316 LDDeELAEALL--AGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPP-YRIECFDIS 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 420 HTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAngetvKWPDAVLIDGGKGQIGVA 499
Cdd:PRK00558 393 HIQGTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEFG-----PLPDLILIDGGKGQLNAA 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 500 VSVWEELGLHIPLVGIAKGPERKAGMEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLSD 579
Cdd:PRK00558 468 KEVLEELGLDIPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDD 547
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 488158345 580 IPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHLH 628
Cdd:PRK00558 548 IPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
22-628 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 881.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 22 FDIPLFLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNF 101
Cdd:COG0322 4 FDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 102 IKALSPKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRDR 181
Cdd:COG0322 84 IKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRSR 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 182 PCLLYQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFI 261
Cdd:COG0322 164 PCLLYQIGRCSAPCVGLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQKV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 262 DSknpNNPNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEPngQDYAEAFVAQHYLGK-SKPDIIISNFS 340
Cdd:COG0322 244 VL---PDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDD--EELLEAFLAQYYLDRpSIPKEILVPEE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 341 VPDA--LKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQMAI----AQRRLQQSSQQHRIDELAKILGMDSDgLNRLE 414
Cdd:COG0322 319 LEDAelLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALerklAERERDEARQERALEELAEALGLPEL-PRRIE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 415 CFDISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAngetvKWPDAVLIDGGKG 494
Cdd:COG0322 398 CFDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDE-----PLPDLILIDGGKG 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 495 QIGVAVSVWEELGL-HIPLVGIAKgpeRKagmEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARV 573
Cdd:COG0322 473 QLNAAREVLEELGLdDIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARL 546
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 488158345 574 TSSLSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHLH 628
Cdd:COG0322 547 KSVLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLH 601
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
27-608 |
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: 567.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 27 FLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNdHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:TIGR00194 4 KLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSvfeHRDRPCLLY 186
Cdd:TIGR00194 83 PRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAKH---NRNRPCLYY 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 187 QIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDskNP 266
Cdd:TIGR00194 160 QIGRCLGPCVKEITEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVS--LT 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 267 NNpNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEpngQDYAEAFVAQHYLGKSK----PDIIISNFSVP 342
Cdd:TIGR00194 238 DL-IDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPGTDL---DELVETFLIQFYQQGYQnrliPSEILVSLSLE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 343 DA--LKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQQHRIDELAKILGMDSdgLNRLECFDISH 420
Cdd:TIGR00194 314 DLklLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPK--IKRIEIFDISH 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 421 TQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEaEANGEtvkWPDAVLIDGGKGQIGVAV 500
Cdd:TIGR00194 392 IDGSQTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQK-KNNLP---LPDLILIDGGKGQLNAAL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 501 SVWEELGL--HIPLVGIAKGpERKAGMEELILPFTGEVFRLppNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLS 578
Cdd:TIGR00194 468 EVLKSLGVvnKPIVIGLAKA-KRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLL 544
|
570 580 590
....*....|....*....|....*....|
gi 488158345 579 DIPGVGSKRRQALLTRFGGLRGVIAASRED 608
Cdd:TIGR00194 545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
400-560 |
1.42e-68 |
|
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: 219.63 E-value: 1.42e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 400 AKILGMDSDgLNRLECFDISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAnge 479
Cdd:pfam08459 1 QEALGLPKL-PRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFG--- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 480 tvKWPDAVLIDGGKGQIGVAVSVWEELGLHIPLVGIAKGPERKagmeeLILPFTGEVFRLPPNSPALHLLQTVRDESHRF 559
Cdd:pfam08459 77 --PLPDLILIDGGKGQLNAALEVLEELGLDIPVIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRF 149
|
.
gi 488158345 560 A 560
Cdd:pfam08459 150 A 150
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
31-111 |
3.13e-40 |
|
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: 141.47 E-value: 3.13e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 31 LPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSPKYN 110
Cdd:cd10434 1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYN 80
|
.
gi 488158345 111 I 111
Cdd:cd10434 81 I 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
35-115 |
9.49e-17 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 75.54 E-value: 9.49e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 35 PGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKND-HSPRIALMVKQVHHIETTITRSEAE-ALILENNFIKALSPKYNIL 112
Cdd:smart00465 2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRkGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNLL 81
|
...
gi 488158345 113 FRD 115
Cdd:smart00465 82 LKG 84
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
22-628 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 902.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 22 FDIPLFLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNF 101
Cdd:PRK00558 2 EFLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 102 IKALSPKYNILFRDDKSYPYLML-SGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRD 180
Cdd:PRK00558 82 IKKYKPRYNVLLRDDKSYPYIKItTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 181 RPCLLYQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQF 260
Cdd:PRK00558 162 RPCLLYQIGRCLAPCVGLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQK 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 261 IDsknPNNPNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEpngQDYAEAFVAQHYLGKSKPDIIISNFS 340
Cdd:PRK00558 242 VS---LKDGEDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVSETEL---EEILEAFLGQFYLQKSIPKEILVPHE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 341 VPD-ALKEALEgeHGKQMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQQHRIDELAKILGMDSDGlNRLECFDIS 419
Cdd:PRK00558 316 LDDeELAEALL--AGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPP-YRIECFDIS 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 420 HTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAngetvKWPDAVLIDGGKGQIGVA 499
Cdd:PRK00558 393 HIQGTATVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEFG-----PLPDLILIDGGKGQLNAA 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 500 VSVWEELGLHIPLVGIAKGPERKAGMEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLSD 579
Cdd:PRK00558 468 KEVLEELGLDIPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDD 547
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 488158345 580 IPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHLH 628
Cdd:PRK00558 548 IPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
22-628 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 881.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 22 FDIPLFLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNF 101
Cdd:COG0322 4 FDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 102 IKALSPKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRDR 181
Cdd:COG0322 84 IKKHKPRYNILLKDDKSYPYIKITNEEFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRSR 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 182 PCLLYQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFI 261
Cdd:COG0322 164 PCLLYQIGRCSAPCVGLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQKV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 262 DSknpNNPNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEPngQDYAEAFVAQHYLGK-SKPDIIISNFS 340
Cdd:COG0322 244 VL---PDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDD--EELLEAFLAQYYLDRpSIPKEILVPEE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 341 VPDA--LKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQMAI----AQRRLQQSSQQHRIDELAKILGMDSDgLNRLE 414
Cdd:COG0322 319 LEDAelLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALerklAERERDEARQERALEELAEALGLPEL-PRRIE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 415 CFDISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAngetvKWPDAVLIDGGKG 494
Cdd:COG0322 398 CFDISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDE-----PLPDLILIDGGKG 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 495 QIGVAVSVWEELGL-HIPLVGIAKgpeRKagmEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARV 573
Cdd:COG0322 473 QLNAAREVLEELGLdDIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARL 546
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 488158345 574 TSSLSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHLH 628
Cdd:COG0322 547 KSVLDEIPGIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLH 601
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
27-608 |
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: 567.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 27 FLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNdHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:TIGR00194 4 KLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSvfeHRDRPCLLY 186
Cdd:TIGR00194 83 PRYNVLLKDDKGYPYIYITHEKYPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAKH---NRNRPCLYY 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 187 QIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDskNP 266
Cdd:TIGR00194 160 QIGRCLGPCVKEITEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVS--LT 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 267 NNpNDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEpngQDYAEAFVAQHYLGKSK----PDIIISNFSVP 342
Cdd:TIGR00194 238 DL-IDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLPGTDL---DELVETFLIQFYQQGYQnrliPSEILVSLSLE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 343 DA--LKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQQHRIDELAKILGMDSdgLNRLECFDISH 420
Cdd:TIGR00194 314 DLklLEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNLPK--IKRIEIFDISH 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 421 TQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEaEANGEtvkWPDAVLIDGGKGQIGVAV 500
Cdd:TIGR00194 392 IDGSQTVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSIQK-KNNLP---LPDLILIDGGKGQLNAAL 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 501 SVWEELGL--HIPLVGIAKGpERKAGMEELILPFTGEVFRLppNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLS 578
Cdd:TIGR00194 468 EVLKSLGVvnKPIVIGLAKA-KRHETDIFLIGDKQGINIDL--NSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLL 544
|
570 580 590
....*....|....*....|....*....|
gi 488158345 579 DIPGVGSKRRQALLTRFGGLRGVIAASRED 608
Cdd:TIGR00194 545 KIPGVGEKRVQKLLKYFGSLKGIKKASVEE 574
|
|
| uvrC |
PRK14669 |
excinuclease ABC subunit C; Provisional |
28-626 |
3.75e-129 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237784 [Multi-domain] Cd Length: 624 Bit Score: 393.51 E-value: 3.75e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 28 LKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYF-QKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:PRK14669 7 IRTLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFsEDKLGNIKTGSLIREAVDIDYILVDNEKEALALENNLIKQYK 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLS-GHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRDRPCLL 185
Cdd:PRK14669 87 PRFNILLRDDKTYPYVKLTlGEKYPRVYVTRRLRKDGAQYYGPFFPANLAYRLVDLIHRHFLVPSCKVDLTRYHPRPCLQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 186 YQIKRCTAPCVGHIS-EEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDSK 264
Cdd:PRK14669 167 FYIHRCLGPCVQGLTtDEAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVEELEEKQRMAAA 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 265 NPNnpnDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEPNGQ----DYAEAFVAQHYL-GKSKPDIIIS-- 337
Cdd:PRK14669 247 KGD---DADVFGYHYENPMVAVNLFHMRGGKIVDRREFFWEDLGEVQVEFEydegLFFSSLLKQIYLdQQYVPREIYVpv 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 338 NFSVPDALKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQQHRIDELAKILGMDSDGLNRLECFD 417
Cdd:PRK14669 324 EFEDREALEELLTEQRHRRIEIRVPQRGDKRSLLDLVEQNAKQSYDQRFRVMKPSSRAIQEALQDALNLPELPSRIECFD 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 418 ISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEaeangETVKWPDAVLIDGGKGQIG 497
Cdd:PRK14669 404 ISHIQGAETVASMVVWEDGKMKKSDYRKFIIKTVVGVDDFASMREVVTRRYSRLQE-----EKQPMPGLVLIDGGLGQLH 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 498 VAVSVWEELGL-HIPLVGIAKgperkagMEELILPF--TGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARVT 574
Cdd:PRK14669 479 AAAEALEAIGItDQPLASIAK-------REEIIYVFgqEDEPIVLDRFSPVLHLVQSIRDEAHRFAITFHRKRRETRDRT 551
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 488158345 575 SSLSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVegISKALAETIYNH 626
Cdd:PRK14669 552 SELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAH 601
|
|
| uvrC |
PRK14668 |
excinuclease ABC subunit C; Provisional |
31-627 |
3.68e-122 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 184785 [Multi-domain] Cd Length: 577 Bit Score: 373.72 E-value: 3.68e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 31 LPKLPGVYRFFdEGGKVLYVGKAVNLKRRVSGYfqKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSPKYN 110
Cdd:PRK14668 13 LPREPGVYQFV-AGGTVLYVGKAVDLRDRVRSY--ADPRSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQPRYN 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 111 ILFRDDKSYPYLMLSGHQYPQMAYYRgtlkKPNQ---YFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRDRPCLLYQ 187
Cdd:PRK14668 90 VRLKDDKSYPLVQLTDHPVPRIEVTR----DPDEgatVFGPYTDKGRVETVVKALRETYGLRGCSDHKYSNRDRPCLDYE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 188 IKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDSKNPN 267
Cdd:PRK14668 166 MGLCTAPCTGEIDEEAYAEDVESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHGGGGEAVSSTG 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 268 NPNDIDLLALAVSDGLVCVHWVSIRGGRHVgDKSFFPDTKNDPEPNGQDYAEAFVAQHYLGKSKPDIIISNFSVPDA-LK 346
Cdd:PRK14668 246 DERAVDVLGVAIEGDRATVARLHAEGGQLV-DRDRHRLEAPDGEDRGAAVLAAFIVQYYAERELPDALLLSERPGDDdVR 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 347 EALEGEhgkQMQFVTKTIGERKVWLKMAEQNAQMAIAqrrlqqssqqhRIDE---LAKILGMDSdgLNRLECFDISHTQG 423
Cdd:PRK14668 325 AWLEAE---GVDVRVPGAGREATLVDLALKNARRRGG-----------RDDEvgaLADALGIDR--PERIEGFDVSHAQG 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 424 EATIASCVVYDEQNIQPSQYRRYNITtaKPGDDYAAMREVLTRRYGKMQEAEANGETvkwPDAVLIDGGKGQIGVAVSVW 503
Cdd:PRK14668 389 RAVVGSNVCFVDGSAETADYRRKKLT--ERNDDYANMRELVRWRAERAVEGRDDRPD---PDLLLIDGGDGQLGAARDAL 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 504 EELGLHIPLVGIAKGperkagmEELILPFTGeVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKarVTSSLSDIPGV 583
Cdd:PRK14668 464 AETGWDVPAIALAKA-------EELVVTPDR-TYDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLRDD--VSTVLDDVPGV 533
|
570 580 590 600
....*....|....*....|....*....|....*....|....
gi 488158345 584 GSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHL 627
Cdd:PRK14668 534 GPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRERL 577
|
|
| uvrC |
PRK14667 |
excinuclease ABC subunit C; Provisional |
27-627 |
2.92e-120 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237783 [Multi-domain] Cd Length: 567 Bit Score: 368.68 E-value: 2.92e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 27 FLKNLPKLPGVYrFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:PRK14667 9 LIEKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQYK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKpNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDsvFEHRDRPCLLY 186
Cdd:PRK14667 88 PKYNVLLKSGSGYPMLLITDDEYPTVKIVRGTGEK-GEYFGPFLPARKARKVKKLIHKLFKLRTCDP--MPKRKEPCMDY 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 187 QIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIdSKNP 266
Cdd:PRK14667 165 HLGLCSGPCCGKISKEDYELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALENLIKGQEV-SGLP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 267 NNPNDIDLLALAVsdglvcVHWVSIRGGRHVGDKSFfpDTKNDPEPNGQdyaeaFVAQHYLGKSKPDIIISNFSVPDALK 346
Cdd:PRK14667 244 IEEADIFYFMGSR------LGLFLVRSSKLVGKEEF--RLESEEQEEEE-----VILGYYYSNYIPQKIITNFELSDNLK 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 347 EALEGEHGKQMQFVTKTIGERKvwlKMAEQNAQMAIAQRRLQqssqqhriDELAKILGMDSdgLNRLECFDISHTQGEAT 426
Cdd:PRK14667 311 QWLSKRKGGDVEFLTLIPKELE---KFIEENIGIKVDLEVLK--------EEFKKTFGFPL--PERIEGFDISHFYGEFT 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 427 IASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEangetVKWPDAVLIDGGKGQIGVAVSVWEEL 506
Cdd:PRK14667 378 VGSCVVWEDGSMNKKEYRRYKIKTVDGIDDYASLREVLTRRARRYKEGE-----NPMPDLWLIDGGKGQLSVGIEVRDRL 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 507 GLHIPLVGIAKgperkagMEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLSDIPGVGSK 586
Cdd:PRK14667 453 GLNIKVFSLAK-------KEEILYTEDGKEIPLKENPILYKVFGLIRDEAHRFALSYNRKLREKEGLKDILDKIKGIGEV 525
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 488158345 587 RRQALLTRFGGLRGVIAASREDLEKVeGISKALAETIYNHL 627
Cdd:PRK14667 526 KKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYL 565
|
|
| uvrC |
PRK14666 |
excinuclease ABC subunit C; Provisional |
28-627 |
7.09e-98 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237782 [Multi-domain] Cd Length: 694 Bit Score: 314.13 E-value: 7.09e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 28 LKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQK-NDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:PRK14666 6 LSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDvSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKHR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLSG-HQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEDSVFEHRDRPCLL 185
Cdd:PRK14666 86 PRYNIVLRDDKQYVLFRLGAkHPYPRLEIVRKARRDGARYFGPFTSASAARETWKTIHRAFPLRRCSDRAFGNRVRACLY 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 186 YQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALgimqsNQFIDSKN 265
Cdd:PRK14666 166 HFMGQCLGPCVNDVPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAV-----ERTVERQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 266 PNNP--NDIDLLALAVSDGLVCVHWVSIRGGRHVGDKSFF---------------------------------------- 303
Cdd:PRK14666 241 AVLPggGDLDVVGLVEAEGGLALGVLFVRQGVLLDGRAFFwpglgfeeapellwsflgqfygpqstipprivvpwlpdte 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 304 ----------------------------------------PDTKNDPEPNGQDYAEAFVAQHYLGKSKPDIIISnfSVPD 343
Cdd:PRK14666 321 gregddlaptavctdagllpdtpllpdapegssdpvvpvaAATPVDASLPDVRTGTAPTSLANVSHADPAVAQP--TQAA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 344 A-------------LKEALEGEHGKQMQFVTKTIGERKVWLKMAEQNAQmaiaqRRLQQSSQQHRIDELAKILGMdSDGL 410
Cdd:PRK14666 399 TlagaapkgathlmLEETLADLRGGPVRIVPPRNPAENRLVDMAMSNAR-----EEARRKAETPLQDLLARALHL-SGPP 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 411 NRLECFDISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKpGDDYAAMREVLTRRYgkmqeaeANGEtvKWPDAVLID 490
Cdd:PRK14666 473 HRIEAVDVSHTGGRNTRVGMVVFEDGKPARDAYRTYAFEDGE-GDDYGTLAAWAGRRV-------ESGP--PWPDLLLVD 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 491 GGKGQIGVAVSVWEELGLH--IPLVGIAKG------PERKAG--MEELILPFTGEVFRLPPNSPALHLLQTVRDESHRFA 560
Cdd:PRK14666 543 GGRGQLAAVVRALEEAGMGglFAVASIAKArteegrADRRAGnvADRIFLPGRANPLPLRAGAPELLFLQHVRDTVHDYA 622
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488158345 561 ITGHRKKRDKARVTSSLSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHL 627
Cdd:PRK14666 623 IGRHRRARAGAALTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689
|
|
| uvrC |
PRK14672 |
excinuclease ABC subunit C; Provisional |
32-623 |
1.48e-81 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173135 [Multi-domain] Cd Length: 691 Bit Score: 271.22 E-value: 1.48e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 32 PKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFqKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSPKYNI 111
Cdd:PRK14672 19 PSTSGVYLWKDVHGVVIYVGKAKSLRTRLTSYF-RCRHDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHTPRYNI 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 112 LFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCedSVFEHRDRPCLLYQIKRC 191
Cdd:PRK14672 98 CLKDGKTYPLLKLTCEPFPRIFRTRQFCQDGARYFGPFPDVQILDSFLKLILRTYKIRTC--TTLRKRKNPCLYYHLKRC 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 192 TAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDSKNPNNPnd 271
Cdd:PRK14672 176 DAPCCGWVSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITHKSLVQDMDERAR-- 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 272 iDLLALAVSDGLVCVHWVSIRGGRHVGDKSFFPDT-KNDPE----------------PNGQDYAEAFVAQHYLGKSKPD- 333
Cdd:PRK14672 254 -DYIAWSSTGAIVTFAVLRMRGGKLNGRELFRTRSlKNEEEilseflityysdhtipPHLFVHSSAGLAEHWLSHKAGTq 332
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 334 -----IIISNFSVP-------------------------DALKEALEGEHGKQMQ----FVTKTIGER------------ 367
Cdd:PRK14672 333 ctvtlIPLHTFPTPqtpsstvttnaptlaasqnsnavqdSGLRSCSETSTMHTLQkahdACTASEGTRentphesahtph 412
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 368 -KVWLKMAEQNAQMAIAqRRLQQSSQQHRIDELAKILGMdSDGLNRLECFDISHTQGEATIASCVVYDEQNIQPSQYRRY 446
Cdd:PRK14672 413 hRAILAMAQLNAHEDIT-RYLKNRGADDALKELQKQLHL-ARIPTLIEGFDISHLGGKYTVASLICFKNGAPDTKNYRLF 490
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 447 NITTAKPG-DDYAAMREVLTRRYGKMQEaeanGETVkwPDAVLIDGGKGQIGVAVSVWEELGLHIPLVGIAKGPerkagm 525
Cdd:PRK14672 491 NLRAHDTRiDDFASMREAIARRYTHTPE----GYTL--PDLILVDGGIGHVSAAQHVLDALGLSIPLVGLAKRA------ 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 526 EELILPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKARVTSSLSDIPGVGSKRRQALLTRFGGLRGVIAAS 605
Cdd:PRK14672 559 EELFIPNSPTPLVLDRRNPALHMLQRIRDEAHRFAITRNRHLRTKKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQSAT 638
|
650
....*....|....*...
gi 488158345 606 REDLEKVEGISKALAETI 623
Cdd:PRK14672 639 PQDIATAIHIPLTQAHTI 656
|
|
| uvrC |
PRK14670 |
excinuclease ABC subunit C; Provisional |
41-623 |
2.44e-70 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173133 [Multi-domain] Cd Length: 574 Bit Score: 238.27 E-value: 2.44e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 41 FDEGGKVLYVGKAVNLKRRVSGYFQKNDhSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSPKYNILFRDDKSYP 120
Cdd:PRK14670 2 YSENNKILYIGKAKNLRSRVKNYFLEKI-SHKTKILMKNVKNIEVITTNSEYEALLLECNLIKTHKPDYNIKLKDDKGYP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 121 YLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCEdsvfEHRDRPCLLYQIKRCTAPCVGHIS 200
Cdd:PRK14670 81 MIRITCEKYPRIFKTRKIINDGSEYFGPYVNVKKLDLVLDLINKTFKTRKCK----KKSKNPCLYFHMGQCLGVCYREDL 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 201 EEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQALGIMQSNQFIDSKNPNNPndiDLLALAVS 280
Cdd:PRK14670 157 EKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKETKRSLIEISQTQIITKINKLSI---DYVYIHPT 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 281 DGLVCVHWVSIRGGRHVGDKSFFPDTKNDPEpngqDYAEAFVAQHYlgkSKPDIIISN-------FSVPDALKEALEGEH 353
Cdd:PRK14670 234 ENLNTIVILKYKDGKLVEKDINFDESIYEED----ELILQFITQYY---TSINMIVPDkihifkkIDTKNITKLINELKN 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 354 GKqMQFVTKTIGERKVWLKMAEQNAQMAIAQRRLQQSSQqhrIDELAKILGMDSdgLNR-LECFDISHTQGEATIASCVV 432
Cdd:PRK14670 307 TK-TEIIYKETKEIIKIMEMAISNAKLALREYENEKNKA---LESLKIILEMDK--LPKtIEGFDIAHLNGQKTVASLVT 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 433 YDEQNIQPSQYRRYNITTAKPG--DDYAAMREVLTRRYGKMQEaeangETVKWPDAVLIDGGKGQIGVAVSVWEELGLH- 509
Cdd:PRK14670 381 FKMGKPFKDGYRVYKINSLLKGeiDDFKAIKEVISRRYSKLIN-----EQLELPNLILIDGGKGQLNAAYSILKGLKIEn 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 510 -IPLVGIAKgperkagMEELI-LPFTGEVFRLPPNSPALHLLQTVRDESHRFAITGHRKKRDKarVTSSLSDIPGVGSKR 587
Cdd:PRK14670 456 kVKVCALAK-------KEETIfLPNKKQGIKLPKGNPALRILQNVRDEAHRKANGFNKKLREN--IKLNYTKIKGIGEKK 526
|
570 580 590
....*....|....*....|....*....|....*.
gi 488158345 588 RQALLTRFGGLRGVIAASREDLEKVEGISKALAETI 623
Cdd:PRK14670 527 AKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKI 562
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
400-560 |
1.42e-68 |
|
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: 219.63 E-value: 1.42e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 400 AKILGMDSDgLNRLECFDISHTQGEATIASCVVYDEQNIQPSQYRRYNITTAKPGDDYAAMREVLTRRYGKMQEAEAnge 479
Cdd:pfam08459 1 QEALGLPKL-PRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFG--- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 480 tvKWPDAVLIDGGKGQIGVAVSVWEELGLHIPLVGIAKGPERKagmeeLILPFTGEVFRLPPNSPALHLLQTVRDESHRF 559
Cdd:pfam08459 77 --PLPDLILIDGGKGQLNAALEVLEELGLDIPVIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRF 149
|
.
gi 488158345 560 A 560
Cdd:pfam08459 150 A 150
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
27-252 |
2.34e-57 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 202.46 E-value: 2.34e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 27 FLKNLPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALS 106
Cdd:PRK07883 210 LADGLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIAAHK 289
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 107 PKYNILFRDDKSYPYLMLSGHQYPQMAYYRGTLKKPNQYFGPYPNSNAVRDSIQVLQKVFMLRTCED--SVFEHRDRPCL 184
Cdd:PRK07883 290 PPYNRRSKFPERRWWVRLTDEAFPRLSVVRAVEDDGAAYLGPFRSRRAAEEAAEALARAFPLRQCTDrlSRRARHGPACA 369
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488158345 185 LYQIKRCTAPCVGHISEEDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQAL 252
Cdd:PRK07883 370 LAELGRCPAPCDGRESAAEYAEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLAAL 437
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
31-111 |
3.13e-40 |
|
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: 141.47 E-value: 3.13e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 31 LPKLPGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSPKYN 110
Cdd:cd10434 1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYN 80
|
.
gi 488158345 111 I 111
Cdd:cd10434 81 I 81
|
|
| PRK10545 |
PRK10545 |
excinuclease Cho; |
27-211 |
5.54e-17 |
|
excinuclease Cho;
Pssm-ID: 182535 Cd Length: 286 Bit Score: 81.64 E-value: 5.54e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 27 FLKNLPKLPGVYRFF-DEGGKVLYVGKAVNLKRRVSGYFQkndhSPRIALMVKQVHHIETTITRSEAEALILENNFIKAL 105
Cdd:PRK10545 27 FLEDLPKLPGVYLFHgESDTMPLYIGKSVNIRSRVLSHLR----TPDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQ 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 106 SPKYNILFRDDKSYPYLMLSGHQyPQMAYYRGT--LKKPNQYfGPYPNSNAVRDSiqvlqkvfmLRTCEDsvfEHR---- 179
Cdd:PRK10545 103 QPLFNKRLRRNRQLCSLQLNEGR-VDVVYAKEVdfSRAPNLF-GLFANRRAALQA---------LQSIAD---EQKlcyg 168
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 488158345 180 ---------DRPCLLYQIKRCTAPCVGHISEEDYHDSVREA 211
Cdd:PRK10545 169 llgleplsrGRACFRSALKRCAGACCGKESHEAHALRLRAS 209
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
35-115 |
9.49e-17 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 75.54 E-value: 9.49e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 35 PGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKND-HSPRIALMVKQVHHIETTITRSEAE-ALILENNFIKALSPKYNIL 112
Cdd:smart00465 2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRkGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNLL 81
|
...
gi 488158345 113 FRD 115
Cdd:smart00465 82 LKG 84
|
|
| MUS81 |
COG1948 |
ERCC4-type crossover junction endonuclease [Replication, recombination and repair]; |
553-624 |
1.99e-11 |
|
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
Pssm-ID: 441551 [Multi-domain] Cd Length: 214 Bit Score: 63.66 E-value: 1.99e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488158345 553 RDESHRFAITGHRKKRD-KARVTSSLSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIY 624
Cdd:COG1948 132 EEEKREVSLHGKKKPKTlREQQLYVVESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVEGIGEKTAERIR 204
|
|
| GIY-YIG |
pfam01541 |
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ... |
35-110 |
2.23e-11 |
|
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: 60.05 E-value: 2.23e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488158345 35 PGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTITRSEAEALILENNFIKALSP-KYN 110
Cdd:pfam01541 2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPnKYN 78
|
|
| GIY-YIG_SF |
cd00719 |
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ... |
36-105 |
3.05e-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: 56.22 E-value: 3.05e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 36 GVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKNDHSPRIALMVKQVHHIETTiTRSEAEALILENNFIKAL 105
Cdd:cd00719 1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVA-PEAESELLDLEAALIKKL 69
|
|
| UVR |
pfam02151 |
UvrB/uvrC motif; |
220-252 |
3.51e-08 |
|
UvrB/uvrC motif;
Pssm-ID: 308001 [Multi-domain] Cd Length: 36 Bit Score: 49.70 E-value: 3.51e-08
10 20 30
....*....|....*....|....*....|...
gi 488158345 220 DELTRTLQHKMQTAAANLQFEEAARYRDQIQAL 252
Cdd:pfam02151 1 KKLIKELEEEMEEAAENEDFEKAAKLRDQINAL 33
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
220-252 |
1.26e-06 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 51.55 E-value: 1.26e-06
10 20 30
....*....|....*....|....*....|...
gi 488158345 220 DELTRTLQHKMQTAAANLQFEEAARYRDQIQAL 252
Cdd:COG0556 622 EKLIKELEKEMKEAAKNLEFEEAARLRDEIKEL 654
|
|
| GIY-YIG_bI1_like |
cd10445 |
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The ... |
35-112 |
1.98e-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: 46.06 E-value: 1.98e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 35 PGVYRFFDEGGKVLYVGKAVNLKRRVSGYFQKN---DHSPRIALMVKQVHH------IETTITRSEAEALILENNFIKAL 105
Cdd:cd10445 1 SGIYIWINKINGKIYVGSSINLYKRLRSYLNPSylkKNSPILRALLKYGLSnftltiLEYYNGENKEELLELEQYYIDLL 80
|
....*..
gi 488158345 106 SPKYNIL 112
Cdd:cd10445 81 KPEYNIL 87
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
202-252 |
2.78e-06 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 50.43 E-value: 2.78e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 488158345 202 EDYHDSVREAATFLNGKTDELTRTLQHKMQTAAANLQFEEAARYRDQIQAL 252
Cdd:PRK05298 594 RDILDSVYKKDKLSKKELEKLIKELEKQMKEAAKNLEFEEAARLRDEIKEL 644
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
577-627 |
6.03e-06 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 43.63 E-value: 6.03e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 488158345 577 LSDIPGVGSKRRQALL-TRFGGLRGVIAASREDLEKVEGISKALAETIYNHL 627
Cdd:pfam14520 4 LLSISGIGPKTALALLsAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILEL 55
|
|
| DisA |
COG1623 |
c-di-AMP synthetase DisA, contains DisA_N, linker and DNA-binding domains [Signal transduction ... |
577-623 |
1.17e-05 |
|
c-di-AMP synthetase DisA, contains DisA_N, linker and DNA-binding domains [Signal transduction mechanisms];
Pssm-ID: 441230 [Multi-domain] Cd Length: 353 Bit Score: 47.82 E-value: 1.17e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 488158345 577 LSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETI 623
Cdd:COG1623 290 LSKIPRLPSAVIENLVEHFGSLQKLLAASIEELDDVEGIGEVRARAI 336
|
|
| HHH_2 |
pfam12826 |
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ... |
572-628 |
2.17e-05 |
|
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: 42.51 E-value: 2.17e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 488158345 572 RVTSSLSdIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHLH 628
Cdd:pfam12826 1 RLLFALG-IRHVGETTAKLLARRFGSLDALAEASLEELLEVDDIGPEIAQSIVEFFA 56
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
577-624 |
8.46e-05 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 45.63 E-value: 8.46e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 488158345 577 LSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIY 624
Cdd:PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIR 764
|
|
| PRK00024 |
PRK00024 |
DNA repair protein RadC; |
575-623 |
1.00e-04 |
|
DNA repair protein RadC;
Pssm-ID: 178801 [Multi-domain] Cd Length: 224 Bit Score: 43.91 E-value: 1.00e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488158345 575 SSLSD------IPGVGSKRR------QALLTRFGGLRGVIAASREDLEKVEGISKALAETI 623
Cdd:PRK00024 22 AALSDaellaiLLRTGTKGKsvldlaRELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQL 82
|
|
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
565-625 |
1.55e-04 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 44.63 E-value: 1.55e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488158345 565 RKKRDKARVTSSLSdIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYN 625
Cdd:COG0272 503 SKKTPLARFLFALG-IRHVGETTAKLLARHFGSLDALMAASEEELAAVDGIGPVVAESIVE 562
|
|
| GIY-YIG_EndoII_Hpy188I_like |
cd10436 |
Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction ... |
35-111 |
1.67e-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: 40.80 E-value: 1.67e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488158345 35 PGVYRFFdEGGKVLYVGKAVNLKRRVSGYfqKNDHSPR--------------------IALMVKQVHHIETTITRSEAEA 94
Cdd:cd10436 1 NGVYAFV-VDGEIVYIGETQDLRKRFNSY--RGGISPRngqttncrinklilkalkkgKVVELYVKQPEELVITLGDPVN 77
|
90
....*....|....*....
gi 488158345 95 L--ILENNFIKALSPKYNI 111
Cdd:cd10436 78 TakGLEDELIEKIKPEWNS 96
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| HHH |
pfam00633 |
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated ... |
598-626 |
2.42e-04 |
|
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: 38.55 E-value: 2.42e-04
10 20
....*....|....*....|....*....
gi 488158345 598 LRGVIAASREDLEKVEGISKALAETIYNH 626
Cdd:pfam00633 2 LEGLIPASVEELLALPGVGPKTAEAILSY 30
|
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| Smf |
COG0758 |
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake ... |
577-628 |
2.52e-04 |
|
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake [Replication, recombination and repair];
Pssm-ID: 440521 [Multi-domain] Cd Length: 360 Bit Score: 43.53 E-value: 2.52e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 488158345 577 LSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVeGISKALAETIYNHLH 628
Cdd:COG0758 10 LSRVPGVGPVTLRRLLAHFGSAEAALEALPSELARL-GLGEKAAEAIRARPD 60
|
|
| PRK13482 |
PRK13482 |
DNA integrity scanning protein DisA; Provisional |
577-627 |
3.26e-04 |
|
DNA integrity scanning protein DisA; Provisional
Pssm-ID: 237395 [Multi-domain] Cd Length: 352 Bit Score: 43.23 E-value: 3.26e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 488158345 577 LSDIPGVGSKRRQALLTRFGGLRGVIAASREDLEKVEGISKALAETIYNHL 627
Cdd:PRK13482 289 LSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGL 339
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|
| McsA |
COG3880 |
Protein-arginine kinase activator protein McsA [Posttranslational modification, protein ... |
226-252 |
2.41e-03 |
|
Protein-arginine kinase activator protein McsA [Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 443088 [Multi-domain] Cd Length: 173 Bit Score: 39.11 E-value: 2.41e-03
10 20
....*....|....*....|....*..
gi 488158345 226 LQHKMQTAAANLQFEEAARYRDQIQAL 252
Cdd:COG3880 138 LKEELQEAVEKEEYEEAAELRDEIREL 164
|
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| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
577-627 |
5.70e-03 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 35.99 E-value: 5.70e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 488158345 577 LSDIPGVGSKRRQALL---TRFGGLRGViaasrEDLEKVEGISKALAETIYNHL 627
Cdd:COG1555 23 LQTLPGIGPKLAQRIVeyrEKNGPFKSV-----EDLLEVKGIGPKTLEKLKPYL 71
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