|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
11-608 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 930.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 11 LATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRP 90
Cdd:PRK00558 8 LKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 91 PYNILLRDDKSYPFVFLSSEDEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRTRPCLQY 170
Cdd:PRK00558 88 RYNVLLRDDKSYPYIKITTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRKRPCLLY 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 171 QIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGNG 250
Cdd:PRK00558 168 QIGRCLAPCVGLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQKVSLKDG 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 251 -DVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAiEEEVGEVLLAFLGQYYLSHqerDLPAELIVNVTHEDfpvlv 329
Cdd:PRK00558 248 eDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVS-ETELEEILEAFLGQFYLQK---SIPKEILVPHELDD----- 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 330 SAIAEA--RGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQHVAARFEALAEALDLAEPPQRLECFDISHSSGEA 407
Cdd:PRK00558 319 EELAEAllAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPPYRIECFDISHIQGTA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVAg 487
Cdd:PRK00558 399 TVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEFGPLPDLILIDGGKGQLNAAKEVLEELGLD- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 488 LILLGVAKGVTRKPGLETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKRRR 567
Cdd:PRK00558 478 IPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDDIPGIGPKRRK 557
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 15597781 568 DLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:PRK00558 558 ALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
5-608 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 912.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 5 FDASAFLATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTL 84
Cdd:COG0322 4 FDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 85 IKEWRPPYNILLRDDKSYPFVFLSSEdEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRT 164
Cdd:COG0322 84 IKKHKPRYNILLKDDKSYPYIKITNE-EFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRS 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 165 RPCLQYQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQS 244
Cdd:COG0322 163 RPCLLYQIGRCSAPCVGLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQK 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 245 ME-GGNGDVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAIEEEVGEVLLAFLGQYYLSHQerDLPAELIVNVTHE 323
Cdd:COG0322 243 VVlPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRP--SIPKEILVPEELE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 324 DFPVLVSAIAEARGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQ----HVAARFEALAEALDLAEPPQRLECFD 399
Cdd:COG0322 321 DAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERErdeaRQERALEELAEALGLPELPRRIECFD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 400 ISHSSGEATVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEV 479
Cdd:COG0322 401 ISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDEPLPDLILIDGGKGQLNAAREV 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 480 LQELAVAGLILLGVAKgvtRKpglETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVP 559
Cdd:COG0322 481 LEELGLDDIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLKSVLDEIP 554
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 15597781 560 GVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:COG0322 555 GIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLHKE 603
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
10-586 |
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: 610.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 10 FLATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSgLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWR 89
Cdd:TIGR00194 4 KLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 90 PPYNILLRDDKSYPFVFLSSEDeYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDsyfRNRTRPCLQ 169
Cdd:TIGR00194 83 PRYNVLLKDDKGYPYIYITHEK-YPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAK---HNRNRPCLY 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 170 YQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGN 249
Cdd:TIGR00194 159 YQIGRCLGPCVKEITEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTD 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 250 G-DVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAiEEEVGEVLLAFLGQYYLSH-QERDLPAELIVNVTHEDFPV 327
Cdd:TIGR00194 239 LiDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLP-GTDLDELVETFLIQFYQQGyQNRLIPSEILVSLSLEDLKL 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 328 LVSAIAEARGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQHVAARFEALAEALDLaEPPQRLECFDISHSSGEA 407
Cdd:TIGR00194 318 LEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNL-PKIKRIEIFDISHIDGSQ 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSR-LKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVA 486
Cdd:TIGR00194 397 TVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSiQKKNNLPLPDLILIDGGKGQLNAALEVLKSLGVV 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 487 G-LILLGVAKgVTRKPGLETLYLNdaSHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKR 565
Cdd:TIGR00194 477 NkPIVIGLAK-AKRHETDIFLIGD--KQGINIDLNSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPGVGEKR 553
|
570 580
....*....|....*....|.
gi 15597781 566 RRDLLKHFGGLQELSRASIDE 586
Cdd:TIGR00194 554 VQKLLKYFGSLKGIKKASVEE 574
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
383-538 |
4.10e-76 |
|
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: 238.89 E-value: 4.10e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 383 AEALDLAEPPQRLECFDISHSSGEATVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPD 462
Cdd:pfam08459 1 QEALGLPKLPRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFGPLPD 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597781 463 ILLVDGGKGQLAMAQEVLQELAVaGLILLGVAKGVTRKpgletLYLNDASHEFTLPADSPALHLIQQIRDEAHRFA 538
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 ... |
16-94 |
3.87e-36 |
|
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: 129.91 E-value: 3.87e-36
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597781 16 NRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNI 94
Cdd:cd10434 3 DSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
17-98 |
1.23e-17 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 77.85 E-value: 1.23e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 17 RPGVYRMFDAEAKLLYVGKAKSLKKRLASYFR-KSGLAPKTAALVARIAQVETTITANETE-ALLLEQTLIKEWRPPYNI 94
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSgSRKGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 15597781 95 LLRD 98
Cdd:smart00465 81 LLKG 84
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| uvrC |
PRK00558 |
excinuclease ABC subunit UvrC; |
11-608 |
0e+00 |
|
excinuclease ABC subunit UvrC;
Pssm-ID: 234792 [Multi-domain] Cd Length: 598 Bit Score: 930.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 11 LATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRP 90
Cdd:PRK00558 8 LKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 91 PYNILLRDDKSYPFVFLSSEDEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRTRPCLQY 170
Cdd:PRK00558 88 RYNVLLRDDKSYPYIKITTNEEFPRLAITRGVAKDKGRYFGPYPSAGAVRETLDLLQKLFPLRTCEDSVFKNRKRPCLLY 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 171 QIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGNG 250
Cdd:PRK00558 168 QIGRCLAPCVGLISKEEYAELVDEAKLFLSGKTDEVLKELEEKMEEASENLEFERAARYRDQIQALRRVQEKQKVSLKDG 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 251 -DVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAiEEEVGEVLLAFLGQYYLSHqerDLPAELIVNVTHEDfpvlv 329
Cdd:PRK00558 248 eDADVIAIAVDGGWACVQVFFVRGGKLLGRRSYFPKVS-ETELEEILEAFLGQFYLQK---SIPKEILVPHELDD----- 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 330 SAIAEA--RGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQHVAARFEALAEALDLAEPPQRLECFDISHSSGEA 407
Cdd:PRK00558 319 EELAEAllAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQQQALEELAELLGLPEPPYRIECFDISHIQGTA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVAg 487
Cdd:PRK00558 399 TVASMVVFEDGGPDKSEYRRYNIKGVTGGDDYAAMREVLTRRYSRLLKEFGPLPDLILIDGGKGQLNAAKEVLEELGLD- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 488 LILLGVAKGVTRKPGLETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKRRR 567
Cdd:PRK00558 478 IPVVGLAKGDKRKAGTEELFFPGEPEPIILPPDSPALYLLQRIRDEAHRFAITFHRKKRSKARLTSALDDIPGIGPKRRK 557
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 15597781 568 DLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:PRK00558 558 ALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHKK 598
|
|
| UvrC |
COG0322 |
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]; |
5-608 |
0e+00 |
|
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
Pssm-ID: 440091 [Multi-domain] Cd Length: 603 Bit Score: 912.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 5 FDASAFLATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTL 84
Cdd:COG0322 4 FDLKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 85 IKEWRPPYNILLRDDKSYPFVFLSSEdEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRT 164
Cdd:COG0322 84 IKKHKPRYNILLKDDKSYPYIKITNE-EFPRIFVTRGVKKDGGRYFGPYPSAGAVRETLDLLQKLFPLRTCSDSLFKNRS 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 165 RPCLQYQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQS 244
Cdd:COG0322 163 RPCLLYQIGRCSAPCVGLISEEEYREDVEQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRALEKVQEKQK 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 245 ME-GGNGDVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAIEEEVGEVLLAFLGQYYLSHQerDLPAELIVNVTHE 323
Cdd:COG0322 243 VVlPDGGDADVIAIARDGGEACVQVFFVRGGRLIGRRSFFLEKVLDEDDEELLEAFLAQYYLDRP--SIPKEILVPEELE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 324 DFPVLVSAIAEARGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQ----HVAARFEALAEALDLAEPPQRLECFD 399
Cdd:COG0322 321 DAELLEEWLSERRGRKVKIRVPQRGEKKKLLELAEKNAREALERKLAERErdeaRQERALEELAEALGLPELPRRIECFD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 400 ISHSSGEATVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEV 479
Cdd:COG0322 401 ISHIQGTNTVASMVVFEDGKPDKSDYRRFKIKTVEGGDDYASMREVLTRRYKRLLEEDEPLPDLILIDGGKGQLNAAREV 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 480 LQELAVAGLILLGVAKgvtRKpglETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVP 559
Cdd:COG0322 481 LEELGLDDIPVIGLAK---RD---EELFLPGDSEPIILPRNSPALYLLQRIRDEAHRFAITFHRKLRSKARLKSVLDEIP 554
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 15597781 560 GVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:COG0322 555 GIGPKRRKALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEYLHKE 603
|
|
| uvrC |
TIGR00194 |
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ... |
10-586 |
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: 610.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 10 FLATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSgLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWR 89
Cdd:TIGR00194 4 KLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 90 PPYNILLRDDKSYPFVFLSSEDeYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDsyfRNRTRPCLQ 169
Cdd:TIGR00194 83 PRYNVLLKDDKGYPYIYITHEK-YPRLLITRKLKQDKGKYFGPFTNAFALRETLDLLLKLFPLRKCAK---HNRNRPCLY 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 170 YQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGN 249
Cdd:TIGR00194 159 YQIGRCLGPCVKEITEEEYQQIVEKIELFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTD 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 250 G-DVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAiEEEVGEVLLAFLGQYYLSH-QERDLPAELIVNVTHEDFPV 327
Cdd:TIGR00194 239 LiDLDIIAVAFDGNVAAIQVFFIRQGKLIGRDQFDFSLP-GTDLDELVETFLIQFYQQGyQNRLIPSEILVSLSLEDLKL 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 328 LVSAIAEARGRELEISYRVRGTRARWQQLAVTNAEQALGARLANRQHVAARFEALAEALDLaEPPQRLECFDISHSSGEA 407
Cdd:TIGR00194 318 LEDLLSEQRGRKINVHQPKKGDKKKLLELAIKNAKYALKQKWTQFERKTQALEDLASLLNL-PKIKRIEIFDISHIDGSQ 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSR-LKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVA 486
Cdd:TIGR00194 397 TVGSMVVFEDGKPLKASYRRYNINSITGGDDYAAMREVLRRRYSSiQKKNNLPLPDLILIDGGKGQLNAALEVLKSLGVV 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 487 G-LILLGVAKgVTRKPGLETLYLNdaSHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKR 565
Cdd:TIGR00194 477 NkPIVIGLAK-AKRHETDIFLIGD--KQGINIDLNSPALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPGVGEKR 553
|
570 580
....*....|....*....|.
gi 15597781 566 RRDLLKHFGGLQELSRASIDE 586
Cdd:TIGR00194 554 VQKLLKYFGSLKGIKKASVEE 574
|
|
| uvrC |
PRK14669 |
excinuclease ABC subunit C; Provisional |
18-608 |
2.11e-145 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237784 [Multi-domain] Cd Length: 624 Bit Score: 434.72 E-value: 2.11e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 18 PGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLA-PKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNILL 96
Cdd:PRK14669 14 PGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGnIKTGSLIREAVDIDYILVDNEKEALALENNLIKQYKPRFNILL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 97 RDDKSYPFVFLSSEDEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRTRPCLQYQIKRCK 176
Cdd:PRK14669 94 RDDKTYPYVKLTLGEKYPRVYVTRRLRKDGAQYYGPFFPANLAYRLVDLIHRHFLVPSCKVDLTRYHPRPCLQFYIHRCL 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 177 GPCV-GLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGNG-DVDI 254
Cdd:PRK14669 174 GPCVqGLTTDEAYAEAVRDVRLFLEGRHSDLARSLRARMEAAALEMQFELAAKYRDLITTVEELEEKQRMAAAKGdDADV 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 255 VAAIVTPGGACVHLISVRGGRVLGSKNFF------PQVAIEEEVGEVLLAFLGQYYLSHQErdLPAELIVNVTHEDFPVL 328
Cdd:PRK14669 254 FGYHYENPMVAVNLFHMRGGKIVDRREFFwedlgeVQVEFEYDEGLFFSSLLKQIYLDQQY--VPREIYVPVEFEDREAL 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 329 VSAIAEARGRELEISYRVRGTRARWQQLAVTNAEQALGARL-ANRQHVAARFEALAEALDLAEPPQRLECFDISHSSGEA 407
Cdd:PRK14669 332 EELLTEQRHRRIEIRVPQRGDKRSLLDLVEQNAKQSYDQRFrVMKPSSRAIQEALQDALNLPELPSRIECFDISHIQGAE 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVAG 487
Cdd:PRK14669 412 TVASMVVWEDGKMKKSDYRKFIIKTVVGVDDFASMREVVTRRYSRLQEEKQPMPGLVLIDGGLGQLHAAAEALEAIGITD 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 488 LILLGVAKgvtRKpglETLYLNDASHE-FTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKRR 566
Cdd:PRK14669 492 QPLASIAK---RE---EIIYVFGQEDEpIVLDRFSPVLHLVQSIRDEAHRFAITFHRKRRETRDRTSELLEIPGVGAKTV 565
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 15597781 567 RDLLKHFGGLQELSRASIDELAKApgISKKLAEQIYAVLHSE 608
Cdd:PRK14669 566 QRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAHFTTE 605
|
|
| uvrC |
PRK14666 |
excinuclease ABC subunit C; Provisional |
11-605 |
3.79e-130 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237782 [Multi-domain] Cd Length: 694 Bit Score: 397.72 E-value: 3.79e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 11 LATCSNRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSG-LAPKTAALVARIAQVETTITANETEALLLEQTLIKEWR 89
Cdd:PRK14666 6 LSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSaLTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKHR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 90 PPYNILLRDDKSYPFVFLSSEDEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRTRPCLQ 169
Cdd:PRK14666 86 PRYNIVLRDDKQYVLFRLGAKHPYPRLEIVRKARRDGARYFGPFTSASAARETWKTIHRAFPLRRCSDRAFGNRVRACLY 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 170 YQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQV-AILRRVQDQQSMEGG 248
Cdd:PRK14666 166 HFMGQCLGPCVNDVPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIrAVERTVERQAAVLPG 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 249 NGDVDIVAAIVTPGGACVHLISVRGGRVLGSKNFFPQVAIEEEVGEVLLAFLGQYYLSH--------------QERDLPA 314
Cdd:PRK14666 246 GGDLDVVGLVEAEGGLALGVLFVRQGVLLDGRAFFWPGLGFEEAPELLWSFLGQFYGPQstipprivvpwlpdTEGREGD 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 315 ELIVNVTHEDFPV-----LVSAIAEARGREL--------------EISYRVRGTR------------------------- 350
Cdd:PRK14666 326 DLAPTAVCTDAGLlpdtpLLPDAPEGSSDPVvpvaaatpvdaslpDVRTGTAPTSlanvshadpavaqptqaatlagaap 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 351 --ARWQQLAVTNAEQALGA-RLANRQHVA-----------ARFEA-----------LAEALDLAEPPQRLECFDISHSSG 405
Cdd:PRK14666 406 kgATHLMLEETLADLRGGPvRIVPPRNPAenrlvdmamsnAREEArrkaetplqdlLARALHLSGPPHRIEAVDVSHTGG 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 406 EATVASCVVFGPEGPLKSDYRRYNIEGvTAGDDYAAMHQALTRrfsRLKDGEgKMPDILLVDGGKGQLAMAQEVLQELAV 485
Cdd:PRK14666 486 RNTRVGMVVFEDGKPARDAYRTYAFED-GEGDDYGTLAAWAGR---RVESGP-PWPDLLLVDGGRGQLAAVVRALEEAGM 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 486 AGLILLG-VAKGVT------RKPG--LETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLE 556
Cdd:PRK14666 561 GGLFAVAsIAKARTeegradRRAGnvADRIFLPGRANPLPLRAGAPELLFLQHVRDTVHDYAIGRHRRARAGAALTGELQ 640
|
650 660 670 680
....*....|....*....|....*....|....*....|....*....
gi 15597781 557 DVPGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVL 605
Cdd:PRK14666 641 RVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689
|
|
| uvrC |
PRK14668 |
excinuclease ABC subunit C; Provisional |
18-601 |
3.68e-110 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 184785 [Multi-domain] Cd Length: 577 Bit Score: 342.13 E-value: 3.68e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 18 PGVYRmFDAEAKLLYVGKAKSLKKRLASYfrksgLAPKTA---ALVARIAQVETTITANETEALLLEQTLIKEWRPPYNI 94
Cdd:PRK14668 17 PGVYQ-FVAGGTVLYVGKAVDLRDRVRSY-----ADPRSErirRMVERADDIDFAVTDTETQALLLEANLIKRHQPRYNV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 95 LLRDDKSYPFVFLSSEdEYPRLSLHRGAKKrKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDSYFRNRTRPCLQYQIKR 174
Cdd:PRK14668 91 RLKDDKSYPLVQLTDH-PVPRIEVTRDPDE-GATVFGPYTDKGRVETVVKALRETYGLRGCSDHKYSNRDRPCLDYEMGL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 175 CKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQ----DQQSMEGGNG 250
Cdd:PRK14668 169 CTAPCTGEIDEEAYAEDVESAERFFEGETGVLADPLRREMEAAAQAQEFERAANLRDRLEAVEAFHggggEAVSSTGDER 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 251 DVDIVAAIVTPGGACV-HLISVRGGRVLGSKNFFPQVAIEEEVGEVLLAFLGQYYlshQERDLPAELIVNVTHEDFPvlV 329
Cdd:PRK14668 249 AVDVLGVAIEGDRATVaRLHAEGGQLVDRDRHRLEAPDGEDRGAAVLAAFIVQYY---AERELPDALLLSERPGDDD--V 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 330 SAIAEARGreleISYRVRGT--RARWQQLAVTNAEQALGArlanRQHVAarfeALAEALDLaEPPQRLECFDISHSSGEA 407
Cdd:PRK14668 324 RAWLEAEG----VDVRVPGAgrEATLVDLALKNARRRGGR----DDEVG----ALADALGI-DRPERIEGFDVSHAQGRA 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 408 TVASCVVFGPEGPLKSDYRRYNIEgvTAGDDYAAMHQALTRRFSRLKDGEGKM--PDILLVDGGKGQLAMAQEVLQEL-- 483
Cdd:PRK14668 391 VVGSNVCFVDGSAETADYRRKKLT--ERNDDYANMRELVRWRAERAVEGRDDRpdPDLLLIDGGDGQLGAARDALAETgw 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 484 ---AVAglillgVAKGVtrkpglETLYLNDASHEFtlPADSPALHLIQQIRDEAHRFAITGHRARRGKArrTSTLEDVPG 560
Cdd:PRK14668 469 dvpAIA------LAKAE------ELVVTPDRTYDW--PDDAPQLHLLQRVRDEAHRFAVQYHQTLRDDV--STVLDDVPG 532
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 15597781 561 VGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQI 601
Cdd:PRK14668 533 VGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETI 573
|
|
| uvrC |
PRK14667 |
excinuclease ABC subunit C; Provisional |
6-601 |
1.01e-109 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 237783 [Multi-domain] Cd Length: 567 Bit Score: 340.56 E-value: 1.01e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 6 DASAFLATCSNRPGVYrMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLI 85
Cdd:PRK14667 5 DALELIEKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 86 KEWRPPYNILLRDDKSYPFVFLsSEDEYPRLSLHRGAKKrKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEDsyFRNRTR 165
Cdd:PRK14667 84 QQYKPKYNVLLKSGSGYPMLLI-TDDEYPTVKIVRGTGE-KGEYFGPFLPARKARKVKKLIHKLFKLRTCDP--MPKRKE 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 166 PCLQYQIKRCKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSM 245
Cdd:PRK14667 160 PCMDYHLGLCSGPCCGKISKEDYELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQILALENLIKGQEV 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 246 EG-GNGDVDIVAAIvtpgGACVHLISVRGGRVLGsKNFFPQVAIEEEVGEVLLAFlgqYYLSHqerdLPAELIVNVTHED 324
Cdd:PRK14667 240 SGlPIEEADIFYFM----GSRLGLFLVRSSKLVG-KEEFRLESEEQEEEEVILGY---YYSNY----IPQKIITNFELSD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 325 fpVLVSAIAEARGRELEISYRVRGtrarwQQLAVTNAEQALGARLANRQhvaarfEALAEALDLaEPPQRLECFDISHSS 404
Cdd:PRK14667 308 --NLKQWLSKRKGGDVEFLTLIPK-----ELEKFIEENIGIKVDLEVLK------EEFKKTFGF-PLPERIEGFDISHFY 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 405 GEATVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEVLQELA 484
Cdd:PRK14667 374 GEFTVGSCVVWEDGSMNKKEYRRYKIKTVDGIDDYASLREVLTRRARRYKEGENPMPDLWLIDGGKGQLSVGIEVRDRLG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 485 VaGLILLGVAKGVtrkpglETLYLNDAShEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPK 564
Cdd:PRK14667 454 L-NIKVFSLAKKE------EILYTEDGK-EIPLKENPILYKVFGLIRDEAHRFALSYNRKLREKEGLKDILDKIKGIGEV 525
|
570 580 590
....*....|....*....|....*....|....*..
gi 15597781 565 RRRDLLKHFGGLQELSRASIDELAKApGISKKLAEQI 601
Cdd:PRK14667 526 KKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEV 561
|
|
| uvrC |
PRK14672 |
excinuclease ABC subunit C; Provisional |
19-607 |
2.04e-90 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173135 [Multi-domain] Cd Length: 691 Bit Score: 293.95 E-value: 2.04e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 19 GVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGlAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNILLRD 98
Cdd:PRK14672 23 GVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCRH-DPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHTPRYNICLKD 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 99 DKSYPFVFLSSEdEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCedSYFRNRTRPCLQYQIKRCKGP 178
Cdd:PRK14672 102 GKTYPLLKLTCE-PFPRIFRTRQFCQDGARYFGPFPDVQILDSFLKLILRTYKIRTC--TTLRKRKNPCLYYHLKRCDAP 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 179 CVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQVAILRRVQDQQSMEGGNGDV-DIVAA 257
Cdd:PRK14672 179 CCGWVSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAIRCITHKSLVQDMDERArDYIAW 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 258 IVTPGGACVHLISVRGGRVLGSKNFFPQVAIEEEvgEVLLAFLGQYYLSHQerdLPAELIVN---------VTHE----- 323
Cdd:PRK14672 259 SSTGAIVTFAVLRMRGGKLNGRELFRTRSLKNEE--EILSEFLITYYSDHT---IPPHLFVHssaglaehwLSHKagtqc 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 324 ----------------------DFPVLVS-----AIAEARGRELEISYRV-------------RGTRARWQQ-------- 355
Cdd:PRK14672 334 tvtliplhtfptpqtpsstvttNAPTLAAsqnsnAVQDSGLRSCSETSTMhtlqkahdactasEGTRENTPHesahtphh 413
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 356 -----LAVTNAEQALGARLANRQHVAArFEALAEALDLAEPPQRLECFDISHSSGEATVASCVVFGPEGPLKSDYRRYNI 430
Cdd:PRK14672 414 railaMAQLNAHEDITRYLKNRGADDA-LKELQKQLHLARIPTLIEGFDISHLGGKYTVASLICFKNGAPDTKNYRLFNL 492
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 431 EG-VTAGDDYAAMHQALTRRFSRLKDGEgKMPDILLVDGGKGQLAMAQEVLQELAVAgLILLGVAKGVtrkpglETLYLN 509
Cdd:PRK14672 493 RAhDTRIDDFASMREAIARRYTHTPEGY-TLPDLILVDGGIGHVSAAQHVLDALGLS-IPLVGLAKRA------EELFIP 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 510 DASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTLEDVPGVGPKRRRDLLKHFGGLQELSRASIDELAK 589
Cdd:PRK14672 565 NSPTPLVLDRRNPALHMLQRIRDEAHRFAITRNRHLRTKKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIAT 644
|
650
....*....|....*...
gi 15597781 590 APGISkklAEQIYAVLHS 607
Cdd:PRK14672 645 AIHIP---LTQAHTILHA 659
|
|
| uvrC |
PRK14670 |
excinuclease ABC subunit C; Provisional |
23-601 |
1.30e-87 |
|
excinuclease ABC subunit C; Provisional
Pssm-ID: 173133 [Multi-domain] Cd Length: 574 Bit Score: 283.34 E-value: 1.30e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 23 MFDAEAKLLYVGKAKSLKKRLASYFRKSgLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNILLRDDKSY 102
Cdd:PRK14670 1 MYSENNKILYIGKAKNLRSRVKNYFLEK-ISHKTKILMKNVKNIEVITTNSEYEALLLECNLIKTHKPDYNIKLKDDKGY 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 103 PFVFLSSEdEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCEdsyfRNRTRPCLQYQIKRCKGPCVGL 182
Cdd:PRK14670 80 PMIRITCE-KYPRIFKTRKIINDGSEYFGPYVNVKKLDLVLDLINKTFKTRKCK----KKSKNPCLYFHMGQCLGVCYRE 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 183 VSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRD-QVAILRRVQDQQSMEGGNGDVDIVAAIVTP 261
Cdd:PRK14670 155 DLEKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKEtKRSLIEISQTQIITKINKLSIDYVYIHPTE 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 262 GGACVHLISVRGGRVLGSKNFFPQVAIEEEvgEVLLAFLGQYYLShqerdlPAELIVNVTH----EDFPVLVSAIAEARG 337
Cdd:PRK14670 235 NLNTIVILKYKDGKLVEKDINFDESIYEED--ELILQFITQYYTS------INMIVPDKIHifkkIDTKNITKLINELKN 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 338 RELEISYRVRGTRARWQQLAVTNAEQALgaRLANRQHVAArFEALAEALDLAEPPQRLECFDISHSSGEATVASCVVFGP 417
Cdd:PRK14670 307 TKTEIIYKETKEIIKIMEMAISNAKLAL--REYENEKNKA-LESLKIILEMDKLPKTIEGFDIAHLNGQKTVASLVTFKM 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 418 EGPLKSDYRRYNIEGVTAG--DDYAAMHQALTRRFSRLKDGEGKMPDILLVDGGKGQLAMAQEVLQELAVAG-LILLGVA 494
Cdd:PRK14670 384 GKPFKDGYRVYKINSLLKGeiDDFKAIKEVISRRYSKLINEQLELPNLILIDGGKGQLNAAYSILKGLKIENkVKVCALA 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 495 KGVtrkpglETLYLNDASHEFTLPADSPALHLIQQIRDEAHRFAITGHRARRGKARRTSTleDVPGVGPKRRRDLLKHFG 574
Cdd:PRK14670 464 KKE------ETIFLPNKKQGIKLPKGNPALRILQNVRDEAHRKANGFNKKLRENIKLNYT--KIKGIGEKKAKKILKSLG 535
|
570 580
....*....|....*....|....*..
gi 15597781 575 GLQELSRASIDELAKAPGISKKLAEQI 601
Cdd:PRK14670 536 TYKDILLLNEDEIAEKMKINIKMAKKI 562
|
|
| UvrC_RNaseH_dom |
pfam08459 |
UvrC RNAse H endonuclease domain; This domain is found in the C subunits of the bacterial and ... |
383-538 |
4.10e-76 |
|
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: 238.89 E-value: 4.10e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 383 AEALDLAEPPQRLECFDISHSSGEATVASCVVFGPEGPLKSDYRRYNIEGVTAGDDYAAMHQALTRRFSRLKDGEGKMPD 462
Cdd:pfam08459 1 QEALGLPKLPRRIECFDISHIQGTDTVASMVVFEDGKPDKSDYRRFNIKTTVGPDDYASMREVLTRRFSRLLEEFGPLPD 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597781 463 ILLVDGGKGQLAMAQEVLQELAVaGLILLGVAKGVTRKpgletLYLNDASHEFTLPADSPALHLIQQIRDEAHRFA 538
Cdd:pfam08459 81 LILIDGGKGQLNAALEVLEELGL-DIPVIGLAKDDKHK-----IDTDGREEEIILPRDSPALHLLQRIRDEAHRFA 150
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
17-282 |
2.70e-48 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 177.42 E-value: 2.70e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 17 RPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNILL 96
Cdd:PRK07883 217 APGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIAAHKPPYNRRS 296
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 97 RDDKSYPFVFLSSEdEYPRLSLHRGAKKRKGRYFGPYPSAGAIRESLNLLQKAFLVRQCED--SYFRNRTRPCLQYQIKR 174
Cdd:PRK07883 297 KFPERRWWVRLTDE-AFPRLSVVRAVEDDGAAYLGPFRSRRAAEEAAEALARAFPLRQCTDrlSRRARHGPACALAELGR 375
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 175 CKGPCVGLVSPEEYAEDVRHSVMFLEGRSNALADELNVGMEQAAMRLDFEKAAELRDQV-AILRRVQDQQSMEGGNGDVD 253
Cdd:PRK07883 376 CPAPCDGRESAAEYAEAVARARAALTGDDDAVLAALRARIDRLAAAERFEEAARLRDRLaALLRALARAQRLAALAAVPE 455
|
250 260
....*....|....*....|....*....
gi 15597781 254 IVAAIVTPGGAcVHLISVRGGRVLGSKNF 282
Cdd:PRK07883 456 LVAARPDGEGG-WELAVVRHGRLAAAGVA 483
|
|
| GIY-YIG_UvrC_Cho |
cd10434 |
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ... |
16-94 |
3.87e-36 |
|
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: 129.91 E-value: 3.87e-36
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597781 16 NRPGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRPPYNI 94
Cdd:cd10434 3 DSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYNI 81
|
|
| GIYc |
smart00465 |
GIY-YIG type nucleases (URI domain); |
17-98 |
1.23e-17 |
|
GIY-YIG type nucleases (URI domain);
Pssm-ID: 214677 [Multi-domain] Cd Length: 84 Bit Score: 77.85 E-value: 1.23e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 17 RPGVYRMFDAEAKLLYVGKAKSLKKRLASYFR-KSGLAPKTAALVARIAQVETTITANETE-ALLLEQTLIKEWRPPYNI 94
Cdd:smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSgSRKGRLLIDALLKYGGNFEFIILESFDEsALELEKYLIKEYKPKYNL 80
|
....
gi 15597781 95 LLRD 98
Cdd:smart00465 81 LLKG 84
|
|
| MUS81 |
COG1948 |
ERCC4-type crossover junction endonuclease [Replication, recombination and repair]; |
555-608 |
2.09e-12 |
|
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
Pssm-ID: 441551 [Multi-domain] Cd Length: 214 Bit Score: 66.74 E-value: 2.09e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 15597781 555 LEDVPGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:COG1948 157 VESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVEGIGEKTAERIREVLDSE 210
|
|
| PRK10545 |
PRK10545 |
excinuclease Cho; |
9-200 |
7.88e-12 |
|
excinuclease Cho;
Pssm-ID: 182535 Cd Length: 286 Bit Score: 66.23 E-value: 7.88e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 9 AFLATCSNRPGVYrMF--DAEAKLLYVGKAKSLKKRLASYFRksglAPKTAALVARIAQVETTITANETEALLLEQTLIK 86
Cdd:PRK10545 26 PFLEDLPKLPGVY-LFhgESDTMPLYIGKSVNIRSRVLSHLR----TPDEAAMLRQSRRISWICTAGEIGALLLEARLIK 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 87 EWRPPYNILLRDDksypfvflssedeyPRL-SLHRGAKKRKGRY------------FGPYPSAGAIRESLNLLqkAFLVR 153
Cdd:PRK10545 101 EQQPLFNKRLRRN--------------RQLcSLQLNEGRVDVVYakevdfsrapnlFGLFANRRAALQALQSI--ADEQK 164
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 15597781 154 QC------EDSyfrNRTRPCLQYQIKRCKGPCVGLVSPEEYAEDVRHSVMFLE 200
Cdd:PRK10545 165 LCygllglEPL---SRGRACFRSALKRCAGACCGKESHEAHALRLRASLERLR 214
|
|
| GIY-YIG |
pfam01541 |
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ... |
18-93 |
1.07e-09 |
|
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: 55.04 E-value: 1.07e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597781 18 PGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITANETEALLLEQTLIKEWRP-PYN 93
Cdd:pfam01541 2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPnKYN 78
|
|
| HHH_5 |
pfam14520 |
Helix-hairpin-helix domain; |
554-605 |
2.08e-09 |
|
Helix-hairpin-helix domain;
Pssm-ID: 434010 [Multi-domain] Cd Length: 57 Bit Score: 53.65 E-value: 2.08e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 15597781 554 TLEDVPGVGPKRRRDLLKH-FGGLQELSRASIDELAKAPGISKKLAEQIYAVL 605
Cdd:pfam14520 3 ELLSISGIGPKTALALLSAgIGTVEDLAEADVDELAEIPGIGEKTAQRIILEL 55
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
540-608 |
1.55e-07 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 54.49 E-value: 1.55e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597781 540 TGHRARRGKARRTSTLEDVPGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:PRK13766 702 GEKKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSE 770
|
|
| GIY-YIG_SF |
cd00719 |
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ... |
19-87 |
2.89e-06 |
|
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: 45.05 E-value: 2.89e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597781 19 GVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVARIAQVETTITAnETEALLLEQTLIKE 87
Cdd:cd00719 1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVAPEA-ESELLDLEAALIKK 68
|
|
| HHH_2 |
pfam12826 |
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ... |
558-608 |
1.52e-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: 42.90 E-value: 1.52e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 15597781 558 VPGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:pfam12826 8 IRHVGETTAKLLARRFGSLDALAEASLEELLEVDDIGPEIAQSIVEFFADP 58
|
|
| GIY-YIG_bI1_like |
cd10445 |
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The ... |
18-96 |
5.05e-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: 42.21 E-value: 5.05e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597781 18 PGVYRMFDAEAKLLYVGKAKSLKKRLASYFRKSGLAPKTAALVA---------RIAQVETTITANETEALLLEQTLIKEW 88
Cdd:cd10445 1 SGIYIWINKINGKIYVGSSINLYKRLRSYLNPSYLKKNSPILRAllkyglsnfTLTILEYYNGENKEELLELEQYYIDLL 80
|
....*...
gi 15597781 89 RPPYNILL 96
Cdd:cd10445 81 KPEYNILK 88
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
205-238 |
8.59e-05 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 45.39 E-value: 8.59e-05
10 20 30
....*....|....*....|....*....|....
gi 15597781 205 ALADELNVGMEQAAMRLDFEKAAELRDQVAILRR 238
Cdd:COG0556 623 KLIKELEKEMKEAAKNLEFEEAARLRDEIKELKK 656
|
|
| Lig |
COG0272 |
NAD-dependent DNA ligase [Replication, recombination and repair]; |
549-608 |
1.33e-04 |
|
NAD-dependent DNA ligase [Replication, recombination and repair];
Pssm-ID: 440042 [Multi-domain] Cd Length: 668 Bit Score: 45.02 E-value: 1.33e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597781 549 ARRTSTLEDV------PGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVLHSE 608
Cdd:COG0272 502 KSKKTPLARFlfalgiRHVGETTAKLLARHFGSLDALMAASEEELAAVDGIGPVVAESIVEFFAEP 567
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
205-238 |
1.76e-04 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 44.65 E-value: 1.76e-04
10 20 30
....*....|....*....|....*....|....
gi 15597781 205 ALADELNVGMEQAAMRLDFEKAAELRDQVAILRR 238
Cdd:PRK05298 613 KLIKELEKQMKEAAKNLEFEEAARLRDEIKELKE 646
|
|
| 5_3_exonuc |
pfam01367 |
5'-3' exonuclease, C-terminal SAM fold; |
558-607 |
3.86e-04 |
|
5'-3' exonuclease, C-terminal SAM fold;
Pssm-ID: 460176 [Multi-domain] Cd Length: 93 Bit Score: 39.66 E-value: 3.86e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 15597781 558 VPGVGPKRRRDLLKHFGGLQELsRASIDELaKAPGISKKLAEQIYAVLHS 607
Cdd:pfam01367 23 VPGIGEKTAAKLLNEYGSLENI-LANADEI-KGGKLREKLRENKEQALLS 70
|
|
| H3TH_53EXO |
cd09898 |
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ... |
558-607 |
4.02e-04 |
|
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.
Pssm-ID: 188618 [Multi-domain] Cd Length: 73 Bit Score: 38.92 E-value: 4.02e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 15597781 558 VPGVGPKRRRDLLKHFGGLQELsRASIDELakAPGISKKLAEQIYAVLHS 607
Cdd:cd09898 21 VPGIGPKTAAKLLQEYGSLENI-LANLDEL--KGKLREKLEENKEQALLS 67
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| UVR |
pfam02151 |
UvrB/uvrC motif; |
214-238 |
4.84e-04 |
|
UvrB/uvrC motif;
Pssm-ID: 308001 [Multi-domain] Cd Length: 36 Bit Score: 37.76 E-value: 4.84e-04
10 20
....*....|....*....|....*
gi 15597781 214 MEQAAMRLDFEKAAELRDQVAILRR 238
Cdd:pfam02151 11 MEEAAENEDFEKAAKLRDQINALKK 35
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| PRK00024 |
PRK00024 |
DNA repair protein RadC; |
560-605 |
5.85e-04 |
|
DNA repair protein RadC;
Pssm-ID: 178801 [Multi-domain] Cd Length: 224 Bit Score: 41.60 E-value: 5.85e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 15597781 560 GVGPKRR------RDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIYAVL 605
Cdd:PRK00024 35 RTGTKGKsvldlaRELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAAL 86
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|
| Smf |
COG0758 |
Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake ... |
558-608 |
6.15e-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: 42.38 E-value: 6.15e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 15597781 558 VPGVGPKRRRDLLKHFGGLQELSRASIDELAKApGISKKLAEQIYAVLHSE 608
Cdd:COG0758 13 VPGVGPVTLRRLLAHFGSAEAALEALPSELARL-GLGEKAAEAIRARPDLA 62
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|
| PRK13482 |
PRK13482 |
DNA integrity scanning protein DisA; Provisional |
569-601 |
1.22e-03 |
|
DNA integrity scanning protein DisA; Provisional
Pssm-ID: 237395 [Multi-domain] Cd Length: 352 Bit Score: 41.30 E-value: 1.22e-03
10 20 30
....*....|....*....|....*....|...
gi 15597781 569 LLKHFGGLQELSRASIDELAKAPGISKKLAEQI 601
Cdd:PRK13482 303 LVEHFGSLQGLLAASIEDLDEVEGIGEVRARAI 335
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|
| HHH |
pfam00633 |
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated ... |
576-604 |
1.24e-03 |
|
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: 36.63 E-value: 1.24e-03
10 20
....*....|....*....|....*....
gi 15597781 576 LQELSRASIDELAKAPGISKKLAEQIYAV 604
Cdd:pfam00633 2 LEGLIPASVEELLALPGVGPKTAEAILSY 30
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|
| ComEA |
COG1555 |
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ... |
553-601 |
2.97e-03 |
|
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];
Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 36.76 E-value: 2.97e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 15597781 553 STLEDVPGVGPKRRRDLLKH---FGGLQelsraSIDELAKAPGISKKLAEQI 601
Cdd:COG1555 21 EELQTLPGIGPKLAQRIVEYrekNGPFK-----SVEDLLEVKGIGPKTLEKL 67
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|
| ligA |
PRK07956 |
NAD-dependent DNA ligase LigA; Validated |
561-602 |
5.60e-03 |
|
NAD-dependent DNA ligase LigA; Validated
Pssm-ID: 236137 [Multi-domain] Cd Length: 665 Bit Score: 39.72 E-value: 5.60e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 15597781 561 VGPKRRRDLLKHFGGLQELSRASIDELAKAPGISKKLAEQIY 602
Cdd:PRK07956 519 VGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIV 560
|
|
| UPF0758_N |
pfam20582 |
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ... |
567-593 |
5.86e-03 |
|
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of the uncharacterized UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with pfam04002.
Pssm-ID: 466731 [Multi-domain] Cd Length: 71 Bit Score: 35.72 E-value: 5.86e-03
10 20
....*....|....*....|....*..
gi 15597781 567 RDLLkHFGGLQELSRASIDELAKAPGI 593
Cdd:pfam20582 46 RRLL-HFGGLRGLLKASVEELMKIKGI 71
|
|
| radA |
PRK04301 |
DNA repair and recombination protein RadA; Validated |
548-601 |
7.78e-03 |
|
DNA repair and recombination protein RadA; Validated
Pssm-ID: 235273 [Multi-domain] Cd Length: 317 Bit Score: 38.71 E-value: 7.78e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 15597781 548 KARRTSTLEDVPGVGPKRRRDLL-KHFGGLQELSRASIDELAKAPGISKKLAEQI 601
Cdd:PRK04301 1 EKMKEKDLEDLPGVGPATAEKLReAGYDTVEAIAVASPKELSEAAGIGESTAAKI 55
|
|
| rad1 |
TIGR00596 |
DNA repair protein (rad1); All proteins in this family for which functions are known are ... |
555-608 |
9.90e-03 |
|
DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273163 [Multi-domain] Cd Length: 814 Bit Score: 39.02 E-value: 9.90e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 15597781 555 LEDVPGVGPKRRRDLLKHFGGLQELSRASIDELAKAPGiSKKLAEQIYAVLHSE 608
Cdd:TIGR00596 759 LLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLRTE 811
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