|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-804 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1635.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:PRK14939 3 MSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:PRK14939 83 DIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGET 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 EKTGTMVRFWPSLETFTNvTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNI 240
Cdd:PRK14939 163 DKTGTEVRFWPSPEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNI 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 241 FYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLI 320
Cdd:PRK14939 242 FYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 321 AVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDL 400
Cdd:PRK14939 322 AVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 401 AGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGR 480
Cdd:PRK14939 402 AGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGR 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 481 DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIA 560
Cdd:PRK14939 482 DEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELA 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 561 LDGATLHTnASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRwvnalvselndk 640
Cdd:PRK14939 562 LEGATLHL-ADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA------------ 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 641 eqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFE 720
Cdd:PRK14939 629 ------------------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFE 672
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 721 QALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 800
Cdd:PRK14939 673 EALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVA 752
|
....
gi 999848431 801 NIDI 804
Cdd:PRK14939 753 NLDV 756
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
5-804 |
0e+00 |
|
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273421 [Multi-domain] Cd Length: 654 Bit Score: 1134.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 5 YDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 84
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 85 EEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG 164
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 165 TMVRFWPSLETFTnVTEFEYEILAKRLRELSFLNSGVSIRLRDKRD--GKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFY 242
Cdd:TIGR01059 160 TTVRFWPDPEIFE-TTEFDFDILAKRLRELAFLNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 243 FSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAV 322
Cdd:TIGR01059 239 IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 323 VSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAG 402
Cdd:TIGR01059 319 ISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 403 LPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDe 482
Cdd:TIGR01059 399 LPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 483 YNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDqyqisiald 562
Cdd:TIGR01059 478 FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD--------- 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 563 gatlhtnasapaLAGEALEKLVSEYnatqkminrmerrypkamlkeliyqptlteadlsdeqtvtrwvnalvsELNDKEQ 642
Cdd:TIGR01059 549 ------------LVGEALEDLKALY------------------------------------------------IYSDKEK 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 643 HGSQWKFDVHtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrglleedafiergerrqpvasfeqa 722
Cdd:TIGR01059 569 EEAKTQIPVH---------------------------------------------------------------------- 578
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 723 ldwlvkESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANI 802
Cdd:TIGR01059 579 ------LGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNL 652
|
..
gi 999848431 803 DI 804
Cdd:TIGR01059 653 DV 654
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-804 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1103.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:COG0187 2 KKSNYDASSIQVLEGLEAVRKRPGMYIGSTDE-RGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 EKTGTMVRFWPSLETFTnVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDG--KEDHFHYEGGIKAFVEYLNKNKTPIHP 238
Cdd:COG0187 161 DRTGTTVRFKPDPEIFE-TTEFDYETLAERLRELAFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHP 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 239 NIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREG 318
Cdd:COG0187 240 EVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 319 LIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGAL 398
Cdd:COG0187 320 LTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 399 DLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGI 478
Cdd:COG0187 400 ESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 479 GrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYqis 558
Cdd:COG0187 480 G-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDEL--- 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 559 ialdgatlhtnasapalagealeklvseynatqkminrmerrypkamLKELiyqptlteadlsdeqtvtrwvnalvseln 638
Cdd:COG0187 556 -----------------------------------------------LKEL----------------------------- 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 639 dkeqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrglleedafiergerrqpvas 718
Cdd:COG0187 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 719 feqaldwlvkESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALK 798
Cdd:COG0187 560 ----------KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKF 629
|
....*.
gi 999848431 799 AANIDI 804
Cdd:COG0187 630 VRNLDI 635
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
35-796 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 812.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 35 GLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGG 114
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 115 LHGVGVSVVNALSQKLELVIQREGKIHRQIYE-HGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRE 193
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 194 LSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNI 273
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 274 PQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVsaTGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQM 353
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 354 NELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKgALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAK 433
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 434 QGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTF 513
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 514 FYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIkddeamdqyqisialdgatlhtnasapalagealeklvseynatqkm 593
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVY----------------------------------------------- 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 594 inrmerrypkamlkeliyqptlteADLSDEQtvtrwvnalvsELNDKEQHGSqwkfdvhtnaeqnlfepivrvrthgvdt 673
Cdd:smart00433 510 ------------------------SFYSLDE-----------YEKWLEKTEG---------------------------- 526
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 674 dypldhefitggeyrrictlgeklrglleedafiergerrqpvasfeqaldwlvkeSRRGLSIQRYKGLGEMNPEQLWET 753
Cdd:smart00433 527 --------------------------------------------------------NKSKYEIQRYKGLGEMNADQLWET 550
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 999848431 754 TMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENA 796
Cdd:smart00433 551 TMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
36-216 |
9.16e-112 |
|
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.
Pssm-ID: 340405 [Multi-domain] Cd Length: 180 Bit Score: 337.59 E-value: 9.16e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 36 LHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGL 115
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 116 HGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNvTEFEYEILAKRLRELS 195
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEK-TEFDFDTLKRRLRELA 159
|
170 180
....*....|....*....|.
gi 999848431 196 FLNSGVSIRLRDKRDGKEDHF 216
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEEVF 180
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
221-377 |
1.12e-66 |
|
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Pssm-ID: 425522 [Multi-domain] Cd Length: 173 Bit Score: 218.64 E-value: 1.12e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 221 GIKAFVEYLNKNKTPIHPNIFYFSTE--KDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMD 298
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 999848431 299 KEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIID 377
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-804 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1635.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:PRK14939 3 MSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:PRK14939 83 DIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGET 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 EKTGTMVRFWPSLETFTNvTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNI 240
Cdd:PRK14939 163 DKTGTEVRFWPSPEIFEN-TEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNI 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 241 FYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLI 320
Cdd:PRK14939 242 FYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 321 AVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDL 400
Cdd:PRK14939 322 AVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 401 AGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGR 480
Cdd:PRK14939 402 AGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGR 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 481 DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIA 560
Cdd:PRK14939 482 DEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELA 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 561 LDGATLHTnASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRwvnalvselndk 640
Cdd:PRK14939 562 LEGATLHL-ADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA------------ 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 641 eqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFE 720
Cdd:PRK14939 629 ------------------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFE 672
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 721 QALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAA 800
Cdd:PRK14939 673 EALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVA 752
|
....
gi 999848431 801 NIDI 804
Cdd:PRK14939 753 NLDV 756
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
5-804 |
0e+00 |
|
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273421 [Multi-domain] Cd Length: 654 Bit Score: 1134.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 5 YDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 84
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 85 EEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG 164
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 165 TMVRFWPSLETFTnVTEFEYEILAKRLRELSFLNSGVSIRLRDKRD--GKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFY 242
Cdd:TIGR01059 160 TTVRFWPDPEIFE-TTEFDFDILAKRLRELAFLNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 243 FSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAV 322
Cdd:TIGR01059 239 IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 323 VSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAG 402
Cdd:TIGR01059 319 ISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 403 LPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDe 482
Cdd:TIGR01059 399 LPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 483 YNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDqyqisiald 562
Cdd:TIGR01059 478 FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD--------- 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 563 gatlhtnasapaLAGEALEKLVSEYnatqkminrmerrypkamlkeliyqptlteadlsdeqtvtrwvnalvsELNDKEQ 642
Cdd:TIGR01059 549 ------------LVGEALEDLKALY------------------------------------------------IYSDKEK 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 643 HGSQWKFDVHtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrglleedafiergerrqpvasfeqa 722
Cdd:TIGR01059 569 EEAKTQIPVH---------------------------------------------------------------------- 578
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 723 ldwlvkESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANI 802
Cdd:TIGR01059 579 ------LGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNL 652
|
..
gi 999848431 803 DI 804
Cdd:TIGR01059 653 DV 654
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-804 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1103.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:COG0187 2 KKSNYDASSIQVLEGLEAVRKRPGMYIGSTDE-RGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 EKTGTMVRFWPSLETFTnVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDG--KEDHFHYEGGIKAFVEYLNKNKTPIHP 238
Cdd:COG0187 161 DRTGTTVRFKPDPEIFE-TTEFDYETLAERLRELAFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHP 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 239 NIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREG 318
Cdd:COG0187 240 EVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 319 LIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGAL 398
Cdd:COG0187 320 LTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 399 DLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGI 478
Cdd:COG0187 400 ESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 479 GrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYqis 558
Cdd:COG0187 480 G-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDEL--- 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 559 ialdgatlhtnasapalagealeklvseynatqkminrmerrypkamLKELiyqptlteadlsdeqtvtrwvnalvseln 638
Cdd:COG0187 556 -----------------------------------------------LKEL----------------------------- 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 639 dkeqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrglleedafiergerrqpvas 718
Cdd:COG0187 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 719 feqaldwlvkESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALK 798
Cdd:COG0187 560 ----------KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKF 629
|
....*.
gi 999848431 799 AANIDI 804
Cdd:COG0187 630 VRNLDI 635
|
|
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-804 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1082.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:PRK05644 4 KAQEYDASQIQVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:PRK05644 83 DIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGET 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 EKTGTMVRFWPSLETFTnVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDG--KEDHFHYEGGIKAFVEYLNKNKTPIHP 238
Cdd:PRK05644 163 DETGTTVTFKPDPEIFE-TTEFDYDTLATRLRELAFLNKGLKITLTDEREGeeKEETFHYEGGIKEYVEYLNRNKEPLHE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 239 NIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREG 318
Cdd:PRK05644 242 EPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 319 LIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGAL 398
Cdd:PRK05644 322 LTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSAL 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 399 DLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGI 478
Cdd:PRK05644 402 ESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 479 GrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEqYIKDDEAMDQyqis 558
Cdd:PRK05644 482 G-DDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDE---- 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 559 ialdgatlhtnasapalagealeklvseynatqkminrmerrypkamlkeliyqptlteadlsdeqtvtrwvnalvseln 638
Cdd:PRK05644 --------------------------------------------------------------------------------
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 639 dkeqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrgLLEEdafiergerrqpvas 718
Cdd:PRK05644 556 -------------------------------------------------------------ILAE--------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 719 feqaldwLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALK 798
Cdd:PRK05644 560 -------LKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKY 632
|
....*.
gi 999848431 799 AANIDI 804
Cdd:PRK05644 633 VRNLDI 638
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-796 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 866.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPT 80
Cdd:PRK05559 4 MTNNYNADSIEVLEGLEPVRKRPGMYIGSTDT-RGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 81 GIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGET 160
Cdd:PRK05559 83 GIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 161 --EKTGTMVRFWPSLETFTNvTEFEYEILAKRLRELSFLNSGVSIRLRDKRdgKEDHFHYEGGIKAFVEYLNKNKTPIHP 238
Cdd:PRK05559 163 gkRKTGTRVRFWPDPKIFDS-PKFSPERLKERLRSKAFLLPGLTITLNDER--ERQTFHYENGLKDYLAELNEGKETLPE 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 239 N-IFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKvSATGDDARE 317
Cdd:PRK05559 240 EfVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVRE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 318 GLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRARemTRRKGA 397
Cdd:PRK05559 319 GLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKKKT 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 398 LDLAgLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCG 477
Cdd:PRK05559 397 SGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIG 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 478 IGrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDqyqi 557
Cdd:PRK05559 476 PG-DSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKE---- 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 558 sialdgatlhtnasapalagEALEKLvseynatqkminrmerrypkamlkeliyqptlteadlsdeqtvtrwvnalvsel 637
Cdd:PRK05559 551 --------------------ELLKKL------------------------------------------------------ 556
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 638 ndkeqhgsqwkfdvhtnaeqnlfepivrvrthgvdtdypldhefitggeyrrictlgeklrglleedafiergerrqpva 717
Cdd:PRK05559 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 999848431 718 sfeqaldwlvKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENA 796
Cdd:PRK05559 557 ----------GKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENG 625
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
35-796 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 812.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 35 GLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGG 114
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 115 LHGVGVSVVNALSQKLELVIQREGKIHRQIYE-HGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRE 193
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 194 LSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNI 273
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 274 PQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVsaTGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQM 353
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 354 NELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKgALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAK 433
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 434 QGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGrDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTF 513
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 514 FYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIkddeamdqyqisialdgatlhtnasapalagealeklvseynatqkm 593
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVY----------------------------------------------- 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 594 inrmerrypkamlkeliyqptlteADLSDEQtvtrwvnalvsELNDKEQHGSqwkfdvhtnaeqnlfepivrvrthgvdt 673
Cdd:smart00433 510 ------------------------SFYSLDE-----------YEKWLEKTEG---------------------------- 526
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 674 dypldhefitggeyrrictlgeklrglleedafiergerrqpvasfeqaldwlvkeSRRGLSIQRYKGLGEMNPEQLWET 753
Cdd:smart00433 527 --------------------------------------------------------NKSKYEIQRYKGLGEMNADQLWET 550
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 999848431 754 TMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENA 796
Cdd:smart00433 551 TMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
3-796 |
4.86e-172 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 519.44 E-value: 4.86e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 3 NSYDSSSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGI 82
Cdd:PTZ00109 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDE-KGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDV 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 83 HPEEGVSAAEVIMTVLHAGGKFDD----------------------------------------NSYKVSGGLHGVGVSV 122
Cdd:PTZ00109 177 SEKTGKSGLETVLTVLHSGGKFQDtfpknsrsdksedkndtksskkgksshvkgpkeakekessQMYEYSSGLHGVGLSV 256
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 123 VNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGE-TEKTGTMVRFWPSLET-FTNVTE-------------FEYEIL 187
Cdd:PTZ00109 257 VNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCpLKKRGTTIHFLPDYKHiFKTHHQhteteeeegckngFNLDLI 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 188 AKRLRELSFLNSGVSIRLRDKRDGKEDHF------HYEGGIKAFVEYLNKNKTPIHP--NIFYFSTEKDGIGVEVALQWN 259
Cdd:PTZ00109 337 KNRIHELSYLNPGLTFYLVDERIANENNFypyetiKHEGGTREFLEELIKDKTPLYKdiNIISIRGVIKNVNVEVSLSWS 416
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 260 DG-FQENIYCFTNNIpQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKD 338
Cdd:PTZ00109 417 LEsYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKT 495
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 339 KLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLA-GLPGKLADCQERDPAL 417
Cdd:PTZ00109 496 KLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILPGKLVDCISDDIER 575
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 418 SELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFD-KMLSSQEVATLITALGCGIGRDEYNPD---------- 486
Cdd:PTZ00109 576 NELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVTWRQYdlshgtkask 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 487 ---------------------KLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQy 545
Cdd:PTZ00109 656 desvqnnnstltkkknslfdtPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQ- 734
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 546 ikddeamdqyqisialdgatlhtnasapalagealeKLVSEYNAtqkminrmerrypkamlKELIYQptlteadLSDEQt 625
Cdd:PTZ00109 735 ------------------------------------FNVSTKNS-----------------KKYIYT-------WSDEE- 753
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 626 vtrwVNALVSELNDKEQHGSQWKFDVHTNAEQNLfepivrvrTHGVDTDYPLDHEFITGGeyrrictlgeklrglleEDA 705
Cdd:PTZ00109 754 ----LNVLIKLLNKDYSSKETTRSVEEKGNAPDL--------DNEYEDEKLDNKNMRENN-----------------VDE 804
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 706 FIERGERRQPVASFEQA----LDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLM 781
Cdd:PTZ00109 805 VELKTELGTNVADTEQTdeldINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLM 884
|
890
....*....|....*
gi 999848431 782 GDAVEPRRAFIEENA 796
Cdd:PTZ00109 885 GEDVQSRKQFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
4-550 |
5.95e-153 |
|
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130127 [Multi-domain] Cd Length: 625 Bit Score: 460.93 E-value: 5.95e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 4 SYDSSSIKVLKGLDAVRKRPGMYIgdtdDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIH 83
Cdd:TIGR01055 3 NYSAKDIEVLDGLEPVRKRPGMYT----DTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIH 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 84 PEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEK- 162
Cdd:TIGR01055 79 PKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKr 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 163 -TGTMVRFWPSLETFTNVtEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFV-EYLNKNKTPIhPNI 240
Cdd:TIGR01055 159 lTGTSVHFTPDPEIFDSL-HFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLsEAVNGDNTLP-PKP 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 241 FYFSTEKDGIGVEVALQW-NDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAkVSATGDDAREGL 319
Cdd:TIGR01055 237 FSGNFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRC 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 320 IAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIdaARAREAARRAREMTRRKGALD 399
Cdd:TIGR01055 316 SYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVRKKLTSG 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 400 LAgLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCgiG 479
Cdd:TIGR01055 394 PA-LPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGI--D 470
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 999848431 480 RDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDE 550
Cdd:TIGR01055 471 PDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEE 541
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
36-216 |
9.16e-112 |
|
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.
Pssm-ID: 340405 [Multi-domain] Cd Length: 180 Bit Score: 337.59 E-value: 9.16e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 36 LHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGL 115
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 116 HGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNvTEFEYEILAKRLRELS 195
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEK-TEFDFDTLKRRLRELA 159
|
170 180
....*....|....*....|.
gi 999848431 196 FLNSGVSIRLRDKRDGKEDHF 216
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEEVF 180
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
220-377 |
1.11e-81 |
|
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Pssm-ID: 238419 [Multi-domain] Cd Length: 172 Bit Score: 258.64 E-value: 1.11e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 220 GGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDK 299
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 999848431 300 EGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIID 377
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
418-532 |
1.83e-77 |
|
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173786 [Multi-domain] Cd Length: 114 Bit Score: 245.26 E-value: 1.83e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 418 SELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGrDEYNPDKLRYHSIIIMT 497
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-EDFDLEKLRYHKIIIMT 79
|
90 100 110
....*....|....*....|....*....|....*
gi 999848431 498 DADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQP 532
Cdd:cd03366 80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
418-532 |
5.79e-69 |
|
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173780 [Multi-domain] Cd Length: 115 Bit Score: 222.77 E-value: 5.79e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 418 SELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMT 497
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 999848431 498 DADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQP 532
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
221-377 |
1.12e-66 |
|
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Pssm-ID: 425522 [Multi-domain] Cd Length: 173 Bit Score: 218.64 E-value: 1.12e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 221 GIKAFVEYLNKNKTPIHPNIFYFSTE--KDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMD 298
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 999848431 299 KEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIID 377
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| GyrB_insert |
pfam18053 |
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ... |
564-729 |
2.44e-64 |
|
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.
Pssm-ID: 465629 Cd Length: 167 Bit Score: 212.38 E-value: 2.44e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 564 ATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQH 643
Cdd:pfam18053 1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 644 GSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQAL 723
Cdd:pfam18053 81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160
|
....*.
gi 999848431 724 DWLVKE 729
Cdd:pfam18053 161 DWLMEE 166
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
22-543 |
2.71e-52 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 197.96 E-value: 2.71e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 22 RPGMYIGDTDDGT----------------------GLHHMVFEVVDNAID----EALAGHCKEIIVTI-HADNSVSVQDD 74
Cdd:PTZ00108 22 RPDTYIGSIETQTedmwvydeeknrmvyktityvpGLYKIFDEILVNAADnkarDKGGHRMTYIKVTIdEENGEISVYND 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 75 GRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ--REGKIHRQIYEHGVPQ- 151
Cdd:PTZ00108 102 GEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVdsKSGKKFKMTWTDNMSKk 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 152 -APLAVTGETEKTGTMVRFWPSLETFtNVTEFEYEILA---KRLRELSFLNSGVSIRLRDKRDGkedhfhyeggIKAFVE 227
Cdd:PTZ00108 182 sEPRITSYDGKKDYTKVTFYPDYAKF-GMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERIA----------IKSFKD 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 228 YLN---KNKTPIHPNIFYFSTEKDGIGVEVALQWNDGfQENIYCFTNNIPQRDGGTHLagfRAAMTRTLNAYMDKEGYSK 304
Cdd:PTZ00108 251 YVDlylPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDG-QFQQVSFVNSICTTKGGTHV---NYILDQLISKLQEKAKKKK 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 305 KAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPtdakivvgkIIDAARAREA 384
Cdd:PTZ00108 327 KKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP---------ILENIVEWAQ 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 385 ARRAREMTRRKGALD---LAGLPgKLADCQERDPALSE---LYLVEGDSAGGSAKQG---RNRKNQAILPLKGKILNVEK 455
Cdd:PTZ00108 398 AKLAAELNKKMKAGKksrILGIP-KLDDANDAGGKNSEectLILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRD 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 456 ARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVE-RGHVYIAQPPL 534
Cdd:PTZ00108 477 ASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFITPI 556
|
570
....*....|
gi 999848431 535 YKV-KKGKQE 543
Cdd:PTZ00108 557 VKAtKKGNQV 566
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
7-545 |
7.65e-50 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 185.34 E-value: 7.65e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 7 SSSIKVLKGLDAVRKRPGMYIGDTDDGT----------------GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHaDN 67
Cdd:PHA02569 1 KDEFKVLSDREHILKRPGMYIGSVAYEAherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 68 SVSVQDDGRGIPTG--IHPE-EGVSAAEVIMTVLHAGGKFDDNSyKVSGGLHGVGVSVVNALSQ---------KLELVIQ 135
Cdd:PHA02569 80 QVTVSDNGRGIPQAmvTTPEgEEIPGPVAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVlfigetcdgKNEVTVN 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 136 REGKIHRQIYEhgvpqaplavTGETEKTGTMVRFWPSLETF--TNVTEFEYEILAKRLRELSFLNSGVSIRLRDKR-DGK 212
Cdd:PHA02569 159 CSNGAENISWS----------TKPGKGKGTSVTFIPDFSHFevNGLDQQYLDIILDRLQTLAVVFPDIKFTFNGKKvSGK 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 213 EDHFHYEGGIKAFVEylnknktpihpnifyfstEKDGIGVEVALQwNDGFQENiyCFTNNIPQRDGGTHLAGFRAAMTRT 292
Cdd:PHA02569 229 FKKYAKQFGDDTIVQ------------------ENDNVSIALAPS-PDGFRQL--SFVNGLHTKNGGHHVDCVMDDICEE 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 293 LnaymdKEGYSKKAKVSATGDDAREGLIAVVSVK-VPDPKFSSQTKDKLVSS--EVKSAVEQQMNELlAEYLLENPTdak 369
Cdd:PHA02569 288 L-----IPMIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHIDLDYKKI-AKQILKTEA--- 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 370 iVVGKIIDAARAREAARRAREMTR-RKGALDL-------AGLPGKLADcqerdpalSELYLVEGDSAGGSAKQGRNRKNQ 441
Cdd:PHA02569 359 -IIMPIIEAALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELH 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 442 AILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEynpDKLRYHSIIIMTDADVDG-SHIRTLLLTFFYRqMPE 520
Cdd:PHA02569 430 GGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKA---ENMNYKNIAIMTDADVDGkGSIYPLLLAFFSR-WPE 505
|
570 580
....*....|....*....|....*
gi 999848431 521 IVERGHVYIAQPPLYKVKKGKQEQY 545
Cdd:PHA02569 506 LFEQGRIRFVKTPVIIAQVGKETKW 530
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
22-542 |
7.41e-46 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 177.98 E-value: 7.41e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 22 RPGMYIGDTDDGT--------------------GLHHMVFEVVDNAIDEALAG-HCKEIIVTIHAD-NSVSVQDDGRGIP 79
Cdd:PLN03128 19 RPDTYIGSTEKHTqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEqNTISVYNNGKGIP 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 80 TGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQ--KLELVIQREGKIHRQIYEHGVPQA--PLA 155
Cdd:PLN03128 99 VEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTefTVETADGNRGKKYKQVFTNNMSVKsePKI 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 156 VTGETEKTGTMVRFWPSLETFTN--VTEFEYEILAKRLRELS-FLNSGVSIRLRDKRDgkedhfhyegGIKAFVEYLN-- 230
Cdd:PLN03128 179 TSCKASENWTKITFKPDLAKFNMtrLDEDVVALMSKRVYDIAgCLGKKLKVELNGKKL----------PVKSFQDYVGly 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 231 ---KNKTPIHPNIFyfstEKDGIGVEVALQWNDG-FQEniYCFTNNIPQRDGGTHLagfrAAMTRTLNAYMdKEGYSKKA 306
Cdd:PLN03128 249 lgpNSREDPLPRIY----EKVNDRWEVCVSLSDGsFQQ--VSFVNSIATIKGGTHV----DYVADQIVKHI-QEKVKKKN 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 307 K--VSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEvksaveqqmNELLAEYLLENPTDAKIVVGKIIDAARAREA 384
Cdd:PLN03128 318 KnaTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRP---------SSFGSKCELSEEFLKKVEKCGVVENILSWAQ 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 385 ARRAREMTRRKGA--LDLAGLPgKLADCQERDPALSE---LYLVEGDSAGGSAKQGR---NRKNQAILPLKGKILNVEKA 456
Cdd:PLN03128 389 FKQQKELKKKDGAkrQRLTGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLsvvGRDHYGVFPLRGKLLNVREA 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 457 RFDKMLSSQEVATLITALGCGIGR--DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHvYIAQ--P 532
Cdd:PLN03128 468 SHKQIMKNAEITNIKQILGLQFGKtyDEENTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIPG-FLVEfiT 546
|
570
....*....|
gi 999848431 533 PLYKVKKGKQ 542
Cdd:PLN03128 547 PIVKATKGGK 556
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
731-793 |
7.47e-41 |
|
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,.
Pssm-ID: 460016 [Multi-domain] Cd Length: 63 Bit Score: 143.67 E-value: 7.47e-41
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 999848431 731 RRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIE 793
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
65-523 |
2.42e-34 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 141.92 E-value: 2.42e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 65 ADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQklELVIQ----REGKI 140
Cdd:PLN03237 109 EQNLISVYNNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFST--EFVIEtadgKRQKK 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 141 HRQIYEH--GVPQAPLAVTGETEKTGTMVRFWPSLETFtNVTEFEYEILA---KRLRELS-FLNSGVSIRLRDKRDGked 214
Cdd:PLN03237 187 YKQVFSNnmGKKSEPVITKCKKSENWTKVTFKPDLAKF-NMTHLEDDVVAlmkKRVVDIAgCLGKTVKVELNGKRIP--- 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 215 hfhyeggIKAFVEYLN---KNKTPIHPNIFYFSTEKDGIGVEVALQWNDG-FQEniYCFTNNIPQRDGGTHLAGFRAAMT 290
Cdd:PLN03237 263 -------VKSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGqFQQ--VSFVNSIATIKGGTHVDYVTNQIA 333
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 291 RTLNAYMDKEgySKKAKVSATgdDAREGLIAVVSVKVPDPKFSSQTKDKLV--SSEVKSAVEqqmnelLAEYLLEnptda 368
Cdd:PLN03237 334 NHVMEAVNKK--NKNANIKAH--NVKNHLWVFVNALIDNPAFDSQTKETLTlrQSSFGSKCE------LSEDFLK----- 398
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 369 KIVVGKIIDAARAREAARRAREMTRRKGA--LDLAGLPgKLADCQE---RDPALSELYLVEGDSAGGSAKQGRN---RKN 440
Cdd:PLN03237 399 KVMKSGIVENLLSWADFKQSKELKKTDGAktTRVTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSvvgRNY 477
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 441 QAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPE 520
Cdd:PLN03237 478 YGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPS 557
|
...
gi 999848431 521 IVE 523
Cdd:PLN03237 558 LLK 560
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
420-524 |
1.67e-24 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 98.91 E-value: 1.67e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 420 LYLVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEY-NPDKLRYHSIII 495
Cdd:cd03365 3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYeSTKSLRYGRLMI 82
|
90 100
....*....|....*....|....*....
gi 999848431 496 MTDADVDGSHIRTLLLTFFYRQMPEIVER 524
Cdd:cd03365 83 MTDQDHDGSHIKGLLINFIHSFWPSLLKI 111
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
222-340 |
6.12e-23 |
|
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.
Pssm-ID: 238202 [Multi-domain] Cd Length: 107 Bit Score: 94.25 E-value: 6.12e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 222 IKAFVEYLNKNKTpiHPNIFYFSTEKDGIGVEVALQWND---GFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNaymd 298
Cdd:cd00329 1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 999848431 299 kegyskkakvsatGDDAREGLIAVVSVKVPD--PKFS-SQTKDKL 340
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
32-142 |
2.05e-18 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 81.54 E-value: 2.05e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 32 DGTGLHHMVFEVVDNAIDEALAGhcKEIIVTIHADN---SVSVQDDGRGIPtgihpeegvsaAEVIMTVLHAGGKFDDNS 108
Cdd:smart00387 2 DPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRS 68
|
90 100 110
....*....|....*....|....*....|....
gi 999848431 109 YKVSGglHGVGVSVVNALSQKLELVIQREGKIHR 142
Cdd:smart00387 69 RKIGG--TGLGLSIVKKLVELHGGEISVESEPGG 100
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
31-175 |
8.16e-16 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 73.94 E-value: 8.16e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 31 DDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPeegvsaaevimtvlHAGGKFDDnSYK 110
Cdd:pfam02518 1 GDELRLRQVLSNLLDNALKHAAKAGEITVTLSEGGELTLTVEDNGIGIPPEDLP--------------RIFEPFST-ADK 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 999848431 111 VSGGLHGVGVSVVNALSQKLelviqrEGKIHRQiyehgvpqaplavtgETEKTGTMVRFWPSLET 175
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELL------GGTITVE---------------SEPGGGTTVTLTLPLAQ 109
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
419-532 |
1.33e-15 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 72.77 E-value: 1.33e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 419 ELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLssqevatlitalgcgigrDEYNPDKLRYHSIIIMTD 498
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKAL------------------KALKELALKAKEVILATD 62
|
90 100 110
....*....|....*....|....*....|....*.
gi 999848431 499 ADVDGSHIRTLLLTFFyrqmpEIVER--GHVYIAQP 532
Cdd:pfam01751 63 PDREGEAIALKLLELK-----ELLENagGRVEFSEL 93
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
35-171 |
4.72e-14 |
|
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.
Pssm-ID: 340407 [Multi-domain] Cd Length: 147 Bit Score: 70.06 E-value: 4.72e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 35 GLHHMVFEVVDNAID-EALAGHCKEIIVTIHAD-NSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVS 112
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPEnNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 999848431 113 GGLHGVGVSVVNALSQK--LELVIQREGKIHRQIYEHGVPQA--PLAVTGETEKTGTMVRFWP 171
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEftVETADSESKKKFKQTWTNNMGKAsePKITPYEKGKDYTKVTFKP 146
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
36-130 |
1.26e-06 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 47.60 E-value: 1.26e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 36 LHHMVFEVVDNAIDEALAGhcKEIIVTIHADNS---VSVQDDGRGIPTGIHPeegvsaaevimtvlHAGGKFDDNSYKVS 112
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE--------------RIFERFYRGDKSRE 64
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90
....*....|....*...
gi 999848431 113 GGLHGVGVSVVNALSQKL 130
Cdd:cd00075 65 GGGTGLGLAIVRRIVEAH 82
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| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
418-521 |
3.17e-05 |
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Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 42.80 E-value: 3.17e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 999848431 418 SELYLVEGDSAGGSAKQGRnRKNQAILPLKGKILNvekarfdkmlssQEVATLITALGcgigrdeynpdklRYHSIIIMT 497
Cdd:cd00188 1 KKLIIVEGPSDALALAQAG-GYGGAVVALGGHALN------------KTRELLKRLLG-------------EAKEVIIAT 54
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90 100
....*....|....*....|....
gi 999848431 498 DADVDGSHIRTLLLTFFYRQMPEI 521
Cdd:cd00188 55 DADREGEAIALRLLELLKSLGKKV 78
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