|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
3-795 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1455.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 3 EQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTQDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGM 82
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 83 PTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVG 162
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 163 DSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEK 242
Cdd:PRK14939 161 ETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPN 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 243 IFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGL 322
Cdd:PRK14939 241 IFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 323 TCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVMD 402
Cdd:PRK14939 321 TAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 403 GLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIG 482
Cdd:PRK14939 401 IAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 483 KEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLLGL 562
Cdd:PRK14939 481 RDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIEL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 563 ALEKAKI-VSDGRTIEGAELADTAKQFLLAKTVIEQESRFVDELVLRAMLHASPIDLTSSENADKAVAelsglldekeaa 641
Cdd:PRK14939 561 ALEGATLhLADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA------------ 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 642 leriegheghrfikitrklhgnvmvsyIEPKFLNSKAYQTLTQTAAALKGLVGEGAKLYKGENEYDADSFETALDILMSV 721
Cdd:PRK14939 629 ---------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDWLLAE 681
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 81311154 722 AQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNID 795
Cdd:PRK14939 682 ARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLD 755
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
4-796 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1052.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 4 QKHEEYGADSIQVLEGLEAVRKRPGMYIGDTqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMP 83
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGST-DERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 84 TGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGD 163
Cdd:COG0187 80 VDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 164 SDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDG--KHESFALSGGVAGFVQYMNRKKTPLHE 241
Cdd:COG0187 160 TDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHP 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 242 KIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREG 321
Cdd:COG0187 240 EVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 322 LTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVM 401
Cdd:COG0187 320 LTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 402 DGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGI 481
Cdd:COG0187 400 ESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 482 GkEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLlg 561
Cdd:COG0187 480 G-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELL-- 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 562 lalekakivsdgrtiegaeladtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavAELSGlldekeaa 641
Cdd:COG0187 557 -------------------------------------------------------------------KELKG-------- 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 642 leriegheghrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsv 721
Cdd:COG0187 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 81311154 722 aQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNIDA 796
Cdd:COG0187 562 -KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
9-795 |
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: 1021.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 9 YGADSIQVLEGLEAVRKRPGMYIGDTQDgSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHP 88
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 89 KEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKG 168
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 169 TTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERD--GKHESFALSGGVAGFVQYMNRKKTPLHEKIFYA 246
Cdd:TIGR01059 160 TTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 247 FGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGLTCVL 326
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 327 SVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVMDGLGL 406
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 407 PGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKeEF 486
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGK-DF 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 487 NPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDqwLLGLALEK 566
Cdd:TIGR01059 479 DLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD--LVGEALED 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 567 AKIVSdgrtiegaELADtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavaelsgllDEKEAALERIE 646
Cdd:TIGR01059 557 LKALY--------IYSD----------------------------------------------------KEKEEAKTQIP 576
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 647 GHEGhrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsvaQKGM 726
Cdd:TIGR01059 577 VHLG------------------------------------------------------------------------RKGI 584
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 81311154 727 SIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNID 795
Cdd:TIGR01059 585 EIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLD 653
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
39-788 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 758.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 39 GLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGG 118
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 119 LHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVR-GETEEPLKIVGDSDKKGTTVRFLAGTETFGNI-EYSFDILAKRIRE 196
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTtDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 197 LSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNI 276
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 277 PQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVEtaGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVI 356
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNIK--GEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 357 NQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGvMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAM 436
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 437 QGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKeEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTF 516
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGK-DFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 517 FYRQMPELVERGYIYIAQPPLYKAKYGKqerylkdelekdqwllglaleKAKIVSDGRtiegaeladtakqfllaktvie 596
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGK---------------------KKYVYSFYS---------------------- 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 597 qesrfvdelvlramlhaspidltssenadkavaelsglLDEKEAALERIEGHeghrfikitrklhgnvmvsyiepkflns 676
Cdd:smart00433 514 --------------------------------------LDEYEKWLEKTEGN---------------------------- 527
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 677 kayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsvaQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLK 756
Cdd:smart00433 528 ----------------------------------------------KSKYEIQRYKGLGEMNADQLWETTMDPERRTLLF 561
|
730 740 750
....*....|....*....|....*....|..
gi 81311154 757 VRIEDAIAADEVFVTLMGDEVEPRRAFIENNA 788
Cdd:smart00433 562 VTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
40-219 |
4.48e-109 |
|
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: 330.27 E-value: 4.48e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 40 LHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGL 119
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 120 HGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSF 199
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170 180
....*....|....*....|
gi 81311154 200 LNNGVDIELTDERDGKHESF 219
Cdd:cd16928 161 LNKGLKIVLEDERTGKEEVF 180
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
224-380 |
3.63e-55 |
|
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: 187.44 E-value: 3.63e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 224 GVAGFVQYMNRKKTPLHEKIFYAFGE--KDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIE 301
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 81311154 302 ANEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVD 380
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
3-795 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1455.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 3 EQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTQDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGM 82
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 83 PTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVG 162
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 163 DSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEK 242
Cdd:PRK14939 161 ETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPN 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 243 IFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGL 322
Cdd:PRK14939 241 IFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 323 TCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVMD 402
Cdd:PRK14939 321 TAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 403 GLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIG 482
Cdd:PRK14939 401 IAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 483 KEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLLGL 562
Cdd:PRK14939 481 RDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIEL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 563 ALEKAKI-VSDGRTIEGAELADTAKQFLLAKTVIEQESRFVDELVLRAMLHASPIDLTSSENADKAVAelsglldekeaa 641
Cdd:PRK14939 561 ALEGATLhLADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA------------ 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 642 leriegheghrfikitrklhgnvmvsyIEPKFLNSKAYQTLTQTAAALKGLVGEGAKLYKGENEYDADSFETALDILMSV 721
Cdd:PRK14939 629 ---------------------------LDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDWLLAE 681
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 81311154 722 AQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNID 795
Cdd:PRK14939 682 ARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLD 755
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
4-796 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1052.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 4 QKHEEYGADSIQVLEGLEAVRKRPGMYIGDTqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMP 83
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGST-DERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 84 TGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGD 163
Cdd:COG0187 80 VDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 164 SDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDG--KHESFALSGGVAGFVQYMNRKKTPLHE 241
Cdd:COG0187 160 TDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHP 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 242 KIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREG 321
Cdd:COG0187 240 EVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 322 LTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVM 401
Cdd:COG0187 320 LTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 402 DGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGI 481
Cdd:COG0187 400 ESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 482 GkEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLlg 561
Cdd:COG0187 480 G-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELL-- 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 562 lalekakivsdgrtiegaeladtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavAELSGlldekeaa 641
Cdd:COG0187 557 -------------------------------------------------------------------KELKG-------- 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 642 leriegheghrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsv 721
Cdd:COG0187 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 81311154 722 aQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNIDA 796
Cdd:COG0187 562 -KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
2-796 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1031.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 2 TEQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRG 81
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGST-GERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 82 MPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIV 161
Cdd:PRK05644 80 IPVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVI 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 162 GDSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDG--KHESFALSGGVAGFVQYMNRKKTPL 239
Cdd:PRK05644 160 GETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGeeKEETFHYEGGIKEYVEYLNRNKEPL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 240 HEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMR 319
Cdd:PRK05644 240 HEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 320 EGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKG 399
Cdd:PRK05644 320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 400 VMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGA 479
Cdd:PRK05644 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGT 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 480 GIGkEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQErYLKDELEKDQWL 559
Cdd:PRK05644 480 GIG-DDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEIL 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 560 lglalekakivsdgrtiegaeladtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavAELSGLLDeke 639
Cdd:PRK05644 558 ---------------------------------------------------------------------AELKLKGN--- 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 640 aaleriegheghrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldilm 719
Cdd:PRK05644 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 81311154 720 svaqKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNIDA 796
Cdd:PRK05644 566 ----PKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
9-795 |
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: 1021.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 9 YGADSIQVLEGLEAVRKRPGMYIGDTQDgSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHP 88
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 89 KEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKG 168
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 169 TTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERD--GKHESFALSGGVAGFVQYMNRKKTPLHEKIFYA 246
Cdd:TIGR01059 160 TTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 247 FGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGLTCVL 326
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 327 SVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGVMDGLGL 406
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 407 PGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKeEF 486
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGK-DF 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 487 NPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDqwLLGLALEK 566
Cdd:TIGR01059 479 DLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD--LVGEALED 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 567 AKIVSdgrtiegaELADtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavaelsgllDEKEAALERIE 646
Cdd:TIGR01059 557 LKALY--------IYSD----------------------------------------------------KEKEEAKTQIP 576
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 647 GHEGhrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsvaQKGM 726
Cdd:TIGR01059 577 VHLG------------------------------------------------------------------------RKGI 584
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 81311154 727 SIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNID 795
Cdd:TIGR01059 585 EIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLD 653
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
2-788 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 825.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 2 TEQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRG 81
Cdd:PRK05559 1 AAMMTNNYNADSIEVLEGLEPVRKRPGMYIGST-DTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 82 MPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIV 161
Cdd:PRK05559 80 IPVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 162 GDSDKK--GTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERdgKHESFALSGGVAGFVQYMNRKKTPL 239
Cdd:PRK05559 160 GTAGKRktGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER--ERQTFHYENGLKDYLAELNEGKETL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 240 HEKIFYAF-GEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKvETAGDDM 318
Cdd:PRK05559 238 PEEFVGSFeGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDV 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 319 REGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDaaRAREAARKAREITRRK 398
Cdd:PRK05559 317 REGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIK--AAQARLRAAKKVKRKK 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 399 gVMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALG 478
Cdd:PRK05559 395 -KTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIG 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 479 AGIGKeEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDElekdqw 558
Cdd:PRK05559 474 IGPGD-SFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDE------ 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 559 llglalekakivsdgrtiegaeladtakqfllaktvieqesrfvdelvlramlhaspidltssenadkavaelsgllDEK 638
Cdd:PRK05559 547 -----------------------------------------------------------------------------EEK 549
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 639 EAALERIEGHEGhrfikitrklhgnvmvsyiepkflnskayqtltqtaaalkglvgegaklykgeneydadsfetaldil 718
Cdd:PRK05559 550 EELLKKLGKKGG-------------------------------------------------------------------- 561
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 719 msvaqkGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNA 788
Cdd:PRK05559 562 ------KPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENG 625
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
39-788 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 758.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 39 GLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGG 118
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 119 LHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVR-GETEEPLKIVGDSDKKGTTVRFLAGTETFGNI-EYSFDILAKRIRE 196
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTtDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 197 LSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNI 276
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 277 PQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVEtaGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVI 356
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNIK--GEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 357 NQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGvMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAM 436
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 437 QGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKeEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTF 516
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGK-DFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 517 FYRQMPELVERGYIYIAQPPLYKAKYGKqerylkdelekdqwllglaleKAKIVSDGRtiegaeladtakqfllaktvie 596
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGK---------------------KKYVYSFYS---------------------- 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 597 qesrfvdelvlramlhaspidltssenadkavaelsglLDEKEAALERIEGHeghrfikitrklhgnvmvsyiepkflns 676
Cdd:smart00433 514 --------------------------------------LDEYEKWLEKTEGN---------------------------- 527
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 677 kayqtltqtaaalkglvgegaklykgeneydadsfetaldilmsvaQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLK 756
Cdd:smart00433 528 ----------------------------------------------KSKYEIQRYKGLGEMNADQLWETTMDPERRTLLF 561
|
730 740 750
....*....|....*....|....*....|..
gi 81311154 757 VRIEDAIAADEVFVTLMGDEVEPRRAFIENNA 788
Cdd:smart00433 562 VTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
4-788 |
2.94e-168 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 509.42 E-value: 2.94e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 4 QKHEEYGADSIQVLEGLEAVRKRPGMYIGDTqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMP 83
Cdd:PTZ00109 95 QRCSEYDADDIVVLEGLEAVRKRPGMYIGNT-DEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIP 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 84 TGIHPKEGRSAAEVIMTVLHAGGKF-----------------DNNS-----------------------YKISGGLHGVG 123
Cdd:PTZ00109 174 CDVSEKTGKSGLETVLTVLHSGGKFqdtfpknsrsdksedknDTKSskkgksshvkgpkeakekessqmYEYSSGLHGVG 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 124 VSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKK-GTTVRFL-------------AGTETFGNIEYSF-- 187
Cdd:PTZ00109 254 LSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLKKrGTTIHFLpdykhifkthhqhTETEEEEGCKNGFnl 333
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 188 DILAKRIRELSFLNNGVDIELTDERDGK------HESFALSGGVAGFVQYMNRKKTPLHEKIFYAF--GEKDGMSVECAM 259
Cdd:PTZ00109 334 DLIKNRIHELSYLNPGLTFYLVDERIANennfypYETIKHEGGTREFLEELIKDKTPLYKDINIISirGVIKNVNVEVSL 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 260 QWN-DSYQESVQCFTNNIpQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQ 338
Cdd:PTZ00109 414 SWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQ 492
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 339 TKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREITRRKGV-MDGLGLPGKLADCQEKD 417
Cdd:PTZ00109 493 TKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNqYYSTILPGKLVDCISDD 572
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 418 PALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFE-KMLASQEVATLITALGAGI--------------- 481
Cdd:PTZ00109 573 IERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVnpvtwrqydlshgtk 652
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 482 -GKEEF---------------NPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQ 545
Cdd:PTZ00109 653 aSKDESvqnnnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRM 732
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 546 ERYlkdelekdqwllglalekakivsdgrtiegaelADTAKQfllAKTVIEQESrfvDELVLRAMlhaspidltssenad 625
Cdd:PTZ00109 733 KQF---------------------------------NVSTKN---SKKYIYTWS---DEELNVLI--------------- 758
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 626 kavaelsGLLDEKEAALERIEGHEghrfikitRKLHGNVMVSYIEPKFLNSKAYQTLTQTAAALKGLVGEGAKlykgene 705
Cdd:PTZ00109 759 -------KLLNKDYSSKETTRSVE--------EKGNAPDLDNEYEDEKLDNKNMRENNVDEVELKTELGTNVA------- 816
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 706 YDADSFETALDILMSVAQKGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIE 785
Cdd:PTZ00109 817 DTEQTDELDINKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIF 896
|
...
gi 81311154 786 NNA 788
Cdd:PTZ00109 897 ENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
9-606 |
1.14e-155 |
|
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: 467.47 E-value: 1.14e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 9 YGADSIQVLEGLEAVRKRPGMYIgdtqDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHP 88
Cdd:TIGR01055 4 YSAKDIEVLDGLEPVRKRPGMYT----DTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 89 KEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKK- 167
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKRl 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 168 -GTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEKIFYA 246
Cdd:TIGR01055 160 tGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLSEAVNGDNTLPPKPFSG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 247 FGEKDGMSVECAMQW-NDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAkVETAGDDMREGLTCV 325
Cdd:TIGR01055 240 NFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSYV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 326 LSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREitrRKGVMDGLG 405
Cdd:TIGR01055 319 LSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPA 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 406 LPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALgaGIGKEE 485
Cdd:TIGR01055 396 LPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVAL--GIDPDS 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 486 FNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLLGLALE 565
Cdd:TIGR01055 474 NDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKK 553
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 81311154 566 KAKIvSDGR-----TIEGAELADTA----KQFLLAKTVIEQESRFVDELV 606
Cdd:TIGR01055 554 KGKP-NVQRfkglgEMNPAQLRETTmdpnTRRLVQLTLDDVQDQRVDKIM 602
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
40-219 |
4.48e-109 |
|
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: 330.27 E-value: 4.48e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 40 LHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGL 119
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 120 HGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSF 199
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170 180
....*....|....*....|
gi 81311154 200 LNNGVDIELTDERDGKHESF 219
Cdd:cd16928 161 LNKGLKIVLEDERTGKEEVF 180
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
421-535 |
6.60e-78 |
|
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: 246.41 E-value: 6.60e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 421 SELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGkEEFNPEKLRYHRIIIMT 500
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-EDFDLEKLRYHKIIIMT 79
|
90 100 110
....*....|....*....|....*....|....*
gi 81311154 501 DADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQP 535
Cdd:cd03366 80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
223-380 |
5.57e-75 |
|
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: 240.93 E-value: 5.57e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 223 GGVAGFVQYMNRKKTPLHEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEA 302
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 81311154 303 NEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVD 380
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
421-535 |
3.57e-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: 223.15 E-value: 3.57e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 421 SELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMT 500
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 81311154 501 DADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQP 535
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 ... |
224-380 |
3.63e-55 |
|
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: 187.44 E-value: 3.63e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 224 GVAGFVQYMNRKKTPLHEKIFYAFGE--KDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIE 301
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 81311154 302 ANEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVD 380
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
12-557 |
9.83e-53 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 193.43 E-value: 9.83e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 12 DSIQVLEGLEAVRKRPGMYIGDTQ--------DGS--------GLHHMVFEVLDNAIDEALAG---HCDKITVTIHaDHS 72
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAyeaherflFGKftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 73 VSVADNGRGMPTGI----HPKE--GRSAAeviMTVLHAGGKFDNNSyKISGGLHGVGVSVVNALSDWVTlTIYRDGKehf 146
Cdd:PHA02569 81 VTVSDNGRGIPQAMvttpEGEEipGPVAA---WTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFI-GETCDGK--- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 147 vRFVRGETEEPLKIVGDSDK----KGTTVRFLAGTETFGNIEYS---FDILAKRIRELS-------FLNNGVDIeltder 212
Cdd:PHA02569 153 -NEVTVNCSNGAENISWSTKpgkgKGTSVTFIPDFSHFEVNGLDqqyLDIILDRLQTLAvvfpdikFTFNGKKV------ 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 213 DGKHESFALSGGVAGFVQymnrkktplhekifyafgEKDGMSVECAMQWNDSYQESvqcFTNNIPQRDGGTHLtalrQVM 292
Cdd:PHA02569 226 SGKFKKYAKQFGDDTIVQ------------------ENDNVSIALAPSPDGFRQLS---FVNGLHTKNGGHHV----DCV 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 293 TRTINSYIEAnEVAKKAKVETAGDDMREGLTCVLSVK-LPDPKFSSQTKDKLVS--GEIGPVVN---EVINQALTDflee 366
Cdd:PHA02569 281 MDDICEELIP-MIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSpfGEIRNHIDldyKKIAKQILK---- 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 367 npNEAkIITgKIVDAARAREAARKAREITR------RKGVMDGL--GLPGKLADcqekdpalSELYLVEGDSAGGSAMQG 438
Cdd:PHA02569 356 --TEA-IIM-PIIEAALARKLAAEKAAETKaakkakKAKVAKHIkaNLIGKDAE--------TTLFLTEGDSAIGYLIEV 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 439 RDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPeklRYHRIIIMTDADVDG-AHIRTLLLTFF 517
Cdd:PHA02569 424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENM---NYKNIAIMTDADVDGkGSIYPLLLAFF 500
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 81311154 518 YRqMPELVERGYIYIAQPPLYKAKYGKQER--YLKDELEKDQ 557
Cdd:PHA02569 501 SR-WPELFEQGRIRFVKTPVIIAQVGKETKwfYSLDEFEKAK 541
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
14-546 |
3.12e-42 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 166.76 E-value: 3.12e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 14 IQVLEGLEAVRKRPGMYIG------------DTQDGS----------GLHHMVFEVLDNAID----EALAGHCDKITVTI 67
Cdd:PTZ00108 10 YQKKTQIEHILLRPDTYIGsietqtedmwvyDEEKNRmvyktityvpGLYKIFDEILVNAADnkarDKGGHRMTYIKVTI 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 68 HADH-SVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIyRDGKEHF 146
Cdd:PTZ00108 90 DEENgEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVEC-VDSKSGK 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 147 VRFVR-----GETEEPlkIVGDSDKKG--TTVRFLAGTETFGNIEYSFDILA---KRIRELSFLNNGVDIELTDERDGkh 216
Cdd:PTZ00108 169 KFKMTwtdnmSKKSEP--RITSYDGKKdyTKVTFYPDYAKFGMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERIA-- 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 217 esfalsggVAGFVQYMN--RKKTPLHEKIFYAFGEKDGM-SVECAMQWNDSYQESVQcFTNNIPQRDGGTHLTALRQVMT 293
Cdd:PTZ00108 245 --------IKSFKDYVDlyLPDGEEGKKPPYPFVYTSVNgRWEVVVSLSDGQFQQVS-FVNSICTTKGGTHVNYILDQLI 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 294 RTINSYIEANevaKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPneaki 373
Cdd:PTZ00108 316 SKLQEKAKKK---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP----- 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 374 ITGKIVDAARAREAARKAREI--TRRKGVMdglGLPgKLADCQEKDPALSE---LYLVEGDSAGGSAMQG---RDRKFQA 445
Cdd:PTZ00108 388 ILENIVEWAQAKLAAELNKKMkaGKKSRIL---GIP-KLDDANDAGGKNSEectLILTEGDSAKALALAGlsvVGRDYYG 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 446 ILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELV 525
Cdd:PTZ00108 464 VFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLL 543
|
570 580
....*....|....*....|...
gi 81311154 526 E-RGYIYIAQPPLYKA-KYGKQE 546
Cdd:PTZ00108 544 KnPGFLKEFITPIVKAtKKGNQV 566
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
724-785 |
1.53e-40 |
|
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: 142.52 E-value: 1.53e-40
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 81311154 724 KGMSIQRYKGLGEMNPEQLWETTMDPAVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIE 785
Cdd:pfam00986 2 KKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
20-545 |
1.26e-38 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 155.25 E-value: 1.26e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 20 LEAVRKRPGMYIGDTQ----------DGS----------GLHHMVFEVLDNAIDEALAG-HCDKITVTIHADH-SVSVAD 77
Cdd:PLN03128 13 LEHILLRPDTYIGSTEkhtqtlwvyeGGEmvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEQnTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 78 NGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYrDGKE--HFVRFVRG--- 152
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETA-DGNRgkKYKQVFTNnms 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 153 ETEEPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDI---LAKRIRELS-FLNNGVDIELTDERdgkhesfaLSggVAGF 228
Cdd:PLN03128 172 VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKK--------LP--VKSF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 229 VQYMN-----RKKTPLHEKIFYAFGekDGMSVeCAMQWNDSYQesvQC-FTNNIPQRDGGTHLTALrqvmTRTINSYIeA 302
Cdd:PLN03128 242 QDYVGlylgpNSREDPLPRIYEKVN--DRWEV-CVSLSDGSFQ---QVsFVNSIATIKGGTHVDYV----ADQIVKHI-Q 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 303 NEVAKKAK--VETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEigpvvnevinqalTDFLEE----NPNEAKIITG 376
Cdd:PLN03128 311 EKVKKKNKnaTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRP-------------SSFGSKcelsEEFLKKVEKC 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 377 KIVDAARAREAARKAREITRRKGVMDG--LGLPgKLADCQEKDPALSE---LYLVEGDSAGGSAMQGRD---RKFQAILP 448
Cdd:PLN03128 378 GVVENILSWAQFKQQKELKKKDGAKRQrlTGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLSvvgRDHYGVFP 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 449 LKGKILNVEKARFEKMLASQEVATLITALGAGIGKE--EFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVE 526
Cdd:PLN03128 457 LRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTydEENTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLK 536
|
570 580
....*....|....*....|
gi 81311154 527 R-GYIYIAQPPLYKAKYGKQ 545
Cdd:PLN03128 537 IpGFLVEFITPIVKATKGGK 556
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
4-526 |
1.08e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 117.66 E-value: 1.08e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 4 QKHEEygadSIQVLEGLEAVrKRPGMYIgdtqdgSGLHHMVFEVLDNAIDEALAG-HCDKITVTIHADHS-VSVADNGRG 81
Cdd:PLN03237 53 EKHTQ----TLWVYETDKMV-QRSVTYV------PGLYKIFDEILVNAADNKQRDpKMDSLRVVIDVEQNlISVYNNGDG 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 82 MPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALS-DWVTLTIyrDGK-EHFVRFV----RGETE 155
Cdd:PLN03237 122 VPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFStEFVIETA--DGKrQKKYKQVfsnnMGKKS 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 156 EPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDILA---KRIRELS-FLNNGVDIELTDERDGkhesfalsggVAGFVQY 231
Cdd:PLN03237 200 EPVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVVAlmkKRVVDIAgCLGKTVKVELNGKRIP----------VKSFSDY 269
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 232 MN------RKKTPLHEKIFYafgEKDGMSVE-CAMQWNDSYQesvQC-FTNNIPQRDGGTHLTALrqvmTRTINSYIeAN 303
Cdd:PLN03237 270 VDlylesaNKSRPENLPRIY---EKVNDRWEvCVSLSEGQFQ---QVsFVNSIATIKGGTHVDYV----TNQIANHV-ME 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 304 EVAKKAK-VETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLV--SGEIGPVVnevinQALTDFLEenpneaKIITGKIVD 380
Cdd:PLN03237 339 AVNKKNKnANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLTlrQSSFGSKC-----ELSEDFLK------KVMKSGIVE 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 381 AARAREAARKAREITRRKGVMDG--LGLPgKLADCQE---KDPALSELYLVEGDSAGGSAMQGR---DRKFQAILPLKGK 452
Cdd:PLN03237 408 NLLSWADFKQSKELKKTDGAKTTrvTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLsvvGRNYYGVFPLRGK 486
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 81311154 453 ILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVE 526
Cdd:PLN03237 487 LLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
|
|
| GyrB_insert |
pfam18053 |
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ... |
576-720 |
2.66e-26 |
|
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: 105.68 E-value: 2.66e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 576 IEGAELADTAKQFLLAKTVIEQESRFVDELVLRAMLHASPID---LTSSENADKAVAELSGLLDEK-------EAALERI 645
Cdd:pfam18053 12 ISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDaedLDDEAAAEAWAAALEARLNQDglggpryRVSVEED 91
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 81311154 646 EGHEGHRfIKITRKLHGNVMVSYIEPKFLNSKAYQTLTQTAAALKGLVGEGAKLYKGENEYDADSFETALDILMS 720
Cdd:pfam18053 92 TERGKYL-LRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEALDWLME 165
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
423-527 |
8.19e-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: 96.99 E-value: 8.19e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 423 LYLVEGDSAGGSAMQGR---DRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEF-NPEKLRYHRIII 498
Cdd:cd03365 3 LILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYeSTKSLRYGRLMI 82
|
90 100
....*....|....*....|....*....
gi 81311154 499 MTDADVDGAHIRTLLLTFFYRQMPELVER 527
Cdd:cd03365 83 MTDQDHDGSHIKGLLINFIHSFWPSLLKI 111
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
228-343 |
1.59e-18 |
|
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: 81.54 E-value: 1.59e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 228 FVQYMNRKKTplHEKIFYAFGEKDGMSVECAMQWND---SYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINsyieane 304
Cdd:cd00329 4 RLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN------- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 81311154 305 vakkakvetaGDDMREGLTCVLSVKLPD--PKFS-SQTKDKL 343
Cdd:cd00329 75 ----------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
36-173 |
3.00e-18 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 80.77 E-value: 3.00e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 36 DGSGLHHMVFEVLDNAIDEALAGhcDKITVTIHADH---SVSVADNGRGMPtgihpkegrsaAEVIMTVLHAGGKFDNNS 112
Cdd:smart00387 2 DPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRS 68
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 81311154 113 YKISGglHGVGVSVVNALSDWVTLTIYRDGKEhfvrfvrgeteeplkivgdsdKKGTTVRF 173
Cdd:smart00387 69 RKIGG--TGLGLSIVKKLVELHGGEISVESEP---------------------GGGTTFTI 106
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
422-535 |
3.30e-16 |
|
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: 74.32 E-value: 3.30e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 422 ELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLasqevatlitalgagigkEEFNPEKLRYHRIIIMTD 501
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKAL------------------KALKELALKAKEVILATD 62
|
90 100 110
....*....|....*....|....*....|....*.
gi 81311154 502 ADVDGAHIRTLLLTFFyrqmpELVER--GYIYIAQP 535
Cdd:pfam01751 63 PDREGEAIALKLLELK-----ELLENagGRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
36-173 |
2.44e-15 |
|
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: 72.40 E-value: 2.44e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 36 DGSGLHHMVFEVLDNAIDEAlaGHCDKITVTIHADH--SVSVADNGRGMPTGIHPkegrsaaevimtvlHAGGKFDnNSY 113
Cdd:pfam02518 2 DELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLP--------------RIFEPFS-TAD 64
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 114 KISGGLHGVGVSVVNALSDWVTLTIYrdgkehfvrfvrgeteeplkiVGDSDKKGTTVRF 173
Cdd:pfam02518 65 KRGGGGTGLGLSIVRKLVELLGGTIT---------------------VESEPGGGTTVTL 103
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
39-131 |
5.62e-08 |
|
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: 52.73 E-value: 5.62e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 39 GLHHMVFEVLDNAID-EALAGHCDKITVTIHAD-HSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKIS 116
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPEnNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90
....*....|....*
gi 81311154 117 GGLHGVGVSVVNALS 131
Cdd:cd16930 84 GGRNGYGAKLCNIFS 98
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
40-132 |
2.97e-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: 46.44 E-value: 2.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 40 LHHMVFEVLDNAIDEALAGhcDKITVTIHADHS---VSVADNGRGMPTGIHPkegrsaaevimtvlHAGGKFDNNSYKIS 116
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE--------------RIFERFYRGDKSRE 64
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90
....*....|....*.
gi 81311154 117 GGLHGVGVSVVNALSD 132
Cdd:cd00075 65 GGGTGLGLAIVRRIVE 80
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| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
421-520 |
3.85e-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: 3.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 81311154 421 SELYLVEGDSAGGSAMQGRDrKFQAILPLKGKILNvekarfekmlasQEVATLITALGagigkeefnpeklRYHRIIIMT 500
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALN------------KTRELLKRLLG-------------EAKEVIIAT 54
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90 100
....*....|....*....|
gi 81311154 501 DADVDGAHIRTLLLTFFYRQ 520
Cdd:cd00188 55 DADREGEAIALRLLELLKSL 74
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