|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-623 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1048.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:PRK14939 128 LSEWLELTIRRDGKIHEQEFEHGVP------------VAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLREL 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNIP 160
Cdd:PRK14939 196 AFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIP 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 161 QRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVA 240
Cdd:PRK14939 276 QRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVN 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 241 KALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSAKQ 320
Cdd:PRK14939 356 EKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQ 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 321 GRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTFF 400
Cdd:PRK14939 436 GRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFF 515
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 401 YRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRLALQGSELVPSkNGAAISGDALGELARSYLLSQSVI 480
Cdd:PRK14939 516 YRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHLA-DGPAISGEALEKLVKEYRAVRKII 594
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 481 GRLSRLYDPAALEAIMDGVSIDLSSEESTEASAKalhaalhdetlknevrvvpsydpvrelrslrverahhgnvrvsvID 560
Cdd:PRK14939 595 DRLERRYPRAVLEALIYAPALDLDDLADEAAVAA--------------------------------------------LD 630
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 167077361 561 EEFQHTADYQQLVTTAKTFEGLIQAGAVIKRGERSMAVTDFKSAMKWLLADAERNVSKQRYKG 623
Cdd:PRK14939 631 ADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDWLLAEARKGLSIQRYKG 693
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-445 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 724.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:COG0187 126 LSERLEVEVKRDGKIYRQRFERGKP------------VGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLREL 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSG--KEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNN 158
Cdd:COG0187 194 AFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNN 273
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:COG0187 274 INTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESV 353
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSA 318
Cdd:COG0187 354 VSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSA 433
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 319 KQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGkDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLT 398
Cdd:COG0187 434 KQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLT 512
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 167077361 399 FFYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRL 445
Cdd:COG0187 513 FFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKEL 559
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-437 |
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: 686.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:TIGR01059 121 LSEWLEVTVFRDGKIYRQEFERGIP------------VGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLREL 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLR--SGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNN 158
Cdd:TIGR01059 189 AFLNSGVKISLEDERdgKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNN 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:TIGR01059 269 INTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESL 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSA 318
Cdd:TIGR01059 349 VYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSA 428
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 319 KQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKdDYNLDKLRYHRIIIMTDADVDGAHIRTLLLT 398
Cdd:TIGR01059 429 KQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGK-DFDLEKLRYHKIIIMTDADVDGSHIRTLLLT 507
|
410 420 430
....*....|....*....|....*....|....*....
gi 167077361 399 FFYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAE 437
Cdd:TIGR01059 508 FFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKE 546
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-435 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 553.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGiaqdrvleqvdGVEVSPMLVTGDTENRGTEVHFMADPTIFG-TVEYHYDILAKRMRE 79
Cdd:smart00433 92 LSTEFEVEVARDGKEYKQSFSNN-----------GKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLRE 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 80 LSFLNNGVRIRLTDLRSGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNI 159
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 160 PQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVetTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVV 239
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 240 AKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGvLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSAK 319
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 320 QGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKdDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTF 399
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGK-DFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
410 420 430
....*....|....*....|....*....|....*.
gi 167077361 400 FYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDD 435
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFY 512
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
106-263 |
2.70e-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: 253.64 E-value: 2.70e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 106 GGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNIPQRDGGTHLTGLRAAMTRVINKYITD 185
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167077361 186 NEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPTDAKIICGKIVE 263
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
107-263 |
1.05e-63 |
|
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: 207.47 E-value: 1.05e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 107 GVKGFVEYINKTKTNLHPTVFFANGE--KDGVGVEVAMQWNDSYNENVLCFTNNIPQRDGGTHLTGLRAAMTRVINKYIT 184
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167077361 185 DNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPTDAKIICGKIVE 263
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-623 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1048.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:PRK14939 128 LSEWLELTIRRDGKIHEQEFEHGVP------------VAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLREL 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNIP 160
Cdd:PRK14939 196 AFLNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIP 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 161 QRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVA 240
Cdd:PRK14939 276 QRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVN 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 241 KALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSAKQ 320
Cdd:PRK14939 356 EKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQ 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 321 GRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTFF 400
Cdd:PRK14939 436 GRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFF 515
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 401 YRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRLALQGSELVPSkNGAAISGDALGELARSYLLSQSVI 480
Cdd:PRK14939 516 YRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHLA-DGPAISGEALEKLVKEYRAVRKII 594
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 481 GRLSRLYDPAALEAIMDGVSIDLSSEESTEASAKalhaalhdetlknevrvvpsydpvrelrslrverahhgnvrvsvID 560
Cdd:PRK14939 595 DRLERRYPRAVLEALIYAPALDLDDLADEAAVAA--------------------------------------------LD 630
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 167077361 561 EEFQHTADYQQLVTTAKTFEGLIQAGAVIKRGERSMAVTDFKSAMKWLLADAERNVSKQRYKG 623
Cdd:PRK14939 631 ADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDWLLAEARKGLSIQRYKG 693
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-445 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 724.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:COG0187 126 LSERLEVEVKRDGKIYRQRFERGKP------------VGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLREL 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSG--KEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNN 158
Cdd:COG0187 194 AFLNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNN 273
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:COG0187 274 INTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESV 353
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSA 318
Cdd:COG0187 354 VSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSA 433
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 319 KQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGkDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLT 398
Cdd:COG0187 434 KQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLT 512
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 167077361 399 FFYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRL 445
Cdd:COG0187 513 FFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKEL 559
|
|
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-445 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 702.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:PRK05644 128 LSTWLEVEVKRDGKIYYQEYERGVP------------VTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLREL 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSG--KEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNN 158
Cdd:PRK05644 196 AFLNKGLKITLTDEREGeeKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANN 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:PRK05644 276 INTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSV 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSA 318
Cdd:PRK05644 356 VSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSA 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 319 KQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGkDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLT 398
Cdd:PRK05644 436 KQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-DDFDISKLRYHKIIIMTDADVDGAHIRTLLLT 514
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 167077361 399 FFYRQMPEMVERGYVYIAQPPLYKIKAGKdERYLKDDAELNAHMLRL 445
Cdd:PRK05644 515 FFYRYMRPLIEAGYVYIAQPPLYKIKKGG-KEYAYSDEELDEILAEL 560
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-437 |
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: 686.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:TIGR01059 121 LSEWLEVTVFRDGKIYRQEFERGIP------------VGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLREL 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLR--SGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNN 158
Cdd:TIGR01059 189 AFLNSGVKISLEDERdgKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNN 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:TIGR01059 269 INTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESL 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSA 318
Cdd:TIGR01059 349 VYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSA 428
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 319 KQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKdDYNLDKLRYHRIIIMTDADVDGAHIRTLLLT 398
Cdd:TIGR01059 429 KQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGK-DFDLEKLRYHKIIIMTDADVDGSHIRTLLLT 507
|
410 420 430
....*....|....*....|....*....|....*....
gi 167077361 399 FFYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAE 437
Cdd:TIGR01059 508 FFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKE 546
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-435 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 553.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGiaqdrvleqvdGVEVSPMLVTGDTENRGTEVHFMADPTIFG-TVEYHYDILAKRMRE 79
Cdd:smart00433 92 LSTEFEVEVARDGKEYKQSFSNN-----------GKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLRE 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 80 LSFLNNGVRIRLTDLRSGKEDDFAFAGGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNI 159
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNI 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 160 PQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVetTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVV 239
Cdd:smart00433 241 ATTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 240 AKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGvLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSAK 319
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 320 QGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKdDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTF 399
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGK-DFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
410 420 430
....*....|....*....|....*....|....*.
gi 167077361 400 FYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDD 435
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFY 512
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-445 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 533.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAQDRvLEQVDGVEvspmlvtgdTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:PRK05559 128 LSSRLEVEVKRDGKVYRQRFEGGDPVGP-LEVVGTAG---------KRKTGTRVRFWPDPKIFDSPKFSPERLKERLRSK 197
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRsgKEDDFAFAGGVKGFVEYINKTKTNLHP-TVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNI 159
Cdd:PRK05559 198 AFLLPGLTITLNDER--ERQTFHYENGLKDYLAELNEGKETLPEeFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLI 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 160 PQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKvETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVV 239
Cdd:PRK05559 276 PTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVV 354
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 240 AKALEEFLLETPTDAKIICGKIVEAARARDAARKAREmtrRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGSAK 319
Cdd:PRK05559 355 KDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVK---RKKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAK 431
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 320 QGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGkDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTF 399
Cdd:PRK05559 432 QARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPG-DSFDLEDLRYGKIIIMTDADVDGAHIATLLLTF 510
|
410 420 430 440
....*....|....*....|....*....|....*....|....*.
gi 167077361 400 FYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRL 445
Cdd:PRK05559 511 FYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKL 556
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
1-423 |
2.43e-91 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 301.80 E-value: 2.43e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTEN-RGTEVHFMAD-PTIFGTVEYHY-------- 70
Cdd:PTZ00109 260 LSSFLKVDVFKGGKIYSIELSKGKV------------TKPLSVFSCPLKkRGTTIHFLPDyKHIFKTHHQHTeteeeegc 327
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 71 ------DILAKRMRELSFLNNGVRIRLTDLRSGKEDDFAF------AGGVKGFVEYINKTKTNLHPTVFFAN--GEKDGV 136
Cdd:PTZ00109 328 kngfnlDLIKNRIHELSYLNPGLTFYLVDERIANENNFYPyetikhEGGTREFLEELIKDKTPLYKDINIISirGVIKNV 407
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 137 GVEVAMQWN-DSYNENVLCFTNNIpQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAKVETTGDDMREGLSCVLSVKVPE 215
Cdd:PTZ00109 408 NVEVSLSWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNG 486
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 216 PKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPTDAKIICGKIVEAARARDAARKAREMTRRKGV-LDGVGLPGKLA 294
Cdd:PTZ00109 487 AEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNqYYSTILPGKLV 566
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 295 DCQEKDPAKCEIYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARYD-KLLSSEQIVTLVTALGCGIGKD---DYN 370
Cdd:PTZ00109 567 DCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrQYD 646
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 371 LD----------------------------KLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPEMVERGYVYIAQPPLYK 422
Cdd:PTZ00109 647 LShgtkaskdesvqnnnstltkkknslfdtPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYR 726
|
.
gi 167077361 423 I 423
Cdd:PTZ00109 727 I 727
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
1-445 |
1.05e-90 |
|
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: 293.36 E-value: 1.05e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGiaqdrvlEQVDGVEVSPmlvTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:TIGR01055 121 LSKRVKIKVYRQGKLYSIAFENG-------AKVTDLISAG---TCGKRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAK 190
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 81 SFLNNGVRIRLTDLRSGKEDDFAFAGGVKGFV-EYINKTKTnLHPTVFFANGEKDGVGVEVAMQWNDSYNENVL-CFTNN 158
Cdd:TIGR01055 191 AVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLsEAVNGDNT-LPPKPFSGNFEGDDEAVEWALLWLPEGGELFMeSYVNL 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 159 IPQRDGGTHLTGLRAAMTRVINKYITDNEIAKKAkVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEV 238
Cdd:TIGR01055 270 IPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGV 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 239 VAKALEEFLLETPTDAKiicgKIVEAARARDAARKAREM-TRRKGVLDGVGLPGKLADCQEKDPAKCEIYIVEGDSAGGS 317
Cdd:TIGR01055 349 IKDAFDLWLNQNVQLAE----HLAEHAISSAQRRKRAAKkVVRKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGS 424
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 318 AKQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDynLDKLRYHRIIIMTDADVDGAHIRTLLL 397
Cdd:TIGR01055 425 AKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDSND--LSQLRYGKICILADADSDGLHIATLLC 502
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 167077361 398 TFFYRQMPEMVERGYVYIAQPPLYKIKAGKDERYLKDDAELNAHMLRL 445
Cdd:TIGR01055 503 ALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKL 550
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
106-263 |
2.70e-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: 253.64 E-value: 2.70e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 106 GGVKGFVEYINKTKTNLHPTVFFANGEKDGVGVEVAMQWNDSYNENVLCFTNNIPQRDGGTHLTGLRAAMTRVINKYITD 185
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167077361 186 NEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPTDAKIICGKIVE 263
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
304-418 |
2.32e-80 |
|
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: 248.72 E-value: 2.32e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 304 CEIYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGkDDYNLDKLRYHRIIIMT 383
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-EDFDLEKLRYHKIIIMT 79
|
90 100 110
....*....|....*....|....*....|....*
gi 167077361 384 DADVDGAHIRTLLLTFFYRQMPEMVERGYVYIAQP 418
Cdd:cd03366 80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
304-418 |
2.07e-71 |
|
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: 225.46 E-value: 2.07e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 304 CEIYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDYNLDKLRYHRIIIMT 383
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 167077361 384 DADVDGAHIRTLLLTFFYRQMPEMVERGYVYIAQP 418
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 ... |
107-263 |
1.05e-63 |
|
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: 207.47 E-value: 1.05e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 107 GVKGFVEYINKTKTNLHPTVFFANGE--KDGVGVEVAMQWNDSYNENVLCFTNNIPQRDGGTHLTGLRAAMTRVINKYIT 184
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167077361 185 DNEIAKKAKVETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPTDAKIICGKIVE 263
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 ... |
451-612 |
2.64e-61 |
|
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: 200.83 E-value: 2.64e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 451 ELVPSKNGAAISGDALGELARSYLLSQSVIGRLSRLYDPAALEAIMDGVSID---LSSEESTEASAKALHAALHDETLK- 526
Cdd:pfam18053 2 ALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDaedLDDEAAAEAWAAALEARLNQDGLGg 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 527 NEVRVVPSYDPVRELRSLRVERAHHGNVRVSVIDEEFQHTADYQQLVTTAKTFEGLIQAGAVIKRGERSMAVTDFKSAMK 606
Cdd:pfam18053 82 PRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEALD 161
|
....*.
gi 167077361 607 WLLADA 612
Cdd:pfam18053 162 WLMEEA 167
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
1-102 |
5.73e-33 |
|
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: 124.57 E-value: 5.73e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 1 LSSWLRLTVRRNGKKHFMEFHRGIAqdrvleqvdgveVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDILAKRMREL 80
Cdd:cd16928 91 LSERLEVEVKRDGKIYRQEFSRGGP------------LTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLREL 158
|
90 100
....*....|....*....|..
gi 167077361 81 SFLNNGVRIRLTDLRSGKEDDF 102
Cdd:cd16928 159 AFLNKGLKIVLEDERTGKEEVF 180
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
52-429 |
1.58e-31 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 131.32 E-value: 1.58e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 52 TEVHFMADPTIFGTVEY---HYDILAKRMRELSFLNNGVRIRLTDLRSGkeddfafaggVKGFVEYIN----KTKTNLHP 124
Cdd:PTZ00108 196 TKVTFYPDYAKFGMTEFdddMLRLLKKRVYDLAGCFGKLKVYLNGERIA----------IKSFKDYVDlylpDGEEGKKP 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 125 TVFFANGEKDGvGVEVAMQWNDSYNENVlCFTNNIPQRDGGTHLTglrAAMTRVINKyITDNEIAK-KAKVETTGDDMRE 203
Cdd:PTZ00108 266 PYPFVYTSVNG-RWEVVVSLSDGQFQQV-SFVNSICTTKGGTHVN---YILDQLISK-LQEKAKKKkKKGKEIKPNQIKN 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 204 GLSCVLSVKVPEPKFSSQTKDKLVSSEVRAPVEEVVAKALEEFLLETPtdakiICGKIVEAARARDAARKAREM--TRRK 281
Cdd:PTZ00108 340 HLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMkaGKKS 414
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 282 GVLdgvGLPgKLADCQE--KDPA-KCEIYIVEGDSAGGSAKQG---RDRKFQAILPLRGKVLNVEKARYDKLLSSEQIVT 355
Cdd:PTZ00108 415 RIL---GIP-KLDDANDagGKNSeECTLILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQN 490
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167077361 356 LVTALGCGIGKDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPEMVE-RGYVYIAQPPLYKI-KAGKDE 429
Cdd:PTZ00108 491 LFKILGLDIGKKYEDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFITPIVKAtKKGNQV 566
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
50-437 |
3.85e-31 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 128.33 E-value: 3.85e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 50 RGTEVHFMADPTIFGTV---EYHYDILAKRMRELS-------FLNNGVRIrltdlrSGKEDDFAFAGGVKGFVEyinktk 119
Cdd:PHA02569 176 KGTSVTFIPDFSHFEVNgldQQYLDIILDRLQTLAvvfpdikFTFNGKKV------SGKFKKYAKQFGDDTIVQ------ 243
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 120 TNLHPTVFFANGEkdgvgvevamqwnDSYNEnvLCFTNNIPQRDGGTHLTGlraamtrVINKyITDN---EIAKKAKVET 196
Cdd:PHA02569 244 ENDNVSIALAPSP-------------DGFRQ--LSFVNGLHTKNGGHHVDC-------VMDD-ICEElipMIKKKHKIEV 300
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 197 TGDDMREGLSCVLSVK-VPEPKFSSQTKDKLVSS--EVRAPVEeVVAKALEEFLLETPTdakiICGKIVEAARARDAARK 273
Cdd:PHA02569 301 TKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEA----IIMPIIEAALARKLAAE 375
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 274 AREMTR------RKGVLDGV--GLPGKLADCQekdpakceIYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARYD 345
Cdd:PHA02569 376 KAAETKaakkakKAKVAKHIkaNLIGKDAETT--------LFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYA 447
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 346 KLLSSEQIVTLVTALGCGIGKDDynlDKLRYHRIIIMTDADVDG-AHIRTLLLTFFYRqMPEMVERGYVYIAQPPLYKIK 424
Cdd:PHA02569 448 DILKNKELFDICAITGLVLGEKA---ENMNYKNIAIMTDADVDGkGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQ 523
|
410
....*....|...
gi 167077361 425 AGKDERYLKDDAE 437
Cdd:PHA02569 524 VGKETKWFYSLDE 536
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
36-410 |
8.74e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 113.26 E-value: 8.74e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 36 VEVSPMLVTGDTENRGTEVHFMADPTIFGTVEYHYDI---LAKRMRELS-FLNNGVRIRLTDLRSGkeddfafaggVKGF 111
Cdd:PLN03128 172 VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKKLP----------VKSF 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 112 VEYIN-----KTKTNLHPTVFFANGEKDGVGVEVAmqwNDSYNEnvLCFTNNIPQRDGGTHLtglrAAMTRVINKYITDn 186
Cdd:PLN03128 242 QDYVGlylgpNSREDPLPRIYEKVNDRWEVCVSLS---DGSFQQ--VSFVNSIATIKGGTHV----DYVADQIVKHIQE- 311
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 187 EIAKKAK--VETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVS------SEVRAPveevvakalEEFLletPTDAKiiC 258
Cdd:PLN03128 312 KVKKKNKnaTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTrpssfgSKCELS---------EEFL---KKVEK--C 377
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 259 GkIVEAARARDAARKAREMTRRKGVLDG--VGLPgKLADCQE---KDPAKCEIYIVEGDSAGGSAKQGRD---RKFQAIL 330
Cdd:PLN03128 378 G-VVENILSWAQFKQQKELKKKDGAKRQrlTGIP-KLDDANDaggKKSKDCTLILTEGDSAKALAMSGLSvvgRDHYGVF 455
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 331 PLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDdYNLD---KLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPEM 407
Cdd:PLN03128 456 PLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKT-YDEEntkSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSL 534
|
...
gi 167077361 408 VER 410
Cdd:PLN03128 535 LKI 537
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
304-410 |
5.96e-25 |
|
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: 100.07 E-value: 5.96e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 304 CEIYIVEGDSAGGSAKQGR---DRKFQAILPLRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDY-NLDKLRYHRI 379
Cdd:cd03365 1 CTLILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYeSTKSLRYGRL 80
|
90 100 110
....*....|....*....|....*....|.
gi 167077361 380 IIMTDADVDGAHIRTLLLTFFYRQMPEMVER 410
Cdd:cd03365 81 MIMTDQDHDGSHIKGLLINFIHSFWPSLLKI 111
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
108-409 |
9.55e-21 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 97.24 E-value: 9.55e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 108 VKGFVEYIN-------KTKTNLHPTVFfangEKDGVGVEVAMQWNDSYNENVlCFTNNIPQRDGGTHLTglraAMTRVIN 180
Cdd:PLN03237 263 VKSFSDYVDlylesanKSRPENLPRIY----EKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHVD----YVTNQIA 333
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 181 KYITdNEIAKKAK-VETTGDDMREGLSCVLSVKVPEPKFSSQTKDKLVsseVRAPVEEVVAKALEEFLletptdAKIICG 259
Cdd:PLN03237 334 NHVM-EAVNKKNKnANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLT---LRQSSFGSKCELSEDFL------KKVMKS 403
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 260 KIVEAARARDAARKAREMTRRKGVLDG--VGLPgKLADCQE---KDPAKCEIYIVEGDSAGGSAKQGR---DRKFQAILP 331
Cdd:PLN03237 404 GIVENLLSWADFKQSKELKKTDGAKTTrvTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLsvvGRNYYGVFP 482
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167077361 332 LRGKVLNVEKARYDKLLSSEQIVTLVTALGCGIGKDDYNLDKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPEMVE 409
Cdd:PLN03237 483 LRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
108-226 |
2.91e-20 |
|
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: 86.16 E-value: 2.91e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 108 VKGFVEYINKTKTnlHPTVFFANGEKDGVGVEVAMQWND---SYNENVLCFTNNIPQRDGGTHLTGLRAAMTRVINkyit 184
Cdd:cd00329 1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 167077361 185 dneiakkakvettGDDMREGLSCVLSVKVP--EPKFS-SQTKDKL 226
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPpsLVDVNvHPTKEEV 106
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
305-418 |
6.68e-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: 73.16 E-value: 6.68e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 305 EIYIVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKARYDKLLSSeqivtlvtalgcgigkddYNLDKLRYHRIIIMTD 384
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA------------------LKELALKAKEVILATD 62
|
90 100 110
....*....|....*....|....*....|....*.
gi 167077361 385 ADVDGAHIRTLLLTFFyrqmpEMVER--GYVYIAQP 418
Cdd:pfam01751 63 PDREGEAIALKLLELK-----ELLENagGRVEFSEL 93
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
304-403 |
9.67e-06 |
|
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: 43.95 E-value: 9.67e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167077361 304 CEIYIVEGDSAGGSAKQGRDrKFQAILPLRGKVLNVEKARYDKLLSseqivtlvtalgcgigkddynldklRYHRIIIMT 383
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG-------------------------EAKEVIIAT 54
|
90 100
....*....|....*....|
gi 167077361 384 DADVDGAHIRTLLLTFFYRQ 403
Cdd:cd00188 55 DADREGEAIALRLLELLKSL 74
|
|
| |
