|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-409 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 772.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVP-GTLNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:PRK05644 107 GGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPvTPLEVIGETDETGTTVTFKPDPEIFETTEFDYD 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGDsdeaeepdaegyvakVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:PRK05644 187 TLATRLRELAFLNKGLKITLTDEREGE---------------EKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKD 251
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:PRK05644 252 GIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHP 331
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:PRK05644 332 EPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLA 411
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:PRK05644 412 DCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLR 491
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:PRK05644 492 YHKIIIMTDA 501
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-409 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 742.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVPGT-LNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:COG0187 105 DGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGpLEKIGKTDRTGTTVRFKPDPEIFETTEFDYE 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGDsdeaeepdaegyvakVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:COG0187 185 TLAERLRELAFLNKGLTITLTDEREEE---------------PKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKD 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:COG0187 250 GIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLP 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:COG0187 330 EPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLA 409
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:COG0187 410 DCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLR 489
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:COG0187 490 YHKIIIMTDA 499
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-409 |
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: 643.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVP-GTLNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:TIGR01059 100 DKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPvGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFD 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERngdsdeaeepdaegyVAKVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:TIGR01059 180 ILAKRLRELAFLNSGVKISLEDER---------------DGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:TIGR01059 245 GIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVP 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:TIGR01059 325 DPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLA 404
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:TIGR01059 405 DCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLR 484
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:TIGR01059 485 YHKIIIMTDA 494
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-409 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 552.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTR--SVPGTLNKGAATRRTGTTITFWADPDIFE-TTVYN 77
Cdd:smart00433 71 DDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNngKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDD 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 78 IETIRRRLQEMAFLNKGLTIVLRDERNGdsdeaeepdaegyvakvKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGE 157
Cdd:smart00433 151 FELLKRRLRELAFLNKGVKITLNDERSD-----------------EEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGE 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 158 APGHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDpaLSGDDIREGLAAIVSVK 237
Cdd:smart00433 214 KDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVK 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 238 VKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELvRRKSAGDIGGLPGK 317
Cdd:smart00433 292 IPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAREL-TRKKKLSSISLPGK 370
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 318 LADCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAK 397
Cdd:smart00433 371 LADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEK 450
|
410
....*....|..
gi 190148862 398 LRYHKIVLMTDA 409
Cdd:smart00433 451 LRYGKIIIMTDA 462
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
131-302 |
2.77e-91 |
|
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: 272.51 E-value: 2.77e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 131 NGLEDFVAHLNKTKDPIYKKLVAFTGEAPGHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARD 210
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 211 KKLLKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSA 290
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAA 160
|
170
....*....|..
gi 190148862 291 QARLAARKAREL 302
Cdd:cd00822 161 KAREAARKAREL 172
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
132-302 |
4.15e-79 |
|
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: 241.37 E-value: 4.15e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 132 GLEDFVAHLNKTKDPIYKKLVAFTGEAP--GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYAR 209
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESPdnRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 210 DKKLLKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQS 289
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160
|
170
....*....|...
gi 190148862 290 AQARLAARKAREL 302
Cdd:pfam00204 161 AKARLAARKAREA 173
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-409 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 772.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVP-GTLNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:PRK05644 107 GGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPvTPLEVIGETDETGTTVTFKPDPEIFETTEFDYD 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGDsdeaeepdaegyvakVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:PRK05644 187 TLATRLRELAFLNKGLKITLTDEREGE---------------EKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKD 251
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:PRK05644 252 GIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHP 331
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:PRK05644 332 EPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLA 411
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:PRK05644 412 DCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLR 491
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:PRK05644 492 YHKIIIMTDA 501
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-409 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 742.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVPGT-LNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:COG0187 105 DGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGpLEKIGKTDRTGTTVRFKPDPEIFETTEFDYE 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGDsdeaeepdaegyvakVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:COG0187 185 TLAERLRELAFLNKGLTITLTDEREEE---------------PKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKD 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:COG0187 250 GIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLP 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:COG0187 330 EPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLA 409
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:COG0187 410 DCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLR 489
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:COG0187 490 YHKIIIMTDA 499
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-409 |
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: 643.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVP-GTLNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:TIGR01059 100 DKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPvGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFD 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERngdsdeaeepdaegyVAKVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:TIGR01059 180 ILAKRLRELAFLNSGVKISLEDER---------------DGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKE 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:TIGR01059 245 GIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVP 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:TIGR01059 325 DPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLA 404
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLR 399
Cdd:TIGR01059 405 DCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLR 484
|
410
....*....|
gi 190148862 400 YHKIVLMTDA 409
Cdd:TIGR01059 485 YHKIIIMTDA 494
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-409 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 642.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVPGT-LNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:PRK14939 107 DQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVApLKVVGETDKTGTEVRFWPSPEIFENTEFDYD 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGdsdeaeepdaegyvakvKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGEAP 159
Cdd:PRK14939 187 ILAKRLRELAFLNSGVRIRLKDERDG-----------------KEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKD 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 160 GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVK 239
Cdd:PRK14939 250 GIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVP 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 240 EPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELVRRKSAGDIGGLPGKLA 319
Cdd:PRK14939 330 DPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLA 409
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 320 DCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGI-HDEFDLAKL 398
Cdd:PRK14939 410 DCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIgRDEFNPDKL 489
|
410
....*....|.
gi 190148862 399 RYHKIVLMTDA 409
Cdd:PRK14939 490 RYHKIIIMTDA 500
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-409 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 552.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTR--SVPGTLNKGAATRRTGTTITFWADPDIFE-TTVYN 77
Cdd:smart00433 71 DDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNngKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDD 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 78 IETIRRRLQEMAFLNKGLTIVLRDERNGdsdeaeepdaegyvakvKEHVFCYPNGLEDFVAHLNKTKDPIYKKLVAFTGE 157
Cdd:smart00433 151 FELLKRRLRELAFLNKGVKITLNDERSD-----------------EEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGE 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 158 APGHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDpaLSGDDIREGLAAIVSVK 237
Cdd:smart00433 214 KDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVK 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 238 VKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKARELvRRKSAGDIGGLPGK 317
Cdd:smart00433 292 IPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAREL-TRKKKLSSISLPGK 370
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 318 LADCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAK 397
Cdd:smart00433 371 LADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEK 450
|
410
....*....|..
gi 190148862 398 LRYHKIVLMTDA 409
Cdd:smart00433 451 LRYGKIIIMTDA 462
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-409 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 535.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVP-GTLNKGAAT--RRTGTTITFWADPDIFETTVYN 77
Cdd:PRK05559 107 SNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPvGPLEVVGTAgkRKTGTRVRFWPDPKIFDSPKFS 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 78 IETIRRRLQEMAFLNKGLTIVLRDERngdsdeaeepdaegyvakvKEHVFCYPNGLEDFVAHLNKTKDPIYKKLV-AFTG 156
Cdd:PRK05559 187 PERLKERLRSKAFLLPGLTITLNDER-------------------ERQTFHYENGLKDYLAELNEGKETLPEEFVgSFEG 247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 157 EAPGHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKeKDPALSGDDIREGLAAIVSV 236
Cdd:PRK05559 248 EAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSV 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 237 KVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLAARKarELVRRKSAgDIGGLPG 316
Cdd:PRK05559 327 KIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAK--KVKRKKKT-SGPALPG 403
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 317 KLADCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLA 396
Cdd:PRK05559 404 KLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSFDLE 483
|
410
....*....|...
gi 190148862 397 KLRYHKIVLMTDA 409
Cdd:PRK05559 484 DLRYGKIIIMTDA 496
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
2-409 |
1.26e-95 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 305.65 E-value: 1.26e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 2 SDSYAVSGGLHGVGVSVVNALSTRLDVEIdtdgFHWDQQYTRSvpgtLNKGAAT----------RRTGTTITFWAD-PDI 70
Cdd:PTZ00109 240 SQMYEYSSGLHGVGLSVVNALSSFLKVDV----FKGGKIYSIE----LSKGKVTkplsvfscplKKRGTTIHFLPDyKHI 311
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 71 FETTV--------------YNIETIRRRLQEMAFLNKGLTIVLRDERNgdSDEAEEPDAEgyvakvkehVFCYPNGLEDF 136
Cdd:PTZ00109 312 FKTHHqhteteeeegckngFNLDLIKNRIHELSYLNPGLTFYLVDERI--ANENNFYPYE---------TIKHEGGTREF 380
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 137 VAHLNKTKDPIYK--KLVAFTGEAPGHALEVAMQWNSG-YTESVYTFANTINThEGGTHEEGFRAALTSTVNKYARDKKL 213
Cdd:PTZ00109 381 LEELIKDKTPLYKdiNIISIRGVIKNVNVEVSLSWSLEsYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGY 459
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 214 LKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQAR 293
Cdd:PTZ00109 460 FKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAF 539
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 294 LAARKARELVRRKSAGDIG-GLPGKLADCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARID-R 371
Cdd:PTZ00109 540 EEAKAAKDLIRQKNNQYYStILPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkK 619
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 372 VLKNTEVQAIITALGTGIH-----------------DEF---------------DLAKLRYHKIVLMTDA 409
Cdd:PTZ00109 620 VFENSEIKLLITSIGLSVNpvtwrqydlshgtkaskDESvqnnnstltkkknslFDTPLRYGKIILLTDA 689
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
131-302 |
2.77e-91 |
|
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: 272.51 E-value: 2.77e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 131 NGLEDFVAHLNKTKDPIYKKLVAFTGEAPGHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARD 210
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 211 KKLLKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSA 290
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAA 160
|
170
....*....|..
gi 190148862 291 QARLAARKAREL 302
Cdd:cd00822 161 KAREAARKAREL 172
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
5-409 |
3.81e-87 |
|
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: 276.80 E-value: 3.81e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 5 YAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTR--SVPGTLNKGAATRR-TGTTITFWADPDIFETTVYNIETI 81
Cdd:TIGR01055 104 YHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENgaKVTDLISAGTCGKRlTGTSVHFTPDPEIFDSLHFSVSRL 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 82 RRRLQEMAFLNKGLTIVLRDERNgdsdeaeepdaegyvakVKEHVFCYPNGLEDFVAHLNKTKDPIYKKLvaFTGEAPG- 160
Cdd:TIGR01055 184 YHILRAKAVLCRGVEIEFEDEVN-----------------NTKALWNYPDGLKDYLSEAVNGDNTLPPKP--FSGNFEGd 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 161 -HALEVAMQW-NSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKeKDPALSGDDIREGLAAIVSVKV 238
Cdd:TIGR01055 245 dEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLP-RGVKLTAEDIWDRCSYVLSIKM 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 239 KEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQSAQARLaaRKARELVRRKSAGDIGgLPGKL 318
Cdd:TIGR01055 324 QDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRK--RAAKKVVRKKLTSGPA-LPGKL 400
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 319 ADCRSTDPSKSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGiHDEFDLAKL 398
Cdd:TIGR01055 401 ADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID-PDSNDLSQL 479
|
410
....*....|.
gi 190148862 399 RYHKIVLMTDA 409
Cdd:TIGR01055 480 RYGKICILADA 490
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
132-302 |
4.15e-79 |
|
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: 241.37 E-value: 4.15e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 132 GLEDFVAHLNKTKDPIYKKLVAFTGEAP--GHALEVAMQWNSGYTESVYTFANTINTHEGGTHEEGFRAALTSTVNKYAR 209
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESPdnRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 210 DKKLLKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLGNTEVKSFVQRISNEWLADWFERNPTEARTIVNKAVQS 289
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160
|
170
....*....|...
gi 190148862 290 AQARLAARKAREL 302
Cdd:pfam00204 161 AKARLAARKAREA 173
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
329-409 |
4.51e-52 |
|
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: 169.76 E-value: 4.51e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 329 SEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAKLRYHKIVLMTD 408
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
.
gi 190148862 409 A 409
Cdd:cd03366 81 A 81
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
1-109 |
1.47e-48 |
|
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: 163.09 E-value: 1.47e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDGFHWDQQYTRSVPGT-LNKGAATRRTGTTITFWADPDIFETTVYNIE 79
Cdd:cd16928 70 DGGSYKVSGGLHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTpLEVIGETKKTGTTVRFWPDPEIFEKTEFDFD 149
|
90 100 110
....*....|....*....|....*....|
gi 190148862 80 TIRRRLQEMAFLNKGLTIVLRDERNGDSDE 109
Cdd:cd16928 150 TLKRRLRELAFLNKGLKIVLEDERTGKEEV 179
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
329-409 |
9.91e-43 |
|
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: 145.73 E-value: 9.91e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 329 SEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIH-DEFDLAKLRYHKIVLMT 407
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
..
gi 190148862 408 DA 409
Cdd:cd01030 81 DA 82
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
1-408 |
1.61e-27 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 115.53 E-value: 1.61e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEIDTDG----FH--WDQQYTRSVPGTL--NKGAATRrtgTTITFWADPDIFE 72
Cdd:PTZ00108 132 DDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKsgkkFKmtWTDNMSKKSEPRItsYDGKKDY---TKVTFYPDYAKFG 208
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 73 TTVYNIETIR---RRLQEMAFLNKGLTIVLRDERNGDSDeaeepdaegyvakVKEHVFCYPngledfvahlnKTKDPIYK 149
Cdd:PTZ00108 209 MTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERIAIKS-------------FKDYVDLYL-----------PDGEEGKK 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 150 KLVAFTGEAPGHALEVAMqwnsGYTESVYT---FANTINTHEGGTHEEGFRAALTSTVNKYAR-DKKLLKEKDPALsgdd 225
Cdd:PTZ00108 265 PPYPFVYTSVNGRWEVVV----SLSDGQFQqvsFVNSICTTKGGTHVNYILDQLISKLQEKAKkKKKKGKEIKPNQ---- 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 226 IREGLAAIVSVKVKEPQFEGQTKTKLgNTEVKSFVQ-RISNEWLADWFERNPteartIVNKAVQSAQARLAArkarELVR 304
Cdd:PTZ00108 337 IKNHLWVFVNCLIVNPSFDSQTKETL-TTKPSKFGStCELSEKLIKYVLKSP-----ILENIVEWAQAKLAA----ELNK 406
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 305 RKSAGDIGGLPG--KLADCRS--TDPSKSEVYIV-EGDSAGGSAKSG-----RDSMtqAILPIRGKIINVEKARIDRVLK 374
Cdd:PTZ00108 407 KMKAGKKSRILGipKLDDANDagGKNSEECTLILtEGDSAKALALAGlsvvgRDYY--GVFPLRGKLLNVRDASLKQLMN 484
|
410 420 430
....*....|....*....|....*....|....*
gi 190148862 375 NTEVQAIITALGTGIHDEFDLAK-LRYHKIVLMTD 408
Cdd:PTZ00108 485 NKEIQNLFKILGLDIGKKYEDPKgLRYGSLMIMTD 519
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
1-408 |
6.83e-21 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 95.16 E-value: 6.83e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 1 DSDSYAVSGGLHGVGVSVVNALSTRLDVEI--DTDGFHWDQQYTR--SVPGT-LNKGAATRRTGTTITFWADPDIFETTV 75
Cdd:PLN03128 124 DDNEKKTTGGRNGYGAKLANIFSTEFTVETadGNRGKKYKQVFTNnmSVKSEpKITSCKASENWTKITFKPDLAKFNMTR 203
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 76 YNIETI---RRRLQEMA-FLNKGLTIVLRDER---NGDSDeaeepdaegYVakvkehvfcypnGLEDFVAHLNKTKDPIY 148
Cdd:PLN03128 204 LDEDVValmSKRVYDIAgCLGKKLKVELNGKKlpvKSFQD---------YV------------GLYLGPNSREDPLPRIY 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 149 KKLvaftgeapGHALEVAMQWNSGYTESVyTFANTINTHEGGTHEEgfraALTSTVNKYARDKKLLKEKDPA-LSGDDIR 227
Cdd:PLN03128 263 EKV--------NDRWEVCVSLSDGSFQQV-SFVNSIATIKGGTHVD----YVADQIVKHIQEKVKKKNKNAThVKPFQIK 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 228 EGLAAIVSVKVKEPQFEGQTKTKLgNTEVKSFVQR--ISNEWLadwfernpteaRTIVNKAVQSAQARLAARKARELVRR 305
Cdd:PLN03128 330 NHLWVFVNCLIENPTFDSQTKETL-TTRPSSFGSKceLSEEFL-----------KKVEKCGVVENILSWAQFKQQKELKK 397
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 306 KSAGDIGGLPG--KLADCRSTDPSKSE---VYIVEGDSAGGSAKSG-----RDSMtqAILPIRGKIINVEKARIDRVLKN 375
Cdd:PLN03128 398 KDGAKRQRLTGipKLDDANDAGGKKSKdctLILTEGDSAKALAMSGlsvvgRDHY--GVFPLRGKLLNVREASHKQIMKN 475
|
410 420 430
....*....|....*....|....*....|....*.
gi 190148862 376 TEVQAIITALG---TGIHDEFDLAKLRYHKIVLMTD 408
Cdd:PLN03128 476 AEITNIKQILGlqfGKTYDEENTKSLRYGHLMIMTD 511
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
133-252 |
9.18e-21 |
|
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: 86.55 E-value: 9.18e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 133 LEDFVAHLNKTKDPiyKKLVAFTGEAPGHALEVAMQWNS---GYTESVYTFANTINTHEGGTHEEGFRAALTSTVNkyar 209
Cdd:cd00329 1 LKDRLAEILGDKVA--DKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 190148862 210 dkkllkekdpalsGDDIREGLAAIVSVKV--KEPQFE-GQTKTKLG 252
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
3-409 |
2.66e-16 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 80.95 E-value: 2.66e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 3 DSYAVSGGLHGVGVSVVNALSTRLdVEIDTDGfhwDQQYT-RSVPGTLNKGAATRRT---GTTITFWADPDIFETTVYN- 77
Cdd:PHA02569 121 DTNRVTGGMNGVGSSLTNFFSVLF-IGETCDG---KNEVTvNCSNGAENISWSTKPGkgkGTSVTFIPDFSHFEVNGLDq 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 78 --IETIRRRLQEMAFLNKGLTIVLrderNGdsdeaeepdaEGYVAKVKEHVFCYPnglEDFVAHLNKtkdpiykKLVAFT 155
Cdd:PHA02569 197 qyLDIILDRLQTLAVVFPDIKFTF----NG----------KKVSGKFKKYAKQFG---DDTIVQEND-------NVSIAL 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 156 GEAPghalevamqwnSGYTESvyTFANTINTHEGGTHEEGFRAALTSTVNKYARDKKLLKEKDPAlsgddIREGLAAIVS 235
Cdd:PHA02569 253 APSP-----------DGFRQL--SFVNGLHTKNGGHHVDCVMDDICEELIPMIKKKHKIEVTKAR-----VKECLTIVLF 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 236 VK-VKEPQFEGQTKTKLGNT--EVKSFVQrISNEWLADWFERNPTEARTIVNKAV---QSAQARLAARKARELVRRKSAG 309
Cdd:PHA02569 315 VRnMSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEAIIMPIIEAALarkLAAEKAAETKAAKKAKKAKVAK 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 310 DI-GGLPGKLADcrstdpskSEVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKNTEVQAIITAlgTG 388
Cdd:PHA02569 394 HIkANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAI--TG 463
|
410 420
....*....|....*....|.
gi 190148862 389 IHDEFDLAKLRYHKIVLMTDA 409
Cdd:PHA02569 464 LVLGEKAENMNYKNIAIMTDA 484
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
179-408 |
1.47e-13 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 72.59 E-value: 1.47e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 179 TFANTINTHEGGTHEEgfraALTSTVNKYARDKKLLKEKDPALSGDDIREGLAAIVSVKVKEPQFEGQTKTKLgNTEVKS 258
Cdd:PLN03237 311 SFVNSIATIKGGTHVD----YVTNQIANHVMEAVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL-TLRQSS 385
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 259 FVQRISnewLADWFERNpTEARTIVNKAVQSAQARlaarKARELVRR--KSAGDIGGLPgKLADCRSTDPSKSE---VYI 333
Cdd:PLN03237 386 FGSKCE---LSEDFLKK-VMKSGIVENLLSWADFK----QSKELKKTdgAKTTRVTGIP-KLEDANEAGGKNSEkctLIL 456
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 190148862 334 VEGDSAGGSAKSGRDSMTQ---AILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDLAK-LRYHKIVLMTD 408
Cdd:PLN03237 457 TEGDSAKALAVAGLSVVGRnyyGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKsLRYGHLMIMTD 535
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
335-408 |
4.05e-13 |
|
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: 65.40 E-value: 4.05e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 190148862 335 EGDSAGGSAKSGRDSM---TQAILPIRGKIINVEKARIDRVLKNTEVQAIITALGTGI--HDEFDLAKLRYHKIVLMTD 408
Cdd:cd03365 7 EGDSAKALAVAGLSVVgrdYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHgkSDYESTKSLRYGRLMIMTD 85
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
330-409 |
2.46e-09 |
|
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: 53.90 E-value: 2.46e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190148862 330 EVYIVEGDSAGGSAKSGRDSMTQAILPIRGKIINVEKARIDRVLKntevqaiitalgtgihdEFDLAKLRYHKIVLMTDA 409
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
|
| |
