|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-393 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 706.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKP-DPLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:PRK05644 108 GGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPvTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDT 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERvaegeEGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:PRK05644 188 LATRLRELAFLNKGLKITLTDER-----EGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:PRK05644 263 DGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKeKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTK 342
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:PRK05644 343 LGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESE 422
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:PRK05644 423 LYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIII 497
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-393 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 671.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKPD-PLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:COG0187 106 GGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVgPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYET 185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERvaegeEGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:COG0187 186 LAERLRELAFLNKGLTITLTDER-----EEEPKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWN 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:COG0187 261 DGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKeKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTK 340
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:COG0187 341 LGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESE 420
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:COG0187 421 LFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIII 495
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-393 |
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: 582.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKP-DPLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:TIGR01059 101 KDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPvGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDI 180
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERVaegeeGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:TIGR01059 181 LAKRLRELAFLNSGVKISLEDERD-----GKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWN 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:TIGR01059 256 DGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKeSKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTK 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:TIGR01059 336 LGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSE 415
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:TIGR01059 416 LYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIII 490
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-393 |
1.20e-179 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 512.49 E-value: 1.20e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHN--SKPDPLEEGETADRTGSAVSFWPDPDVFE-TTDFDF 77
Cdd:smart00433 72 DDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNngKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDF 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 78 QTICRRLQEMAFLNRALSIHLLDERVAEgeegkprEVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQ 157
Cdd:smart00433 152 ELLKRRLRELAFLNKGVKITLNDERSDE-------EKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQ 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 158 WNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLKgDEKLSGEDIREGLAAIISVKLANPQFEGQTKT 237
Cdd:smart00433 225 YTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLK-EKNIKGEDVREGLTAFISVKIPEPQFEGQTKE 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 238 KLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLlESGSMPGKLADCQSTDPRES 317
Cdd:smart00433 304 KLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKL-SSISLPGKLADASSAGPKKC 382
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 318 EVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:smart00433 383 ELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIII 458
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
120-273 |
8.06e-76 |
|
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: 232.45 E-value: 8.06e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 120 GGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGAD 199
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 200 KKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQK 273
Cdd:cd00822 81 NNLLKkKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
121-273 |
1.98e-66 |
|
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Pssm-ID: 425522 [Multi-domain] Cd Length: 173 Bit Score: 208.62 E-value: 1.98e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 121 GIADFVRHLNASKNPMHKTVVEFAAE--EEGMSVEIAMQWNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGA 198
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 199 DKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQK 273
Cdd:pfam00204 81 KKGLLKkKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-393 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 706.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKP-DPLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:PRK05644 108 GGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPvTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDT 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERvaegeEGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:PRK05644 188 LATRLRELAFLNKGLKITLTDER-----EGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYN 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:PRK05644 263 DGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKeKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTK 342
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:PRK05644 343 LGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESE 422
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:PRK05644 423 LYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIII 497
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-393 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 671.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKPD-PLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:COG0187 106 GGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVgPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYET 185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERvaegeEGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:COG0187 186 LAERLRELAFLNKGLTITLTDER-----EEEPKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWN 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:COG0187 261 DGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKeKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTK 340
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:COG0187 341 LGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESE 420
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:COG0187 421 LFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIII 495
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-393 |
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: 582.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKP-DPLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:TIGR01059 101 KDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPvGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDI 180
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERVaegeeGKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWN 159
Cdd:TIGR01059 181 LAKRLRELAFLNSGVKISLEDERD-----GKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWN 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 160 ESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTK 238
Cdd:TIGR01059 256 DGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKeSKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTK 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 239 LGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESE 318
Cdd:TIGR01059 336 LGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSE 415
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 319 VFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:TIGR01059 416 LYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIII 490
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
2-393 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 582.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 2 KAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKPD-PLEEGETADRTGSAVSFWPDPDVFETTDFDFQTI 80
Cdd:PRK14939 109 NSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVaPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDIL 188
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 81 CRRLQEMAFLNRALSIHLLDERvaegeegKPREVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWNE 160
Cdd:PRK14939 189 AKRLRELAFLNSGVRIRLKDER-------DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWND 261
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 161 SYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKL 239
Cdd:PRK14939 262 SYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKkAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKL 341
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 240 GNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTDPRESEV 319
Cdd:PRK14939 342 VSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSEL 421
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 320 FIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGI-HDDFDMEKLRYHKVVL 393
Cdd:PRK14939 422 YLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIgRDEFNPDKLRYHKIII 496
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
1-393 |
1.20e-179 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 512.49 E-value: 1.20e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHN--SKPDPLEEGETADRTGSAVSFWPDPDVFE-TTDFDF 77
Cdd:smart00433 72 DDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNngKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDF 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 78 QTICRRLQEMAFLNRALSIHLLDERVAEgeegkprEVTFYYEGGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQ 157
Cdd:smart00433 152 ELLKRRLRELAFLNKGVKITLNDERSDE-------EKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQ 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 158 WNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLKgDEKLSGEDIREGLAAIISVKLANPQFEGQTKT 237
Cdd:smart00433 225 YTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLK-EKNIKGEDVREGLTAFISVKIPEPQFEGQTKE 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 238 KLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRKSLlESGSMPGKLADCQSTDPRES 317
Cdd:smart00433 304 KLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKL-SSISLPGKLADASSAGPKKC 382
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 318 EVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:smart00433 383 ELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIII 458
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-393 |
3.58e-169 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 486.92 E-value: 3.58e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKP-DPLEEGETA--DRTGSAVSFWPDPDVFETTDFDF 77
Cdd:PRK05559 108 NKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPvGPLEVVGTAgkRKTGTRVRFWPDPKIFDSPKFSP 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 78 QTICRRLQEMAFLNRALSIHLLDERVaegeegkprEVTFYYEGGIADFVRHLNASKNPMHKTVVE-FAAEEEGMSVEIAM 156
Cdd:PRK05559 188 ERLKERLRSKAFLLPGLTITLNDERE---------RQTFHYENGLKDYLAELNEGKETLPEEFVGsFEGEAEGEAVEWAL 258
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 157 QWNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLKGDEKLSGEDIREGLAAIISVKLANPQFEGQTK 236
Cdd:PRK05559 259 QWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKKLEGEDVREGLAAVLSVKIPEPQFEGQTK 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 237 TKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKasQAARARIAAQQARKLARRKSLLESgSMPGKLADCQSTDPRE 316
Cdd:PRK05559 339 EKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEK--AIKAAQARLRAAKKVKRKKKTSGP-ALPGKLADCTSQDPER 415
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 188529762 317 SEVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDFDMEKLRYHKVVL 393
Cdd:PRK05559 416 TELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSFDLEDLRYGKIII 492
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
2-380 |
9.86e-89 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 286.78 E-value: 9.86e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 2 KAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSK-PDPLEEGETA-DRTGSAVSFWPD-PDVFETT----- 73
Cdd:PTZ00109 241 QMYEYSSGLHGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKvTKPLSVFSCPlKKRGTTIHFLPDyKHIFKTHhqhte 320
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 74 ---------DFDFQTICRRLQEMAFLNRALSIHLLDERVAEgEEGKPREVTFYYEGGIADFVRHLNASKNPMHK--TVVE 142
Cdd:PTZ00109 321 teeeegcknGFNLDLIKNRIHELSYLNPGLTFYLVDERIAN-ENNFYPYETIKHEGGTREFLEELIKDKTPLYKdiNIIS 399
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 143 FAAEEEGMSVEIAMQWN-ESYGESVYTFANTINThEGGTHEEGFRAALTSVVN----RYGADKKLLKgdeKLSGEDIREG 217
Cdd:PTZ00109 400 IRGVIKNVNVEVSLSWSlESYTALIKSFANNVST-TAGTHIDGFKYAITRCVNgnikKNGYFKGNFV---NIPGEFIREG 475
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 218 LAAIISVKLANPQFEGQTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQKASQAARARIAAQQARKLARRK-SL 296
Cdd:PTZ00109 476 MTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKnNQ 555
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 297 LESGSMPGKLADCQSTDPRESEVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARID-RVLKNNEVQALITALGT 375
Cdd:PTZ00109 556 YYSTILPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGL 635
|
....*
gi 188529762 376 GIHDD 380
Cdd:PTZ00109 636 SVNPV 640
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
2-393 |
8.01e-80 |
|
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: 257.15 E-value: 8.01e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 2 KAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHN-SKPDPLEEGETADR--TGSAVSFWPDPDVFETTDFDFQ 78
Cdd:TIGR01055 102 KNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENgAKVTDLISAGTCGKrlTGTSVHFTPDPEIFDSLHFSVS 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 79 TICRRLQEMAFLNRALSIHLLDERvaegeegKPREVTFYYEGGIADFVrhlnASKNPMHKTVVE--FAAEEEG--MSVEI 154
Cdd:TIGR01055 182 RLYHILRAKAVLCRGVEIEFEDEV-------NNTKALWNYPDGLKDYL----SEAVNGDNTLPPkpFSGNFEGddEAVEW 250
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 155 AMQWNESYGESVY-TFANTINTHEGGTHEEGFRAALTSVVNRYGADKKLLKGDEKLSGEDIREGLAAIISVKLANPQFEG 233
Cdd:TIGR01055 251 ALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAG 330
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 234 QTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQkasQAARARIAAQQARKLARRKSLLESGSMPGKLADCQSTD 313
Cdd:TIGR01055 331 QTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAE---HAISSAQRRKRAAKKVVRKKLTSGPALPGKLADCTRQD 407
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 314 PRESEVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGiHDDFDMEKLRYHKVVL 393
Cdd:TIGR01055 408 LEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID-PDSNDLSQLRYGKICI 486
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
120-273 |
8.06e-76 |
|
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: 232.45 E-value: 8.06e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 120 GGIADFVRHLNASKNPMHKTVVEFAAEEEGMSVEIAMQWNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGAD 199
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188529762 200 KKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQK 273
Cdd:cd00822 81 NNLLKkKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
121-273 |
1.98e-66 |
|
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Pssm-ID: 425522 [Multi-domain] Cd Length: 173 Bit Score: 208.62 E-value: 1.98e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 121 GIADFVRHLNASKNPMHKTVVEFAAE--EEGMSVEIAMQWNESYGESVYTFANTINTHEGGTHEEGFRAALTSVVNRYGA 198
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 199 DKKLLK-GDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKLGNTPVKSFVQRVSNDRLVDWFDRNPAEAKTIIQK 273
Cdd:pfam00204 81 KKGLLKkKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
1-109 |
3.65e-44 |
|
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: 151.15 E-value: 3.65e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 1 GKAYAVSGGLHGVGVSVVNALSTRMAVEIHKSGFVWRQQYHNSKPD-PLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:cd16928 71 GGSYKVSGGLHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLtPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDT 150
|
90 100 110
....*....|....*....|....*....|
gi 188529762 80 ICRRLQEMAFLNRALSIHLLDERVAEGEEG 109
Cdd:cd16928 151 LKRRLRELAFLNKGLKIVLEDERTGKEEVF 180
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
317-393 |
6.55e-41 |
|
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: 140.33 E-value: 6.55e-41
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188529762 317 SEVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIH-DDFDMEKLRYHKVVL 393
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIII 78
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
6-393 |
1.48e-23 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 103.20 E-value: 1.48e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 6 VSGGLHGVGVSVVNALSTRMAVEI--HKSGFVWRQQYHN---SKPDPL--EEGETADRTgsAVSFWPDPDVFETTDFDFQ 78
Cdd:PTZ00108 138 VTGGRNGFGAKLTNIFSTKFTVECvdSKSGKKFKMTWTDnmsKKSEPRitSYDGKKDYT--KVTFYPDYAKFGMTEFDDD 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 79 TI---CRRLQEMAFLNRALSIHLLDERVaegeegkprevtfyyegGIADF---VRHLNASKNPMHKTVVEFAAEEEGMSV 152
Cdd:PTZ00108 216 MLrllKKRVYDLAGCFGKLKVYLNGERI-----------------AIKSFkdyVDLYLPDGEEGKKPPYPFVYTSVNGRW 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 153 EIAMQWNESYGESVyTFANTINTHEGGTHEEGFRAALTSVVNRYGADKKllKGDEKLSGEDIREGLAAIISVKLANPQFE 232
Cdd:PTZ00108 279 EVVVSLSDGQFQQV-SFVNSICTTKGGTHVNYILDQLISKLQEKAKKKK--KKGKEIKPNQIKNHLWVFVNCLIVNPSFD 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 233 GQTKTKLgNTPVKSFVQ-RVSNDRLVDWFDRNPaeaktIIQKASQAARARIAAQQARKL-ARRKSLLESgsMPgKLADCQ 310
Cdd:PTZ00108 356 SQTKETL-TTKPSKFGStCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMkAGKKSRILG--IP-KLDDAN 426
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 311 STDPRESEV---FIVEGDSA-----GGSAKQGRDprTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGIHDDF- 381
Cdd:PTZ00108 427 DAGGKNSEEctlILTEGDSAkalalAGLSVVGRD--YYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYe 504
|
410
....*....|..
gi 188529762 382 DMEKLRYHKVVL 393
Cdd:PTZ00108 505 DPKGLRYGSLMI 516
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
122-240 |
3.14e-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: 87.70 E-value: 3.14e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 122 IADFVRHLNasKNPMHKTVVEFAAEEEGMSVEIAMQWNE---SYGESVYTFANTINTHEGGTHEEGFRAALTSVVNryga 198
Cdd:cd00329 1 LKDRLAEIL--GDKVADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 188529762 199 dkkllkgdeklsGEDIREGLAAIISVKLAN--PQFE-GQTKTKLG 240
Cdd:cd00329 75 ------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEVR 107
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
6-393 |
6.13e-18 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 85.92 E-value: 6.13e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 6 VSGGLHGVGVSVVNALSTRMAVEI------HKSGFVWRQQYHNsKPDPLEEGETADRTGSAVSFWPDPDVFETTDFDFQT 79
Cdd:PLN03128 130 TTGGRNGYGAKLANIFSTEFTVETadgnrgKKYKQVFTNNMSV-KSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDV 208
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 80 I---CRRLQEMA-FLNRALSIHLLDERVaegeegkprEVtfyyeGGIADFVR-HLNASKNPMHKTVvefAAEEEGMSVEI 154
Cdd:PLN03128 209 ValmSKRVYDIAgCLGKKLKVELNGKKL---------PV-----KSFQDYVGlYLGPNSREDPLPR---IYEKVNDRWEV 271
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 155 AMQWNESYGESVyTFANTINTHEGGTHEEgfraALTSVVNRYGAD--KKLLKGDEKLSGEDIREGLAAIISVKLANPQFE 232
Cdd:PLN03128 272 CVSLSDGSFQQV-SFVNSIATIKGGTHVD----YVADQIVKHIQEkvKKKNKNATHVKPFQIKNHLWVFVNCLIENPTFD 346
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 233 GQTKTKLGNTPV---------KSFVQRVSNDRLVD----W--FDRNPAEAKTIIQKasqaarariaaqqarklaRRKSLl 297
Cdd:PLN03128 347 SQTKETLTTRPSsfgskcelsEEFLKKVEKCGVVEnilsWaqFKQQKELKKKDGAK------------------RQRLT- 407
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 298 esgSMPgKLADCQ---STDPRESEVFIVEGDSA-----GGSAKQGRDprTQAILPVRGKILNVEKARIDRVLKNNEVQAL 369
Cdd:PLN03128 408 ---GIP-KLDDANdagGKKSKDCTLILTEGDSAkalamSGLSVVGRD--HYGVFPLRGKLLNVREASHKQIMKNAEITNI 481
|
410 420
....*....|....*....|....*..
gi 188529762 370 ITALGTGIHDDFDME---KLRYHKVVL 393
Cdd:PLN03128 482 KQILGLQFGKTYDEEntkSLRYGHLMI 508
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
323-393 |
2.96e-11 |
|
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: 60.39 E-value: 2.96e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 323 EGDSAGGSAKQGR---DPRTQAILPVRGKILNVEKARIDRVLKNNEVQALITALGTGI--HDDFDMEKLRYHKVVL 393
Cdd:cd03365 7 EGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHgkSDYESTKSLRYGRLMI 82
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
6-391 |
5.45e-11 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 64.00 E-value: 5.45e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 6 VSGGLHGVGVSVVNALSTRmaveihksgFVwrqqyhnskpdpleeGETAD------------------RT------GSAV 61
Cdd:PHA02569 125 VTGGMNGVGSSLTNFFSVL---------FI---------------GETCDgknevtvncsngaeniswSTkpgkgkGTSV 180
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 62 SFWPDPDVFETTDFDFQT---ICRRLQemaflnrALSIHLLDervaegeegkpreVTFYYEGGIADFVRHLNASKNPMHK 138
Cdd:PHA02569 181 TFIPDFSHFEVNGLDQQYldiILDRLQ-------TLAVVFPD-------------IKFTFNGKKVSGKFKKYAKQFGDDT 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 139 TVVEFaaeeEGMSVEIAmqwNESYGESVYTFANTINTHEGGTHEEGFRAALTSvvnrygadkKLLKGDEK-----LSGED 213
Cdd:PHA02569 241 IVQEN----DNVSIALA---PSPDGFRQLSFVNGLHTKNGGHHVDCVMDDICE---------ELIPMIKKkhkieVTKAR 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 214 IREGLAAIISVK-LANPQFEGQTKTKLGNT--PVKSFVQrVSNDRLVDWFDRNPAEAKTIIQKA--SQAARARIAAQQAR 288
Cdd:PHA02569 305 VKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEAIIMPIIEAAlaRKLAAEKAAETKAA 383
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 289 KLARRKSLLE--SGSMPGKLAdcqstdprESEVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNNEV 366
Cdd:PHA02569 384 KKAKKAKVAKhiKANLIGKDA--------ETTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKEL 455
|
410 420
....*....|....*....|....*
gi 188529762 367 qALITALgTGIHDDFDMEKLRYHKV 391
Cdd:PHA02569 456 -FDICAI-TGLVLGEKAENMNYKNI 478
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
318-393 |
8.96e-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: 52.36 E-value: 8.96e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188529762 318 EVFIVEGDSAGGSAKQGRDPRTQAILPVRGKILNVEKARIDRVLKNnevqalitalgtgihddFDMEKLRYHKVVL 393
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVIL 59
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
6-388 |
1.13e-06 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 51.02 E-value: 1.13e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 6 VSGGLHGVGVSVVNALSTRMAVEIH--KSGFVWRQQYHNS---KPDPL----EEGETADRtgsaVSFWPDPDVFETTDFD 76
Cdd:PLN03237 155 TTGGRNGYGAKLTNIFSTEFVIETAdgKRQKKYKQVFSNNmgkKSEPVitkcKKSENWTK----VTFKPDLAKFNMTHLE 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 77 FQTI---CRRLQEMA-FLNRALSIHLLDERVAEGeegkprevtfyyegGIADFVRHLNASKNPMHKTVVEFAAEEEGMSV 152
Cdd:PLN03237 231 DDVValmKKRVVDIAgCLGKTVKVELNGKRIPVK--------------SFSDYVDLYLESANKSRPENLPRIYEKVNDRW 296
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 153 EIAMQWNESYGESVyTFANTINTHEGGTHEEgfraALTSVVNRY--GADKKLLKgDEKLSGEDIREGLAAIISVKLANPQ 230
Cdd:PLN03237 297 EVCVSLSEGQFQQV-SFVNSIATIKGGTHVD----YVTNQIANHvmEAVNKKNK-NANIKAHNVKNHLWVFVNALIDNPA 370
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 231 FEGQTKTKLgNTPVKSF----------VQRVSN----DRLVDW--FDRNPAEAKTIIQKasqaarariaaqqarklARRK 294
Cdd:PLN03237 371 FDSQTKETL-TLRQSSFgskcelsedfLKKVMKsgivENLLSWadFKQSKELKKTDGAK-----------------TTRV 432
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188529762 295 SLLEsgsmpgKLADCQSTDPRESE---VFIVEGDSA-----GGSAKQGRDprTQAILPVRGKILNVEKARIDRVLKNNEV 366
Cdd:PLN03237 433 TGIP------KLEDANEAGGKNSEkctLILTEGDSAkalavAGLSVVGRN--YYGVFPLRGKLLNVREASHKQIMNNAEI 504
|
410 420
....*....|....*....|...
gi 188529762 367 QALITALGTGIHDDFDMEK-LRY 388
Cdd:PLN03237 505 ENIKQILGLQHGKQYESVKsLRY 527
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
169-247 |
6.20e-03 |
|
TopoIIA_Trans_ScTopoIIA: 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 Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. 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. 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.
Pssm-ID: 239563 [Multi-domain] Cd Length: 153 Bit Score: 36.88 E-value: 6.20e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 188529762 169 FANTINTHEGGTHEEGFRAALTSVVNryGADKKLLKGDEKLSGEDIREGLAAIISVKLANPQFEGQTKTKLgNTPVKSF 247
Cdd:cd03481 49 FVNSIATTKGGTHVDYVADQIVKKLD--EVVKKKNKGGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL-TTKPKSF 124
|
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| |
