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Conserved domains on  [gi|818607703|gb|KKS56649|]
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MAG: gyrase subunit B protein [Candidatus Magasanikbacteria bacterium GW2011_GWA2_42_32]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOP2c super family cl40739
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 15-448 0e+00

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


The actual alignment was detected with superfamily member PRK05644:

Pssm-ID: 454823 [Multi-domain]  Cd Length: 638  Bit Score: 718.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   15 ANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPV 94
Cdd:PRK05644    3 EKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   95 DIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA 174
Cdd:PRK05644   83 DIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGET 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  175 KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKENSQSyIFYFEGGISSYVRHLNRQQEPKH 254
Cdd:PRK05644  163 DETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEE-TFHYEGGIKEYVEYLNRNKEPLH 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  255 DNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVR 334
Cdd:PRK05644  241 EEPIYFEGE-KDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  335 EGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKG 414
Cdd:PRK05644  320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399

                         410       420       430
                  ....*....|....*....|....*....|....
gi 818607703  415 ALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:PRK05644  400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGG 433
GyrB super family cl43054
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
785-1023 3.30e-134

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0187:

Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 419.05  E-value: 3.30e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:COG0187   432 SAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLL 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIVAEFTKNKeakikivakkkeeaeetegteespeges 944
Cdd:COG0187   512 TFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKGKK---------------------------- 563

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:COG0187   564 -------KVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
Intein_splicing super family cl38470
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
 456-784 2.28e-11

Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.


The actual alignment was detected with superfamily member pfam14890:

Pssm-ID: 434290 [Multi-domain]  Cd Length: 378  Bit Score: 66.72  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   456 IALADGR-NLSFKELVKEEeqGKNNYCYTIKDDGdIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKFMM---RNG 531
Cdd:pfam14890    1 IILEDGGeQVTIGELVEKE--GFNVWAINLDDLK-LEVASVKHAWKLGYKGPLYEITLSNGRKIKATPDHKFFVirdNLG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   532 SYIEAQNLKPEISLMPLVRKLSkiEGRITIKGYEMVL----------------NPQNHKWIFTHLLSDKYNLEKKiYNLD 595
Cdd:pfam14890   78 WVKRADELKEGDYIAVPRKLPS--SGLPNMELLELLLwlgilghlieitgdgcILKRHYIVYTEKYKYTREIPLK-ELIE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   596 DGEHKHHKNFNKLNNNPD-NIVRMPKEENKKIQAEKVKNFFKQHPEQKELLTNLARQEWTNKELL----QWRSQKTKEQW 670
Cdd:pfam14890  155 WIEEELFGDVINPRIKPErKFWYQVGLVAGDGLTHDKKNPIAKWLESLEIFGLLSYNKFIPEFVFslpkGAIASFIRGYF 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   671 TAE--FREKRKLAY-----------TQTYLNHS--LSFAKKMQENGQDIFATYERERANLPK--------RNNNLLKLDT 727
Cdd:pfam14890  235 DTDgcISKRNPGIYlsstserlaedVQLLLLSLgiNARLSKINGKGRNVYHVLITGKSSLEKfkekigayLQIKKEKLEE 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818607703   728 LLNRFFNGNRN-----ALQEAVVN---FNHKIKRIEKISKKIDVYDIEIPKTHNFaLASGIFVHN 784
Cdd:pfam14890  315 ILNKYKQSNAEssevkDFLEWLINsdvYWDKVKSIEVLDEEEYVYDLTVEGYHNF-VANGIIVHN 378
 
Name Accession Description Interval E-value
gyrB PRK05644
DNA gyrase subunit B; Validated
 15-448 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 718.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   15 ANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPV 94
Cdd:PRK05644    3 EKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   95 DIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA 174
Cdd:PRK05644   83 DIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGET 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  175 KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKENSQSyIFYFEGGISSYVRHLNRQQEPKH 254
Cdd:PRK05644  163 DETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEE-TFHYEGGIKEYVEYLNRNKEPLH 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  255 DNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVR 334
Cdd:PRK05644  241 EEPIYFEGE-KDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  335 EGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKG 414
Cdd:PRK05644  320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399

                         410       420       430
                  ....*....|....*....|....*....|....
gi 818607703  415 ALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:PRK05644  400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGG 433
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
15-448 0e+00

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 716.81  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   15 ANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPV 94
Cdd:COG0187     1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   95 DIHKQFKVSALELVLTKLHAggkfggggykvsggLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA 174
Cdd:COG0187    81 DIHPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  175 KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKEnSQSYIFYFEGGISSYVRHLNRQQEPKH 254
Cdd:COG0187   161 DRTGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEE-PKEETFHYEGGIKDFVEYLNEDKEPLH 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  255 DNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVR 334
Cdd:COG0187   239 PEVIYFEGE-KDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVR 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  335 EGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKG 414
Cdd:COG0187   318 EGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKS 397

                         410       420       430
                  ....*....|....*....|....*....|....
gi 818607703  415 ALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:COG0187   398 ALESSGLPGKLADCSSKDPEESELFIVEGDSAGG 431
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 20-448 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: 598.96  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    20 YTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQ 99
Cdd:TIGR01059    1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   100 FKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKAKDHGT 179
Cdd:TIGR01059   81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   180 IITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDkENSQSYIFYFEGGISSYVRHLNRQQEPKHDNIFY 259
Cdd:TIGR01059  161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERD-GKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   260 IDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVREGLTT 339
Cdd:TIGR01059  239 IKGE-KEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTA 317

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   340 VISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKGALEGF 419
Cdd:TIGR01059  318 VISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG 397

                          410       420
                   ....*....|....*....|....*....
gi 818607703   420 TLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:TIGR01059  398 GLPGKLADCSSKDPSKSELYIVEGDSAGG 426
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 49-448 1.58e-152

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 465.11  E-value: 1.58e-152
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703     49 GLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGG 128
Cdd:smart00433    1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    129 LHGVGVSVVNALSTWMKAEVHRDGGVFVQEY-AYGKPQYKVKQAGKAKDHGTIITFQPDPKTFTETTEFDWKTILDHLRQ 207
Cdd:smart00433   81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    208 QAYLTKGVKIIVVDERDKENSQsyiFYFEGGISSYVRHLNRQQEPKHDNIFYIDKKLDDDlQVEIALRYVEDFKELIFAF 287
Cdd:smart00433  161 LAFLNKGVKITLNDERSDEEKT---FLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNI-RVEVAFQYTDGYSENIVSF 236

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    288 ANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKdeNLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAV 367
Cdd:smart00433  237 VNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGV 314

                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    368 ETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTvIRKGALEGFTLPGKLADCSTKDATVSELYIVEGDSAG 447
Cdd:smart00433  315 EKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAREL-TRKKKLSSISLPGKLADASSAGPKKCELFLVEGDSAG 393


                    .
gi 818607703    448 G 448
Cdd:smart00433  394 G 394
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
785-1023 3.30e-134

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 419.05  E-value: 3.30e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:COG0187   432 SAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLL 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIVAEFTKNKeakikivakkkeeaeetegteespeges 944
Cdd:COG0187   512 TFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKGKK---------------------------- 563

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:COG0187   564 -------KVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
gyrB PRK05644
DNA gyrase subunit B; Validated
 785-1023 6.10e-133

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 415.65  E-value: 6.10e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:PRK05644  434 SAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLL 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEfRYAFSDEERDKIVAEFTKNKEAkikivakkkeeaeetegteespeges 944
Cdd:PRK05644  514 TFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAELKLKGNP-------------------------- 566

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:PRK05644  567 -------KYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 785-1023 9.71e-111

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: 357.44  E-value: 9.71e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:TIGR01059  427 SAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIIIMTDADVDGSHIRTLLL 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDkIVAEFTKNKEAKIKIVAKKKEEAEETEGTEESPEGes 944
Cdd:TIGR01059  507 TFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD-LVGEALEDLKALYIYSDKEKEEAKTQIPVHLGRKG-- 583

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703   945 satiggikINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:TIGR01059  584 --------IEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLDV 654
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 785-1016 9.04e-90

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 299.47  E-value: 9.04e-90
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:smart00433  395 SAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLL 474

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFS---DEERDKIVAEFTKNKeakikivakkkeeaeetegteespe 941
Cdd:smart00433  475 TFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFyslDEYEKWLEKTEGNKS------------------------- 529

                           170       180       190       200       210       220       230
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818607703    942 gessatiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAK 1016
Cdd:smart00433  530 ----------KYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 50-226 1.29e-76

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: 248.99  E-value: 1.29e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   50 LHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGL 129
Cdd:cd16928     1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  130 HGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKAKDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQA 209
Cdd:cd16928    81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159

                         170
                  ....*....|....*..
gi 818607703  210 YLTKGVKIIVVDERDKE 226
Cdd:cd16928   160 FLNKGLKIVLEDERTGK 176
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 238-409 3.22e-68

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: 225.57  E-value: 3.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   238 GISSYVRHLNRQQEPKHDNIFYIDK-KLDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYAR 316
Cdd:pfam00204    1 GLKDFVEELNKDKKPLHKEIIYFEGeSPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   317 GKTILKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILA 396
Cdd:pfam00204   81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160

                          170
                   ....*....|...
gi 818607703   397 AKARVAAKIARDT 409
Cdd:pfam00204  161 AKARLAARKAREA 173
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 785-885 2.23e-61

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: 204.04  E-value: 2.23e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:cd03366    14 SAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTDADVDGAHIRTLLL 93

                          90       100
                  ....*....|....*....|.
gi 818607703  865 TLFFRHFPQLITNGHIFIAQP 885
Cdd:cd03366    94 TFFFRYMRPLIENGHVYIAQP 114
DNA_gyraseB_C pfam00986
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 952-1012 1.40e-40

DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,.


Pssm-ID: 460016 [Multi-domain]  Cd Length: 63  Bit Score: 143.29  E-value: 1.40e-40
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818607703   952 KINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQ 1012
Cdd:pfam00986    3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
Intein_splicing pfam14890
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
 456-784 2.28e-11

Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.


Pssm-ID: 434290 [Multi-domain]  Cd Length: 378  Bit Score: 66.72  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   456 IALADGR-NLSFKELVKEEeqGKNNYCYTIKDDGdIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKFMM---RNG 531
Cdd:pfam14890    1 IILEDGGeQVTIGELVEKE--GFNVWAINLDDLK-LEVASVKHAWKLGYKGPLYEITLSNGRKIKATPDHKFFVirdNLG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   532 SYIEAQNLKPEISLMPLVRKLSkiEGRITIKGYEMVL----------------NPQNHKWIFTHLLSDKYNLEKKiYNLD 595
Cdd:pfam14890   78 WVKRADELKEGDYIAVPRKLPS--SGLPNMELLELLLwlgilghlieitgdgcILKRHYIVYTEKYKYTREIPLK-ELIE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   596 DGEHKHHKNFNKLNNNPD-NIVRMPKEENKKIQAEKVKNFFKQHPEQKELLTNLARQEWTNKELL----QWRSQKTKEQW 670
Cdd:pfam14890  155 WIEEELFGDVINPRIKPErKFWYQVGLVAGDGLTHDKKNPIAKWLESLEIFGLLSYNKFIPEFVFslpkGAIASFIRGYF 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   671 TAE--FREKRKLAY-----------TQTYLNHS--LSFAKKMQENGQDIFATYERERANLPK--------RNNNLLKLDT 727
Cdd:pfam14890  235 DTDgcISKRNPGIYlsstserlaedVQLLLLSLgiNARLSKINGKGRNVYHVLITGKSSLEKfkekigayLQIKKEKLEE 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818607703   728 LLNRFFNGNRN-----ALQEAVVN---FNHKIKRIEKISKKIDVYDIEIPKTHNFaLASGIFVHN 784
Cdd:pfam14890  315 ILNKYKQSNAEssevkDFLEWLINsdvYWDKVKSIEVLDEEEYVYDLTVEGYHNF-VANGIIVHN 378
Hint cd00081
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
 449-564 1.16e-10

Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.


Pssm-ID: 238035 [Multi-domain]  Cd Length: 136  Bit Score: 60.36  E-value: 1.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  449 CWDGDTKIALADGRNLSFKELVKEeeqgKNNYCYTIKDDGDIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKFMM 528
Cdd:cd00081     1 CFTGDTLVLLEDGGRKKIEELVEK----KGDKVLALDETGKLVFSKVLKVLRRDYEKKFYKIKTESGREITLTPDHLLFV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 818607703  529 RNGS---YIEAQNLKPEISLMPLVR-KLSKIEgRITIKGY 564
Cdd:cd00081    77 LEDGelkWVFASDLKPGDYVLVPVLeKVKEIE-EIEYTGG 115
intein_Nterm TIGR01445
intein N-terminal splicing region; This model is based on interated search results, starting ...
 451-527 5.67e-10

intein N-terminal splicing region; This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein.


Pssm-ID: 273629 [Multi-domain]  Cd Length: 81  Bit Score: 56.56  E-value: 5.67e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   451 DGDTKIALADGRNLSFKELVKEEeqgKNNYCYTIKDDGDIGIEKILNPRI-----TKKNAEVIKIILDNAEELICTPDHK 525
Cdd:TIGR01445    2 TGDTKVLTEDGETVKIGELVEKE---KDEKEPIKVKVLSLDGGKIVKARPvvvwkRRAEGKLIRIKTENGREIKATPDHP 78


                   ..
gi 818607703   526 FM 527
Cdd:TIGR01445   79 FL 80
HintN smart00306
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
 448-541 6.60e-10

Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.


Pssm-ID: 197642 [Multi-domain]  Cd Length: 100  Bit Score: 56.89  E-value: 6.60e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    448 GCWDGDTKIALADGRNLSFKELVKEEE-QGKNNycytikDDGDIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKF 526
Cdd:smart00306    1 GCFPGDTLVLTEDGGIKKIEELEEGDKvLALDE------GTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLL 74

                            90
                    ....*....|....*...
gi 818607703    527 MMRNGS---YIEAQNLKP 541
Cdd:smart00306   75 LVRDGGklvWVFASELKP 92
Hop COG1372
Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, ...
 443-909 4.56e-08

Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440983 [Multi-domain]  Cd Length: 866  Bit Score: 57.21  E-value: 4.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  443 GDSAGGCWDGDTKIALADGRNLSFKELVkeeEQGKNNYCYTIKDDGdigiEKILNPRITK--KNA--EVIKIILDNAEEL 518
Cdd:COG1372    92 DTGTGVCLTGDTLVLTADGRLVPIGELV---GSGEDVEVLSLDLDT----GKLVWAPVTKvfKTGvkPVYRIRTRSGREI 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  519 ICTPDHKFMMRNGsYIEAQNLKPEiSLMPLVRKLSkIEGRITIKGyemVLNPqNHKWIFTHLLSDKYNLEKK---IYNLD 595
Cdd:COG1372   165 RATPDHPFLTLSG-WKEAGELKPG-DRVAVPRHLP-SFGEEELPD---SLDE-ELAYLLGLLLGDGSLSKRGagrFTNAD 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  596 DGEHKHHKN-FNKLNNNPDNIVRMPKEENKK----IQAEKVKNFFKQhpeqkellTNLARQEWTNKELLQWRSQKTKEQW 670
Cdd:COG1372   238 EELLEDVAEaAEELFGRADEGPRVEARRATVyevrVSSKPLAELLEE--------LGLFGKRSGEKRIPDFVFRLSREQI 309

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  671 tAEF------------REKRKLAYTQTylnhSLSFAKKMQE--NGQDIFAT-YERERANLPKRN---------NNLLKLD 726
Cdd:COG1372   310 -RAFlrglfdadgsvsNRGGRIRLSTT----SRRLAEQVQLllLRLGIVSRiYERRRPDGKGRTayrlrisggDNLRRFA 384

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  727 TLLNRFFNGNRNALQEA-------------VVNFNH------------------------------KIKRIEKISKKiDV 763
Cdd:COG1372   385 ERIGFGSSRKQERLAELlaalrrrkddlvrARELANgrrlsrerlrrlaledealealadsdvywdEVVSIEPVGEE-DV 463

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  764 YDIEIPKTHNFaLASGIFVHNSAKQG--------RNRENQAILPLRGKILNIERARI---DKILTNNELKSLIIAMGTNI 832
Cdd:COG1372   464 YDLTVPGTHNF-VANGIVVHNSGGALddvgaavlDEDLLGGEPEEGEAGGAAEDKDRaktGATTLAAGDLLVERDVEAEP 542

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818607703  833 GEMFDISKLRYHRIVIMTDADVDGAHIRTLLLTLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIV 909
Cdd:COG1372   543 EEIEDVISGEGRILERAALLAVALDELEDELEEARAAAALKAKKAELAALLKETEPLVETEEEEEALLLEGAREIEL 619
 
Name Accession Description Interval E-value
gyrB PRK05644
DNA gyrase subunit B; Validated
 15-448 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 718.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   15 ANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPV 94
Cdd:PRK05644    3 EKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   95 DIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA 174
Cdd:PRK05644   83 DIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGET 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  175 KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKENSQSyIFYFEGGISSYVRHLNRQQEPKH 254
Cdd:PRK05644  163 DETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEE-TFHYEGGIKEYVEYLNRNKEPLH 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  255 DNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVR 334
Cdd:PRK05644  241 EEPIYFEGE-KDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  335 EGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKG 414
Cdd:PRK05644  320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399

                         410       420       430
                  ....*....|....*....|....*....|....
gi 818607703  415 ALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:PRK05644  400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGG 433
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
15-448 0e+00

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 716.81  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   15 ANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPV 94
Cdd:COG0187     1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   95 DIHKQFKVSALELVLTKLHAggkfggggykvsggLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA 174
Cdd:COG0187    81 DIHPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  175 KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKEnSQSYIFYFEGGISSYVRHLNRQQEPKH 254
Cdd:COG0187   161 DRTGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEE-PKEETFHYEGGIKDFVEYLNEDKEPLH 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  255 DNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVR 334
Cdd:COG0187   239 PEVIYFEGE-KDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVR 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  335 EGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKG 414
Cdd:COG0187   318 EGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKS 397

                         410       420       430
                  ....*....|....*....|....*....|....
gi 818607703  415 ALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:COG0187   398 ALESSGLPGKLADCSSKDPEESELFIVEGDSAGG 431
gyrB PRK14939
DNA gyrase subunit B; Provisional
 14-448 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 619.03  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   14 PANAGGYTAQQITVLEGLEPVRQRPGMYIGSTG-STGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGI 92
Cdd:PRK14939    1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   93 PVDIHKQFKVSALELVLTKLHAggkfggggykvsggLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAG 172
Cdd:PRK14939   81 PTDIHPEEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  173 KAKDHGTIITFQPDPKTFTeTTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKENSqsyIFYFEGGISSYVRHLNRQQEP 252
Cdd:PRK14939  161 ETDKTGTEVRFWPSPEIFE-NTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEE---EFHYEGGIKAFVEYLNRNKTP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  253 KHDNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGED 332
Cdd:PRK14939  237 LHPNIFYFSGE-KDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDD 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  333 VREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIR 412
Cdd:PRK14939  316 AREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRR 395

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 818607703  413 KGALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:PRK14939  396 KGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGG 431
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 20-448 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: 598.96  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    20 YTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQ 99
Cdd:TIGR01059    1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   100 FKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKAKDHGT 179
Cdd:TIGR01059   81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   180 IITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDkENSQSYIFYFEGGISSYVRHLNRQQEPKHDNIFY 259
Cdd:TIGR01059  161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERD-GKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   260 IDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVREGLTT 339
Cdd:TIGR01059  239 IKGE-KEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTA 317

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   340 VISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKGALEGF 419
Cdd:TIGR01059  318 VISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG 397

                          410       420
                   ....*....|....*....|....*....
gi 818607703   420 TLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:TIGR01059  398 GLPGKLADCSSKDPSKSELYIVEGDSAGG 426
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 14-448 7.31e-175

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 524.67  E-value: 7.31e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   14 PANAGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIP 93
Cdd:PRK05559    2 AMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   94 VDIHKQFKVSALELVLTKLHAggkfggggykvsggLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGK 173
Cdd:PRK05559   82 VGIHPEEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGT 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  174 A--KDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQAYLTKGVKIIVVDERDKEnsqsyIFYFEGGISSYVRHLNRQQE 251
Cdd:PRK05559  162 AgkRKTGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ-----TFHYENGLKDYLAELNEGKE 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  252 PKHDNIFYIDKKLDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARgKTILKEKDENLTGE 331
Cdd:PRK05559  236 TLPEEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAE-KRNLLPKGKKLEGE 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  332 DVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAakiARDTVI 411
Cdd:PRK05559  315 DVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLR---AAKKVK 391

                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 818607703  412 RKGALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:PRK05559  392 RKKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGG 428
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 49-448 1.58e-152

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 465.11  E-value: 1.58e-152
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703     49 GLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGG 128
Cdd:smart00433    1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    129 LHGVGVSVVNALSTWMKAEVHRDGGVFVQEY-AYGKPQYKVKQAGKAKDHGTIITFQPDPKTFTETTEFDWKTILDHLRQ 207
Cdd:smart00433   81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    208 QAYLTKGVKIIVVDERDKENSQsyiFYFEGGISSYVRHLNRQQEPKHDNIFYIDKKLDDDlQVEIALRYVEDFKELIFAF 287
Cdd:smart00433  161 LAFLNKGVKITLNDERSDEEKT---FLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNI-RVEVAFQYTDGYSENIVSF 236

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    288 ANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKdeNLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAV 367
Cdd:smart00433  237 VNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGV 314

                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    368 ETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTvIRKGALEGFTLPGKLADCSTKDATVSELYIVEGDSAG 447
Cdd:smart00433  315 EKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAREL-TRKKKLSSISLPGKLADASSAGPKKCELFLVEGDSAG 393


                    .
gi 818607703    448 G 448
Cdd:smart00433  394 G 394
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
785-1023 3.30e-134

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 419.05  E-value: 3.30e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:COG0187   432 SAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLL 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIVAEFTKNKeakikivakkkeeaeetegteespeges 944
Cdd:COG0187   512 TFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKGKK---------------------------- 563

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:COG0187   564 -------KVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
parE_Gpos TIGR01058
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ...
 17-448 9.19e-134

DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step 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. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130130 [Multi-domain]  Cd Length: 637  Bit Score: 417.73  E-value: 9.19e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    17 AGGYTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDI 96
Cdd:TIGR01058    2 ASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    97 HKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEY-AYGKPQYKVKQAGKAK 175
Cdd:TIGR01058   82 HQDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFeNGGKIVQSLKKIGTTK 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   176 DHGTIITFQPDPKTFTeTTEFDWKTILDHLRQQAYLTKGVKIIVVDERdkeNSQSYIFYFEGGISSYVRHLNRQQEPKHD 255
Cdd:TIGR01058  162 KTGTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKR---TNKTTVFFYENGLVDFVDYINETKETLSQ 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   256 NIFYidKKLDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVRE 335
Cdd:TIGR01058  238 VTYF--EGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIRE 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   336 GLTTVISVKL--KNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTV--I 411
Cdd:TIGR01058  316 GLSAIISVRIpeELIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKksG 395

                          410       420       430
                   ....*....|....*....|....*....|....*..
gi 818607703   412 RKGALEGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:TIGR01058  396 KKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGG 432
gyrB PRK05644
DNA gyrase subunit B; Validated
 785-1023 6.10e-133

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 415.65  E-value: 6.10e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:PRK05644  434 SAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLL 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEfRYAFSDEERDKIVAEFTKNKEAkikivakkkeeaeetegteespeges 944
Cdd:PRK05644  514 TFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAELKLKGNP-------------------------- 566

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:PRK05644  567 -------KYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
gyrB PRK14939
DNA gyrase subunit B; Provisional
 785-1023 2.67e-113

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 367.50  E-value: 2.67e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIG-EMFDISKLRYHRIVIMTDADVDGAHIRTLL 863
Cdd:PRK14939  432 SAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLL 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  864 LTLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDK------------------------------------ 907
Cdd:PRK14939  512 LTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDylielalegatlhladgpaisgealeklvkeyravr 591

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  908 -------------IVAEFTKNKEAKIKIVAKKKEEAEETEGTEESPE-----------------------GESSATIGGI 951
Cdd:PRK14939  592 kiidrlerrypraVLEALIYAPALDLDDLADEAAVAALDADFLTSAEyrrlvelaeklrglieegaylerGERKQPVSSF 671

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  952 K-------------INIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSV 1018
Cdd:PRK14939  672 EealdwllaearkgLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNV 751


                  ....*
gi 818607703 1019 KELDI 1023
Cdd:PRK14939  752 ANLDV 756
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 785-1023 9.71e-111

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: 357.44  E-value: 9.71e-111
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:TIGR01059  427 SAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIIIMTDADVDGSHIRTLLL 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDkIVAEFTKNKEAKIKIVAKKKEEAEETEGTEESPEGes 944
Cdd:TIGR01059  507 TFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD-LVGEALEDLKALYIYSDKEKEEAKTQIPVHLGRKG-- 583

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703   945 satiggikINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKSVKELDI 1023
Cdd:TIGR01059  584 --------IEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLDV 654
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 777-1021 8.37e-105

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 340.93  E-value: 8.37e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  777 ASGifvhnSAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDG 856
Cdd:PRK05559  426 AGG-----SAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSFDLEDLRYGKIIIMTDADVDG 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  857 AHIRTLLLTLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIVAEFTKnkeakikivakkkeeaeetegt 936
Cdd:PRK05559  501 AHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKLGK---------------------- 558

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  937 eespegessatiGGIKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAK 1016
Cdd:PRK05559  559 ------------KGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGD 626


                  ....*
gi 818607703 1017 SVKEL 1021
Cdd:PRK05559  627 FAEEE 631
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 20-448 2.56e-93

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: 309.93  E-value: 2.56e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    20 YTAQQITVLEGLEPVRQRPGMYigsTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQ 99
Cdd:TIGR01055    4 YSAKDIEVLDGLEPVRKRPGMY---TDTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   100 FKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA--KDH 177
Cdd:TIGR01055   81 EGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCgkRLT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   178 GTIITFQPDPKTFTEtTEFDWKTILDHLRQQAYLTKGVKIIVVDErdKENSQSyIFYFEGGISSYVRHLNRQQEPKHDNI 257
Cdd:TIGR01055  161 GTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKA-LWNYPDGLKDYLSEAVNGDNTLPPKP 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   258 FyIDKKLDDDLQVEIALRYVEDFKELIF-AFANNIYNPEGGMHLVGFRTALTRTLNAYARGKTILkEKDENLTGEDVREG 336
Cdd:TIGR01055  237 F-SGNFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNL-PRGVKLTAEDIWDR 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   337 LTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARvaaKIARDTVIRKGAL 416
Cdd:TIGR01055  315 CSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRR---KRAAKKVVRKKLT 391

                          410       420       430
                   ....*....|....*....|....*....|..
gi 818607703   417 EGFTLPGKLADCSTKDATVSELYIVEGDSAGG 448
Cdd:TIGR01055  392 SGPALPGKLADCTRQDLEGTELFLVEGDSAGG 423
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 20-448 2.16e-90

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 309.12  E-value: 2.16e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   20 YTAQQITVLEGLEPVRQRPGMYIGSTGSTGLHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQ 99
Cdd:PTZ00109  100 YDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEK 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  100 FKVSALELVLTKLH----------------------------------------AGGKFGGGGYKVSGGLHGVGVSVVNA 139
Cdd:PTZ00109  180 TGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSVVNA 259

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  140 LSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKA-KDHGTIITFQPDPKTF-------TETTE-------FDWKTILDH 204
Cdd:PTZ00109  260 LSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPlKKRGTTIHFLPDYKHIfkthhqhTETEEeegckngFNLDLIKNR 339

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  205 LRQQAYLTKGVKIIVVDER--DKENSQSY-IFYFEGGISSYVRHLNRQQEPKHDNIFYID-KKLDDDLQVEIALRYV-ED 279
Cdd:PTZ00109  340 IHELSYLNPGLTFYLVDERiaNENNFYPYeTIKHEGGTREFLEELIKDKTPLYKDINIISiRGVIKNVNVEVSLSWSlES 419

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  280 FKELIFAFANNIyNPEGGMHLVGFRTALTRTLNAYARGKTILKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLG 359
Cdd:PTZ00109  420 YTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLG 498

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  360 NPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILAAKARVAAKIARDTVIRKGA-LEGFTLPGKLADCSTKDATVSEL 438
Cdd:PTZ00109  499 NHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNqYYSTILPGKLVDCISDDIERNEL 578

                         490
                  ....*....|
gi 818607703  439 YIVEGDSAGG 448
Cdd:PTZ00109  579 FIVEGESAAG 588
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 785-1016 9.04e-90

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 299.47  E-value: 9.04e-90
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:smart00433  395 SAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLL 474

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFS---DEERDKIVAEFTKNKeakikivakkkeeaeetegteespe 941
Cdd:smart00433  475 TFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFyslDEYEKWLEKTEGNKS------------------------- 529

                           170       180       190       200       210       220       230
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818607703    942 gessatiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAK 1016
Cdd:smart00433  530 ----------KYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 50-226 1.29e-76

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: 248.99  E-value: 1.29e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   50 LHHLIWEVVDNSLDEAMAGHCDQITVKILPGNKISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGL 129
Cdd:cd16928     1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  130 HGVGVSVVNALSTWMKAEVHRDGGVFVQEYAYGKPQYKVKQAGKAKDHGTIITFQPDPKTFtETTEFDWKTILDHLRQQA 209
Cdd:cd16928    81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159

                         170
                  ....*....|....*..
gi 818607703  210 YLTKGVKIIVVDERDKE 226
Cdd:cd16928   160 FLNKGLKIVLEDERTGK 176
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 237-409 2.19e-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: 247.86  E-value: 2.19e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  237 GGISSYVRHLNRQQEPKHDNIFYIDKKlDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYAR 316
Cdd:cd00822     1 GGLKDFVEELNKDKEPLHEEPIYIEGE-KDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  317 GKTILKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILA 396
Cdd:cd00822    80 KNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILA 159

                         170
                  ....*....|...
gi 818607703  397 AKARVAAKIARDT 409
Cdd:cd00822   160 AKAREAARKAREL 172
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 238-409 3.22e-68

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: 225.57  E-value: 3.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   238 GISSYVRHLNRQQEPKHDNIFYIDK-KLDDDLQVEIALRYVEDFKELIFAFANNIYNPEGGMHLVGFRTALTRTLNAYAR 316
Cdd:pfam00204    1 GLKDFVEELNKDKKPLHKEIIYFEGeSPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   317 GKTILKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILA 396
Cdd:pfam00204   81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160

                          170
                   ....*....|...
gi 818607703   397 AKARVAAKIARDT 409
Cdd:pfam00204  161 AKARLAARKAREA 173
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 785-885 2.23e-61

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: 204.04  E-value: 2.23e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:cd03366    14 SAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTDADVDGAHIRTLLL 93

                          90       100
                  ....*....|....*....|.
gi 818607703  865 TLFFRHFPQLITNGHIFIAQP 885
Cdd:cd03366    94 TFFFRYMRPLIENGHVYIAQP 114
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 785-1012 4.44e-57

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: 208.62  E-value: 4.44e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNiGEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:TIGR01055  424 SAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID-PDSNDLSQLRYGKICILADADSDGLHIATLLC 502

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   865 TLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIVAEFTKNKEakikivakkkeeaeetegteespeges 944
Cdd:TIGR01055  503 ALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKKKKG--------------------------- 555

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818607703   945 satiggiKINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAE--KADEIFDILMGDEV-EPRRKFIQ 1012
Cdd:TIGR01055  556 -------KPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQdqRVDKIMDMLLAKKRsEDRFNWLQ 619
TOPRIM_TopoIIA_like cd01030
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 785-885 1.43e-51

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: 176.54  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEM-FDISKLRYHRIVIMTDADVDGAHIRTLL 863
Cdd:cd01030    14 SAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDdFDLDKLRYGKIIIMTDADVDGSHIRTLL 93

                          90       100
                  ....*....|....*....|..
gi 818607703  864 LTLFFRHFPQLITNGHIFIAQP 885
Cdd:cd01030    94 LTFFYRFWPSLLENGFLYIAQT 115
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 785-1017 1.46e-50

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 193.56  E-value: 1.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  785 SAKQGRNRENQAILPLRGKILNIERARID-KILTNNELKSLIIAMGTNIG------------------------------ 833
Cdd:PTZ00109  589 NAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNpvtwrqydlshgtkaskdesvqnnnstltk 668

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  834 --EMFDISKLRYHRIVIMTDADVDGAHIRTLLLTLFFRHFPQLITNGHIFIAQPPLFKV------------QSGKEFRYA 899
Cdd:PTZ00109  669 kkNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqfnvstKNSKKYIYT 748

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  900 FSDEERDKIVAEFTKNKEAKIKIVAKKKEEAEETEGTEESPEG---------------------------ESSATIGGIK 952
Cdd:PTZ00109  749 WSDEELNVLIKLLNKDYSSKETTRSVEEKGNAPDLDNEYEDEKldnknmrennvdevelktelgtnvadtEQTDELDINK 828

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818607703  953 --------INIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQTHAKS 1017
Cdd:PTZ00109  829 affkfskhYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFENSPA 901
DNA_gyraseB_C pfam00986
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 952-1012 1.40e-40

DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,.


Pssm-ID: 460016 [Multi-domain]  Cd Length: 63  Bit Score: 143.29  E-value: 1.40e-40
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818607703   952 KINIQRYKGLGEMNPDQLWETTMDPTTRTMRKITIEDAEKADEIFDILMGDEVEPRRKFIQ 1012
Cdd:pfam00986    3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 23-448 4.43e-21

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 98.67  E-value: 4.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   23 QQITVLEGLEPVRQRPGMYIGSTGST-----------------GLHHLIWEVVDNSLDEAMAG---HCDQITVKIlPGNK 82
Cdd:PHA02569    2 DEFKVLSDREHILKRPGMYIGSVAYEaherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   83 ISVTDNGRGIPVDIhkqFKVSALELVLTKLHAGGKFG-----GGGYKVSGGLHGVGVSVVNALSTWMKAEVHrDGGVFVQ 157
Cdd:PHA02569   81 VTVSDNGRGIPQAM---VTTPEGEEIPGPVAAWTRTKagsnfDDTNRVTGGMNGVGSSLTNFFSVLFIGETC-DGKNEVT 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  158 EYAYGKPQYKVKQAGKAKDHGTIITFQPDPKTFtETTEFDWKT---ILDHLRQQAYLTKGVKiivvderdkensqsyiFY 234
Cdd:PHA02569  157 VNCSNGAENISWSTKPGKGKGTSVTFIPDFSHF-EVNGLDQQYldiILDRLQTLAVVFPDIK----------------FT 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  235 FEGGISSyvrhlnrQQEPKHDNIFYIDKKLDDDLQVEIAL-RYVEDFKELifAFANNIYNPEGGMHLVGFRTALTRTLNa 313
Cdd:PHA02569  220 FNGKKVS-------GKFKKYAKQFGDDTIVQENDNVSIALaPSPDGFRQL--SFVNGLHTKNGGHHVDCVMDDICEELI- 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  314 yargKTILKEKDENLTGEDVREGLTTVISVK-LKNPQFEGQTKAKLGNP--EVKTAVETVFGEsfsiwLEEHPKDAEAII 390
Cdd:PHA02569  290 ----PMIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHIDLDYKK-----IAKQILKTEAII 360

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818607703  391 GKCILAAKAR-VAAKIARDTVIRKGALEG-------FTLPGKLADcstkdatvSELYIVEGDSAGG 448
Cdd:PHA02569  361 MPIIEAALARkLAAEKAAETKAAKKAKKAkvakhikANLIGKDAE--------TTLFLTEGDSAIG 418
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 792-875 4.12e-17

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: 78.11  E-value: 4.12e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  792 RENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMF--DISKLRYHRIVIMTDADVDGAHIRTLLLTLFFR 869
Cdd:cd03365    24 RDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHS 103


                  ....*.
gi 818607703  870 HFPQLI 875
Cdd:cd03365   104 FWPSLL 109
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 790-1012 4.48e-16

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 82.88  E-value: 4.48e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  790 RNRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEmfDISKLRYHRIVIMTDADVDG-AHIRTLLLTlFF 868
Cdd:PHA02569  424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGE--KAENMNYKNIAIMTDADVDGkGSIYPLLLA-FF 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  869 RHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSdeerdkiVAEFTKNKEAKIkivakkkeeaeetegteespegessati 948
Cdd:PHA02569  501 SRWPELFEQGRIRFVKTPVIIAQVGKETKWFYS-------LDEFEKAKDSLK---------------------------- 545

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818607703  949 ggiKINIQRYKGLGEMNPDQLWETTMDPttrTMRKITIEDAEKadEIFDILMGDEVEPRRKFIQ 1012
Cdd:PHA02569  546 ---KWSIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPDDWK--ELFEMLFGDDADLRKDWMS 601
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 22-446 1.86e-14

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 78.55  E-value: 1.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   22 AQQITVLEGLEPVRQRPGMYIGSTGST-----------------------GLHHLIWEV----VDNSLDEAMAGHCDQIT 74
Cdd:PTZ00108    7 EERYQKKTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   75 VKILPGNK-ISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAEV--HRD 151
Cdd:PTZ00108   87 VTIDEENGeISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSKS 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  152 GGVFVQEYAYG---KPQYKVKQAGKAKDHgTIITFQPDPKTFtETTEFDwKTILDHLRQQAY----LTKGVKIIVVDERD 224
Cdd:PTZ00108  167 GKKFKMTWTDNmskKSEPRITSYDGKKDY-TKVTFYPDYAKF-GMTEFD-DDMLRLLKKRVYdlagCFGKLKVYLNGERI 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  225 KENS-QSYI-FYFEGGISSYVRHLNRQQEPKHDnifyidkkldddlQVEIALRYVED-FKelIFAFANNIYNPEGGMHLV 301
Cdd:PTZ00108  244 AIKSfKDYVdLYLPDGEEGKKPPYPFVYTSVNG-------------RWEVVVSLSDGqFQ--QVSFVNSICTTKGGTHVN 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  302 GFRTALTRTLNAYARGKtilKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLGNPEVKTAVETVFGESFSIWLEE 381
Cdd:PTZ00108  309 YILDQLISKLQEKAKKK---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLK 385

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818607703  382 HPkdaeaIIGKCILAAKARVAAKIARDT-VIRKGALEGFTlpgKLADCS---TKDATVSELYIVEGDSA 446
Cdd:PTZ00108  386 SP-----ILENIVEWAQAKLAAELNKKMkAGKKSRILGIP---KLDDANdagGKNSEECTLILTEGDSA 446
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 791-875 2.65e-14

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 77.83  E-value: 2.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  791 NRENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFD---ISKLRYHRIVIMTDADVDGAHIRTLLLTLF 867
Cdd:PLN03128  448 GRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDeenTKSLRYGHLMIMTDQDHDGSHIKGLIINFF 527


                  ....*...
gi 818607703  868 FRHFPQLI 875
Cdd:PLN03128  528 HSFWPSLL 535
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 31-446 3.48e-14

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 77.44  E-value: 3.48e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   31 LEPVRQRPGMYIGST-----------GST----------GLHHLIWEVVDNSLDEAMAG-HCDQITVKILPG-NKISVTD 87
Cdd:PLN03128   13 LEHILLRPDTYIGSTekhtqtlwvyeGGEmvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEqNTISVYN 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   88 NGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTwmkaevhrdggVFVQEYAYGKPQYK 167
Cdd:PLN03128   93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFST-----------EFTVETADGNRGKK 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  168 VKQ---------------AGKAKDHGTIITFQPDPKTFTeTTEFDwKTILDHLRQQAY-----LTKGVKIIVVDERDKEN 227
Cdd:PLN03128  162 YKQvftnnmsvksepkitSCKASENWTKITFKPDLAKFN-MTRLD-EDVVALMSKRVYdiagcLGKKLKVELNGKKLPVK 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  228 SqsyifyfeggISSYVRhLNRQQEPKHDNIFYIDKKLDDDLQVEIALryvEDFKELIFAFANNIYNPEGGMHLvgfrTAL 307
Cdd:PLN03128  240 S----------FQDYVG-LYLGPNSREDPLPRIYEKVNDRWEVCVSL---SDGSFQQVSFVNSIATIKGGTHV----DYV 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  308 TRTLNAYARGKTILKEKD-ENLTGEDVREGLTTVISVKLKNPQFEGQTKAKLgnpevkTAVETVFGESFSIWLEEHPKDA 386
Cdd:PLN03128  302 ADQIVKHIQEKVKKKNKNaTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL------TTRPSSFGSKCELSEEFLKKVE 375

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818607703  387 EAIIGKCILA-AKARVAAKIARDTVIRKGALEGFTlpgKLADCS---TKDATVSELYIVEGDSA 446
Cdd:PLN03128  376 KCGVVENILSwAQFKQQKELKKKDGAKRQRLTGIP---KLDDANdagGKKSKDCTLILTEGDSA 436
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 792-891 4.28e-14

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 77.39  E-value: 4.28e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  792 RENQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMF-DISKLRYHRIVIMTDADVDGAHIRTLLLTLFFRH 870
Cdd:PTZ00108  459 RDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHF 538

                          90       100
                  ....*....|....*....|....
gi 818607703  871 FPQLI-TNGHI--FIAqpPLFKVQ 891
Cdd:PTZ00108  539 WPSLLkNPGFLkeFIT--PIVKAT 560
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 47-151 2.69e-12

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 64.31  E-value: 2.69e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    47 STGLHHLIWEVVDNSLDEAmaGHCDQITVKILPGNK--ISVTDNGRGIPVDIHkqfkvsalELVLTKLhaggkfgGGGYK 124
Cdd:pfam02518    3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDL--------PRIFEPF-------STADK 65

                           90       100
                   ....*....|....*....|....*..
gi 818607703   125 VSGGLHGVGVSVVNALSTWMKAEVHRD 151
Cdd:pfam02518   66 RGGGGTGLGLSIVRKLVELLGGTITVE 92
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 789-875 8.43e-12

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 69.89  E-value: 8.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  789 GRNRenQAILPLRGKILNIERARIDKILTNNELKSLIIAMGTNIGEMFD-ISKLRYHRIVIMTDADVDGAHIRTLLLTLF 867
Cdd:PLN03237  474 GRNY--YGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYEsVKSLRYGHLMIMTDQDHDGSHIKGLLINFI 551


                  ....*...
gi 818607703  868 FRHFPQLI 875
Cdd:PLN03237  552 HSFWPSLL 559
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 21-446 9.58e-12

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 69.51  E-value: 9.58e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   21 TAQQITVLEGLEPVrQRPGMYIgstgsTGLHHLIWEVVDNSLDEAMAG-HCDQITVKI-LPGNKISVTDNGRGIPVDIHK 98
Cdd:PLN03237   55 HTQTLWVYETDKMV-QRSVTYV-----PGLYKIFDEILVNAADNKQRDpKMDSLRVVIdVEQNLISVYNNGDGVPVEIHQ 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   99 QFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTwmkaevhrdggVFVQEYAYGKPQYKVKQA------- 171
Cdd:PLN03237  129 EEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFST-----------EFVIETADGKRQKKYKQVfsnnmgk 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  172 --------GKAKDHGTIITFQPDPKTFTETTEFDWKTILdhLRQQAY-----LTKGVKIIVVDERDKENSqsyifyfegg 238
Cdd:PLN03237  198 ksepvitkCKKSENWTKVTFKPDLAKFNMTHLEDDVVAL--MKKRVVdiagcLGKTVKVELNGKRIPVKS---------- 265

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  239 ISSYVR-HLNRQQEPKHDNIFYIDKKLDDDLQVEIALRYVEdFKELifAFANNIYNPEGGMHLvgfrTALTRTLNAYARG 317
Cdd:PLN03237  266 FSDYVDlYLESANKSRPENLPRIYEKVNDRWEVCVSLSEGQ-FQQV--SFVNSIATIKGGTHV----DYVTNQIANHVME 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  318 KTILKEKDENLTGEDVREGLTTVISVKLKNPQFEGQTKaklgnpEVKTAVETVFGESFSIWLEEHPKDAEAIIGKCILA- 396
Cdd:PLN03237  339 AVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTK------ETLTLRQSSFGSKCELSEDFLKKVMKSGIVENLLSw 412

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 818607703  397 AKARVAAKIARDTVIRKGALEGFTLPGKLADCSTKDATVSELYIVEGDSA 446
Cdd:PLN03237  413 ADFKQSKELKKTDGAKTTRVTGIPKLEDANEAGGKNSEKCTLILTEGDSA 462
Intein_splicing pfam14890
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
 456-784 2.28e-11

Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.


Pssm-ID: 434290 [Multi-domain]  Cd Length: 378  Bit Score: 66.72  E-value: 2.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   456 IALADGR-NLSFKELVKEEeqGKNNYCYTIKDDGdIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKFMM---RNG 531
Cdd:pfam14890    1 IILEDGGeQVTIGELVEKE--GFNVWAINLDDLK-LEVASVKHAWKLGYKGPLYEITLSNGRKIKATPDHKFFVirdNLG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   532 SYIEAQNLKPEISLMPLVRKLSkiEGRITIKGYEMVL----------------NPQNHKWIFTHLLSDKYNLEKKiYNLD 595
Cdd:pfam14890   78 WVKRADELKEGDYIAVPRKLPS--SGLPNMELLELLLwlgilghlieitgdgcILKRHYIVYTEKYKYTREIPLK-ELIE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   596 DGEHKHHKNFNKLNNNPD-NIVRMPKEENKKIQAEKVKNFFKQHPEQKELLTNLARQEWTNKELL----QWRSQKTKEQW 670
Cdd:pfam14890  155 WIEEELFGDVINPRIKPErKFWYQVGLVAGDGLTHDKKNPIAKWLESLEIFGLLSYNKFIPEFVFslpkGAIASFIRGYF 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   671 TAE--FREKRKLAY-----------TQTYLNHS--LSFAKKMQENGQDIFATYERERANLPK--------RNNNLLKLDT 727
Cdd:pfam14890  235 DTDgcISKRNPGIYlsstserlaedVQLLLLSLgiNARLSKINGKGRNVYHVLITGKSSLEKfkekigayLQIKKEKLEE 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818607703   728 LLNRFFNGNRN-----ALQEAVVN---FNHKIKRIEKISKKIDVYDIEIPKTHNFaLASGIFVHN 784
Cdd:pfam14890  315 ILNKYKQSNAEssevkDFLEWLINsdvYWDKVKSIEVLDEEEYVYDLTVEGYHNF-VANGIIVHN 378
Hint cd00081
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
 449-564 1.16e-10

Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.


Pssm-ID: 238035 [Multi-domain]  Cd Length: 136  Bit Score: 60.36  E-value: 1.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  449 CWDGDTKIALADGRNLSFKELVKEeeqgKNNYCYTIKDDGDIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKFMM 528
Cdd:cd00081     1 CFTGDTLVLLEDGGRKKIEELVEK----KGDKVLALDETGKLVFSKVLKVLRRDYEKKFYKIKTESGREITLTPDHLLFV 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 818607703  529 RNGS---YIEAQNLKPEISLMPLVR-KLSKIEgRITIKGY 564
Cdd:cd00081    77 LEDGelkWVFASDLKPGDYVLVPVLeKVKEIE-EIEYTGG 115
intein_Nterm TIGR01445
intein N-terminal splicing region; This model is based on interated search results, starting ...
 451-527 5.67e-10

intein N-terminal splicing region; This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein.


Pssm-ID: 273629 [Multi-domain]  Cd Length: 81  Bit Score: 56.56  E-value: 5.67e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   451 DGDTKIALADGRNLSFKELVKEEeqgKNNYCYTIKDDGDIGIEKILNPRI-----TKKNAEVIKIILDNAEELICTPDHK 525
Cdd:TIGR01445    2 TGDTKVLTEDGETVKIGELVEKE---KDEKEPIKVKVLSLDGGKIVKARPvvvwkRRAEGKLIRIKTENGREIKATPDHP 78


                   ..
gi 818607703   526 FM 527
Cdd:TIGR01445   79 FL 80
HintN smart00306
Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. ...
 448-541 6.60e-10

Hint (Hedgehog/Intein) domain N-terminal region; Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.


Pssm-ID: 197642 [Multi-domain]  Cd Length: 100  Bit Score: 56.89  E-value: 6.60e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703    448 GCWDGDTKIALADGRNLSFKELVKEEE-QGKNNycytikDDGDIGIEKILNPRITKKNAEVIKIILDNAEELICTPDHKF 526
Cdd:smart00306    1 GCFPGDTLVLTEDGGIKKIEELEEGDKvLALDE------GTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLL 74

                            90
                    ....*....|....*...
gi 818607703    527 MMRNGS---YIEAQNLKP 541
Cdd:smart00306   75 LVRDGGklvWVFASELKP 92
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 785-885 1.01e-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: 56.21  E-value: 1.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   785 SAKQGRNRENQAILPLRGKILNIERARIDKILtnnelksliiamgtnigEMFDISKLRYHRIVIMTDADVDGAHIRTLLL 864
Cdd:pfam01751   13 ALEKALGGGFQAVVAVLGHLLSLEKGPKKKAL-----------------KALKELALKAKEVILATDPDREGEAIALKLL 75

                           90       100
                   ....*....|....*....|...
gi 818607703   865 TLFfrhfpQLITN--GHIFIAQP 885
Cdd:pfam01751   76 ELK-----ELLENagGRVEFSEL 93
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 49-152 4.05e-09

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 55.35  E-value: 4.05e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703     49 GLHHLIWEVVDNSLDEAMAGhcDQITVKILPGN---KISVTDNGRGIPVDIhkqfkvsaLELVLTKLHAGGKFGGGGYKv 125
Cdd:smart00387    5 RLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPED--------LEKIFEPFFRTDKRSRKIGG- 73

                            90       100
                    ....*....|....*....|....*..
gi 818607703    126 sgglHGVGVSVVNALSTWMKAEVHRDG 152
Cdd:smart00387   74 ----TGLGLSIVKKLVELHGGEISVES 96
Hop COG1372
Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, ...
 443-909 4.56e-08

Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440983 [Multi-domain]  Cd Length: 866  Bit Score: 57.21  E-value: 4.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  443 GDSAGGCWDGDTKIALADGRNLSFKELVkeeEQGKNNYCYTIKDDGdigiEKILNPRITK--KNA--EVIKIILDNAEEL 518
Cdd:COG1372    92 DTGTGVCLTGDTLVLTADGRLVPIGELV---GSGEDVEVLSLDLDT----GKLVWAPVTKvfKTGvkPVYRIRTRSGREI 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  519 ICTPDHKFMMRNGsYIEAQNLKPEiSLMPLVRKLSkIEGRITIKGyemVLNPqNHKWIFTHLLSDKYNLEKK---IYNLD 595
Cdd:COG1372   165 RATPDHPFLTLSG-WKEAGELKPG-DRVAVPRHLP-SFGEEELPD---SLDE-ELAYLLGLLLGDGSLSKRGagrFTNAD 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  596 DGEHKHHKN-FNKLNNNPDNIVRMPKEENKK----IQAEKVKNFFKQhpeqkellTNLARQEWTNKELLQWRSQKTKEQW 670
Cdd:COG1372   238 EELLEDVAEaAEELFGRADEGPRVEARRATVyevrVSSKPLAELLEE--------LGLFGKRSGEKRIPDFVFRLSREQI 309

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  671 tAEF------------REKRKLAYTQTylnhSLSFAKKMQE--NGQDIFAT-YERERANLPKRN---------NNLLKLD 726
Cdd:COG1372   310 -RAFlrglfdadgsvsNRGGRIRLSTT----SRRLAEQVQLllLRLGIVSRiYERRRPDGKGRTayrlrisggDNLRRFA 384

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  727 TLLNRFFNGNRNALQEA-------------VVNFNH------------------------------KIKRIEKISKKiDV 763
Cdd:COG1372   385 ERIGFGSSRKQERLAELlaalrrrkddlvrARELANgrrlsrerlrrlaledealealadsdvywdEVVSIEPVGEE-DV 463

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703  764 YDIEIPKTHNFaLASGIFVHNSAKQG--------RNRENQAILPLRGKILNIERARI---DKILTNNELKSLIIAMGTNI 832
Cdd:COG1372   464 YDLTVPGTHNF-VANGIVVHNSGGALddvgaavlDEDLLGGEPEEGEAGGAAEDKDRaktGATTLAAGDLLVERDVEAEP 542

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818607703  833 GEMFDISKLRYHRIVIMTDADVDGAHIRTLLLTLFFRHFPQLITNGHIFIAQPPLFKVQSGKEFRYAFSDEERDKIV 909
Cdd:COG1372   543 EEIEDVISGEGRILERAALLAVALDELEDELEEARAAAALKAKKAELAALLKETEPLVETEEEEEALLLEGAREIEL 619
HintC smart00305
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
 750-788 8.76e-07

Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.


Pssm-ID: 197641  Cd Length: 46  Bit Score: 46.40  E-value: 8.76e-07
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 818607703    750 KIKRIEKISKKiDVYDIEIPKTHNFaLASGIFVHNSAKQ 788
Cdd:smart00305    8 RVKSIEETEYT-GVYDPTVTENHNF-IANGILVHNCAEI 44
Hint cd00081
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
 744-784 3.18e-06

Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.


Pssm-ID: 238035 [Multi-domain]  Cd Length: 136  Bit Score: 47.65  E-value: 3.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 818607703  744 VVNFNHKIKRIEKISKKIDVYDIEIPKTHNFaLASGIFVHN 784
Cdd:cd00081    97 LVPVLEKVKEIEEIEYTGGVYDLTVEDNHNF-IANGVLVHN 136
HATPase_TopII-like cd16930
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ...
 73-186 6.72e-05

Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.


Pssm-ID: 340407 [Multi-domain]  Cd Length: 147  Bit Score: 43.87  E-value: 6.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818607703   73 ITVKILP-GNKISVTDNGRGIPVDIHKQFKVSALELVLTKLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWMKAE-VHR 150
Cdd:cd16930    29 IKVTIDPeNNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFTVEtADS 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 818607703  151 DGG-VFVQEYA-----YGKPqyKVKQAGKAKDHgTIITFQPD 186
Cdd:cd16930   109 ESKkKFKQTWTnnmgkASEP--KITPYEKGKDY-TKVTFKPD 147
intein_Cterm TIGR01443
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
 762-783 7.32e-04

intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.


Pssm-ID: 213622 [Multi-domain]  Cd Length: 21  Bit Score: 37.78  E-value: 7.32e-04
                           10        20
                   ....*....|....*....|..
gi 818607703   762 DVYDIEIPKTHNFaLASGIFVH 783
Cdd:TIGR01443    1 YVYDLTVEGNHNF-IANGIVVH 21
HNH_3 pfam13392
HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in ...
 594-623 1.23e-03

HNH endonuclease; This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases.


Pssm-ID: 433169  Cd Length: 46  Bit Score: 37.57  E-value: 1.23e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 818607703   594 LDDGEHKHHKNFNKLNNNPDNIVRMPKEEN 623
Cdd:pfam13392   15 IPDGMVVDHIDGDRRNNRPENLRLVTRREN 44
mutL PRK00095
DNA mismatch repair endonuclease MutL;
56-95 1.51e-03

DNA mismatch repair endonuclease MutL;


Pssm-ID: 234630 [Multi-domain]  Cd Length: 617  Bit Score: 42.51  E-value: 1.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 818607703   56 EVVDNSLDeamAGhCDQITVKILPG--NKISVTDNGRGIPVD 95
Cdd:PRK00095   29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGISKE 66
HATPase_MutL-MLH-PMS-like cd16926
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ...
 56-95 3.13e-03

Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.


Pssm-ID: 340403 [Multi-domain]  Cd Length: 188  Bit Score: 39.73  E-value: 3.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 818607703   56 EVVDNSLDeamAGhCDQITVKILPG--NKISVTDNGRGIPVD 95
Cdd:cd16926    20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGISRE 57
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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