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Conserved domains on  [gi|765018477|ref|WP_044584590|]
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GyrI-like domain-containing protein [Bacillus bombysepticus]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 10007405)

AraC family transcriptional regulator containing an AraC family helix-turn-helix (HTH) DNA-binding domain, may regulate the expression of genes with diverse biological functions including metabolism, stress response, and virulence

CATH:  1.10.10.10
Gene Ontology:  GO:0043565|GO:0003677|GO:0006355|GO:0003700
PubMed:  9409145|33837749|12596232|10473770|15808743|11282467

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-295 8.61e-62

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


:

Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 197.39  E-value: 8.61e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   1 MENKQSRNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYRADmT 80
Cdd:COG3449    2 MKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSA-I 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  81 ITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYRNDNSKNCKDVRGIPQYNECKKvrgNVEIVTADDINVAYIRHTGTYEEL 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPLDPPRLEPMM---DVEIKELPPRRVAYLRHRGPYEEI 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 161 AIAFpemiEKLFRYAaKKNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISgESTVETNDVGIMVIPSGKYAVGHFEI 240
Cdd:COG3449  158 GEAF----ERLIAWA-KARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVP-EDVALPGGVEVKTIPGGRYAVLRHKG 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 765018477 241 FQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQENKHIVDIYVPIEP 295
Cdd:COG3449  232 PYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-295 8.61e-62

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 197.39  E-value: 8.61e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   1 MENKQSRNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYRADmT 80
Cdd:COG3449    2 MKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSA-I 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  81 ITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYRNDNSKNCKDVRGIPQYNECKKvrgNVEIVTADDINVAYIRHTGTYEEL 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPLDPPRLEPMM---DVEIKELPPRRVAYLRHRGPYEEI 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 161 AIAFpemiEKLFRYAaKKNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISgESTVETNDVGIMVIPSGKYAVGHFEI 240
Cdd:COG3449  158 GEAF----ERLIAWA-KARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVP-EDVALPGGVEVKTIPGGRYAVLRHKG 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 765018477 241 FQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQENKHIVDIYVPIEP 295
Cdd:COG3449  232 PYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 137-294 2.73e-34

Bacterial transcription activator, effector binding domain; This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.


Pssm-ID: 214874 [Multi-domain]  Cd Length: 158  Bit Score: 122.20  E-value: 2.73e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   137 NVEIVTADDINVAYIRHTGTYEELAIafPEMIEKLFRYA-AKKNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISGE 215
Cdd:smart00871   1 EVRIVELPAFKVAGLRHRGPNEDEKI--PELWQRLIQWAkELGLLPVGNSGEPYGVYYDDPDDTPDGEFRYDAGVEVSDE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   216 STVEtNDVGIMVIPSGKYAVGHFEI-FQDEYKGAWDFLYGEWLPNSGYKPRDSYP-FEMYKNDPRQHQENKHIVDIYVPI 293
Cdd:smart00871  79 VEAP-EGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWLPNSGYELRDAGPdFEVYLNDPPDTDPEELVTEIYIPV 157


                   .
gi 765018477   294 E 294
Cdd:smart00871 158 K 158
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 137-293 1.74e-33

GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 119.82  E-value: 1.74e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  137 NVEIVTADDINVAYIRHTGTYEELAIafPEMIEKLFRYAAKkNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISgES 216
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNEEGI--GALWEELCAWASE-NGLSPAPSPLIGVSYDDPEVTEDEELRYDAGVAVP-IP 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 765018477  217 TVETNDVGIMVIPSGKYAVGHFEIFQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQENKHIVDIYVPI 293
Cdd:pfam06445  77 VEGPEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWLPESGYERRDGPSFEIYLNDPREVPEEELKTEIYIPV 153
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 1-112 6.15e-20

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 87.78  E-value: 6.15e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   1 MENKQSRNEyvRRIHKVQDYIESNIDS-SLSIEELADIAGFSKYHFHRIF--KGIVdepLSRYVNRLKLER-ATHLLTYR 76
Cdd:PRK09685 188 RESVQPRRE--RQFQKVVALIDQSIQEeILRPEWIAGELGISVRSLYRLFaeQGLV---VAQYIRNRRLDRcADDLRPAA 262

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 765018477  77 ADMTITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK09685 263 DDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 4-112 7.61e-14

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 70.86  E-value: 7.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477    4 KQSRNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLtyRADMTITD 83
Cdd:TIGR04094 277 EISINHHSPLIRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLL--RSQIPVSE 354

                          90       100
                  ....*....|....*....|....*....
gi 765018477   84 IAYHFGFTDSAVFSRTFKNYYGVSPSQYR 112
Cdd:TIGR04094 355 VSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
viru_reg_Rsp NF033869
AraC family transcriptional regulator Rsp; Rsp (repressor of surface proteins), as described ...
 20-112 5.52e-08

AraC family transcriptional regulator Rsp; Rsp (repressor of surface proteins), as described in Staphylococcus aureus, is a large protein with an AraC-like helix-turn-helix DNA-binding domain. Regulatory targets include the accessory gene regulator (agr) operon, which in turn regulates a large number of virulence factors.


Pssm-ID: 411433 [Multi-domain]  Cd Length: 701  Bit Score: 53.96  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  20 YIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTDSAVFSRT 99
Cdd:NF033869 155 FIHDHISSNLSLRDVAQHCNISESYCSNLFVRYLNMNFKDYFTSLKLCHAIQLLL-STNHSINAISELSGFSSHTNFTNQ 233

                         90
                 ....*....|...
gi 765018477 100 FKNYYGVSPSQYR 112
Cdd:NF033869 234 FKNYLNFSPKQFR 246
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-295 8.61e-62

DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 197.39  E-value: 8.61e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   1 MENKQSRNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYRADmT 80
Cdd:COG3449    2 MKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSA-I 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  81 ITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYRNDNSKNCKDVRGIPQYNECKKvrgNVEIVTADDINVAYIRHTGTYEEL 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAKLLALPPLDPPRLEPMM---DVEIKELPPRRVAYLRHRGPYEEI 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 161 AIAFpemiEKLFRYAaKKNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISgESTVETNDVGIMVIPSGKYAVGHFEI 240
Cdd:COG3449  158 GEAF----ERLIAWA-KARGLLPPDSRTIGIYYDDPDITPPEKLRYDACVTVP-EDVALPGGVEVKTIPGGRYAVLRHKG 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 765018477 241 FQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQENKHIVDIYVPIEP 295
Cdd:COG3449  232 PYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 137-294 2.73e-34

Bacterial transcription activator, effector binding domain; This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA.


Pssm-ID: 214874 [Multi-domain]  Cd Length: 158  Bit Score: 122.20  E-value: 2.73e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   137 NVEIVTADDINVAYIRHTGTYEELAIafPEMIEKLFRYA-AKKNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISGE 215
Cdd:smart00871   1 EVRIVELPAFKVAGLRHRGPNEDEKI--PELWQRLIQWAkELGLLPVGNSGEPYGVYYDDPDDTPDGEFRYDAGVEVSDE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   216 STVEtNDVGIMVIPSGKYAVGHFEI-FQDEYKGAWDFLYGEWLPNSGYKPRDSYP-FEMYKNDPRQHQENKHIVDIYVPI 293
Cdd:smart00871  79 VEAP-EGVETKTIPAGKYAVFTHKGgSYDEIQEAWEAIYGEWLPNSGYELRDAGPdFEVYLNDPPDTDPEELVTEIYIPV 157


                   .
gi 765018477   294 E 294
Cdd:smart00871 158 K 158
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 137-293 1.74e-33

GyrI-like small molecule binding domain; This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira.


Pssm-ID: 428947  Cd Length: 153  Bit Score: 119.82  E-value: 1.74e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  137 NVEIVTADDINVAYIRHTGTYEELAIafPEMIEKLFRYAAKkNDHVFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISgES 216
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNEEGI--GALWEELCAWASE-NGLSPAPSPLIGVSYDDPEVTEDEELRYDAGVAVP-IP 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 765018477  217 TVETNDVGIMVIPSGKYAVGHFEIFQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQENKHIVDIYVPI 293
Cdd:pfam06445  77 VEGPEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWLPESGYERRDGPSFEIYLNDPREVPEEELKTEIYIPV 153
Cass2 pfam14526
Integron-associated effector binding protein; This family contains Cass2 from Vibrio cholerae, ...
 139-293 1.32e-31

Integron-associated effector binding protein; This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species.


Pssm-ID: 434016 [Multi-domain]  Cd Length: 149  Bit Score: 114.76  E-value: 1.32e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  139 EIVTADDINVAYIRHTGTYEELAiaFPEMIEKLFRYAAKKND--HVFEDTKVLTIYHDHHEFTEdhHLRTSLCVTISGES 216
Cdd:pfam14526   1 EIVELPSFTVAGIRYEGPNEYED--HNKEIGKFWEEFNEDGRlpNIKKDDKSYGIYVDYEDEEN--EFDYYAGVEVPSFS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 765018477  217 TVETNDVgIMVIPSGKYAVGHFEI-FQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRQHQEnkhiVDIYVPI 293
Cdd:pfam14526  77 ELPEGLV-VIEIPGGKYAVFTIEGdFPDAIAEAWTRIYGWLLPNSGYERAGGPDFEVYKENGDENMK----IELYIPV 149
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 12-113 2.97e-30

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 116.03  E-value: 2.97e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  12 RRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFT 91
Cdd:COG4977  210 PRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLE-TTDLSIEEIAAACGFG 288

                         90       100
                 ....*....|....*....|..
gi 765018477  92 DSAVFSRTFKNYYGVSPSQYRN 113
Cdd:COG4977  289 SASHFRRAFRRRFGVSPSAYRR 310
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
21-118 7.87e-27

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 105.63  E-value: 7.87e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  21 IESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTDSAVFSRTF 100
Cdd:COG2207  161 LLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLA-ETDLSISEIAYELGFSSQSHFSRAF 239

                         90
                 ....*....|....*...
gi 765018477 101 KNYYGVSPSQYRNDNSKN 118
Cdd:COG2207  240 KKRFGVTPSEYRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
29-112 5.67e-26

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 98.01  E-value: 5.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477    29 LSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTDSAVFSRTFKNYYGVSP 108
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLR-DTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 765018477   109 SQYR 112
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
34-113 1.26e-24

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 94.58  E-value: 1.26e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   34 LADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYRADMTITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYRN 113
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 1-112 6.15e-20

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 87.78  E-value: 6.15e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   1 MENKQSRNEyvRRIHKVQDYIESNIDS-SLSIEELADIAGFSKYHFHRIF--KGIVdepLSRYVNRLKLER-ATHLLTYR 76
Cdd:PRK09685 188 RESVQPRRE--RQFQKVVALIDQSIQEeILRPEWIAGELGISVRSLYRLFaeQGLV---VAQYIRNRRLDRcADDLRPAA 262

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 765018477  77 ADMTITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK09685 263 DDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
7-115 2.43e-17

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 76.68  E-value: 2.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   7 RNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAY 86
Cdd:PRK11511   4 RNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLK-ESNEPILYLAE 82

                         90       100
                 ....*....|....*....|....*....
gi 765018477  87 HFGFTDSAVFSRTFKNYYGVSPSQYRNDN 115
Cdd:PRK11511  83 RYGFESQQTLTRTFKNYFDVPPHKYRMTN 111
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 19-113 2.54e-17

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 80.87  E-value: 2.54e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  19 DYIESNIDSSLSIEELADIAGFSKYHFHRIFK---GIVdePLSrYVNRLKLERATHLLTyrADMTITDIAYHFGFTDSAV 95
Cdd:COG2169   91 RLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKahtGVT--PKA-YARARRLLRARQLLQ--TGLSVTDAAYAAGFGSLSR 165

                         90
                 ....*....|....*...
gi 765018477  96 FSRTFKNYYGVSPSQYRN 113
Cdd:COG2169  166 FYEAFKKLLGMTPSAYRR 183
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
14-113 3.34e-17

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 75.73  E-value: 3.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  14 IHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTDS 93
Cdd:PRK10219   7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELR-TTERPIFDIAMDLGYVSQ 85

                         90       100
                 ....*....|....*....|
gi 765018477  94 AVFSRTFKNYYGVSPSQYRN 113
Cdd:PRK10219  86 QTFSRVFRRQFDRTPSDYRH 105
YdeE COG3708
Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription] ...
 137-294 6.40e-17

Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription];


Pssm-ID: 442922  Cd Length: 157  Bit Score: 76.21  E-value: 6.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 137 NVEIVTADDINVA--YIRHTGTYEELAIAFPEMIEKLFRYAAKKNDHVFEDTKVLTIYHDHHEftEDHHLRTSLCVTISG 214
Cdd:COG3708    2 EYRIVEKPAFKLVglSARTSNSDEEANEEIPALWQRFLPEGLAEIPNLSNPGGLYGVCTDYES--DEGEFDYLAGVEVSS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 215 ESTVeTNDVGIMVIPSGKYAVghFEI---FQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYknDPRQHQENKHIVDIYV 291
Cdd:COG3708   80 FDEV-PEGLETLEIPAGTYAV--FTHkgpMPEALQETWQYIYSEWLPSSGYERADGPDFEVY--DERDDPSPDSEVEIWI 154


                 ...
gi 765018477 292 PIE 294
Cdd:COG3708  155 PIK 157
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
138-289 1.18e-15

GyrI-like small molecule binding domain [Signal transduction mechanisms];


Pssm-ID: 444003  Cd Length: 144  Bit Score: 72.34  E-value: 1.18e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 138 VEIVTADDINVAYIRHTGTYEELAIAFPEMIEKLFRYAAKKNdhVFEDTKVLTIYHDhhefTEDHHLRTSLCVTISGEST 217
Cdd:COG4978    1 VEVKELPAQPVASIRATVPMDELGELIGEAFGELFAYLAENG--IEPAGPPFAIYHD----TDEDDVDVEVGVPVAGPLP 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 765018477 218 vETNDVGIMVIPSGKYAV----GHFeifqDEYKGAWDFLyGEWLPNSGYKPRDSyPFEMYKNDPRQHQ-ENKHIVDI 289
Cdd:COG4978   75 -GTGDIKVGTLPAGKAATathrGPY----DTLDEAYEAL-LAWIEENGLEVAGP-PREVYLTDPGNEPdPEEWVTEI 144
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
12-112 7.15e-15

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 73.17  E-value: 7.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  12 RRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYrADMTITDIAYHFGFT 91
Cdd:PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRH-SDASVTDIAYRCGFG 249

                         90       100
                 ....*....|....*....|.
gi 765018477  92 DSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK13503 250 DSNHFSTLFRREFSWSPRDIR 270
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 4-112 7.61e-14

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 70.86  E-value: 7.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477    4 KQSRNEYVRRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLtyRADMTITD 83
Cdd:TIGR04094 277 EISINHHSPLIRAVIQYINLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLL--RSQIPVSE 354

                          90       100
                  ....*....|....*....|....*....
gi 765018477   84 IAYHFGFTDSAVFSRTFKNYYGVSPSQYR 112
Cdd:TIGR04094 355 VSNELGFYDLSHFSRTFKKHTGVSPKQYQ 383
PRK10016 PRK10016
DNA gyrase inhibitor SbmC;
137-295 2.09e-12

DNA gyrase inhibitor SbmC;


Pssm-ID: 182195  Cd Length: 156  Bit Score: 63.92  E-value: 2.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 137 NVEIVTADDINVAYIRHTGTYEELAiafPEMIEKLFRYAAKKNdhvFEDTKVLTIYHDHHEFTEDHHLRTSLCVTISGES 216
Cdd:PRK10016   2 NYEIKQEQKRTIAGFHLVGPWEQTV---KQGFEQLMMWVDSHN---IVPKEWVAVYYDNPDEVPAEKLRCDTVVTVPDDF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477 217 TVETNDVGIMV--IPSGKYAVGHFEIFQDEYKGAWDFLYGEWLPNSGYKPRDSYPFEMYKNDPRqhQENKHIVDIYVPIE 294
Cdd:PRK10016  76 VLPENSEGVILteIPGGQYAVAVARVVDDDFAKPWYQFFNSLLQDSAYQMAPKPCFEVYLNDGA--EDGYWDIEMYVPVQ 153


                 .
gi 765018477 295 P 295
Cdd:PRK10016 154 K 154
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
13-113 4.61e-11

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 62.30  E-value: 4.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  13 RIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLtYRADMTITDIAYHFGFTD 92
Cdd:PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLL-QTTRMPIATIGRNVGYDD 262

                         90       100
                 ....*....|....*....|.
gi 765018477  93 SAVFSRTFKNYYGVSPSQYRN 113
Cdd:PRK10572 263 QLYFSRVFKKCTGASPSEFRA 283
PRK10371 PRK10371
transcriptional regulator MelR;
3-112 2.69e-10

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 59.83  E-value: 2.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477   3 NKQSRNEYVRR-IHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTI 81
Cdd:PRK10371 181 HKNSVSRHAQFyVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLS-DTDKSI 259

                         90       100       110
                 ....*....|....*....|....*....|.
gi 765018477  82 TDIAYHFGFTDSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK10371 260 LDIALTAGFRSSSRFYSTFGKYVGMSPQQYR 290
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
14-112 4.80e-10

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 59.25  E-value: 4.80e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  14 IHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHL--LTYRAdmtITDIAYHFGFT 91
Cdd:PRK15121   7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVAlrLTSRP---ILDIALQYRFD 83

                         90       100
                 ....*....|....*....|.
gi 765018477  92 DSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK15121  84 SQQTFTRAFKKQFAQTPALYR 104
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 78-113 5.83e-09

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 51.00  E-value: 5.83e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 765018477   78 DMTITDIAYHFGFtDSAVFSRTFKNYYGVSPSQYRN 113
Cdd:pfam00165   8 NLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
viru_reg_Rsp NF033869
AraC family transcriptional regulator Rsp; Rsp (repressor of surface proteins), as described ...
 20-112 5.52e-08

AraC family transcriptional regulator Rsp; Rsp (repressor of surface proteins), as described in Staphylococcus aureus, is a large protein with an AraC-like helix-turn-helix DNA-binding domain. Regulatory targets include the accessory gene regulator (agr) operon, which in turn regulates a large number of virulence factors.


Pssm-ID: 411433 [Multi-domain]  Cd Length: 701  Bit Score: 53.96  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  20 YIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTDSAVFSRT 99
Cdd:NF033869 155 FIHDHISSNLSLRDVAQHCNISESYCSNLFVRYLNMNFKDYFTSLKLCHAIQLLL-STNHSINAISELSGFSSHTNFTNQ 233

                         90
                 ....*....|...
gi 765018477 100 FKNYYGVSPSQYR 112
Cdd:NF033869 234 FKNYLNFSPKQFR 246
ftrA PRK09393
transcriptional activator FtrA; Provisional
 12-112 1.08e-07

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 52.27  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  12 RRIHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYRAdMTITDIAYHFGFT 91
Cdd:PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSA-LSIDQIAERAGFG 296

                         90       100
                 ....*....|....*....|.
gi 765018477  92 DSAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK09393 297 SEESLRHHFRRRAATSPAAYR 317
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
26-113 1.20e-07

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 52.10  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  26 DSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLtyRADMTITDIAYHFGFTDSAVFSRTFKNYYG 105
Cdd:PRK15435  97 ETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREAL--AKGESVTTSILNAGFPDSSSYYRKADETLG 174


                 ....*...
gi 765018477 106 VSPSQYRN 113
Cdd:PRK15435 175 MTAKQFRH 182
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 21-62 3.97e-06

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 42.91  E-value: 3.97e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 765018477   21 IESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVN 62
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
14-117 4.79e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 47.40  E-value: 4.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  14 IHKVQDYIESNIDSSLSIEELADIAGFSKYHFHRIFKGIVDEPLSRYVNRLKLERATHLLTYrADMTITDIAYHFGFTDS 93
Cdd:PRK13500 208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQH-SRLLISDISTECGFEDS 286

                         90       100
                 ....*....|....*....|....
gi 765018477  94 AVFSRTFKNYYGVSPSQYRNDNSK 117
Cdd:PRK13500 287 NYFSVVFTRETGMTPSQWRHLNSQ 310
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
19-112 1.46e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 42.58  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 765018477  19 DYIESNIDSSLSIEelADIAGFSKYH------FHRIFKGIVDEPLSRYVNRLKLERATHLLTyRADMTITDIAYHFGFTD 92
Cdd:PRK13501 179 DLIMSALQQSLGAY--FDMADFCHKNqlversLKQLFRQQTGMSISHYLRQIRLCHAKCLLR-GSEHRISDIAARCGFED 255

                         90       100
                 ....*....|....*....|
gi 765018477  93 SAVFSRTFKNYYGVSPSQYR 112
Cdd:PRK13501 256 SNYFSAVFTREAGMTPRDYR 275
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
57-113 2.09e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.88  E-value: 2.09e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 765018477  57 LSRYVNRLKLERATHLLTYrADMTITDIAYHFGFTDSAVFSRTFKNYYGVSPSQYRN 113
Cdd:PRK13502 221 INQYLRQVRICHAQYLLQH-SPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRH 276
 
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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