NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489529555|ref|WP_003434289|]
View 

GyrI-like domain-containing protein [Clostridioides difficile]

Protein Classification

GyrI-like domain-containing protein( domain architecture ID 10007405)

GyrI-like domain-containing protein adopts a beta-barrel fold similar to the effector-binding region of AraC/XylS transcription activators and may bind a small molecule; similar to Escherichia coli probable transcriptional regulator YgiV

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-305 2.23e-63

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


:

Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 201.62  E-value: 2.23e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   1 MTNAKSKKEYLNRICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLIHRTDMT 80
Cdd:COG3449    1 MMKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  81 VTDIAHYFGFTDSAVFSRAFKNYYKISPIKYRNNYSKnckepykisqynRSISKPKCKNTREVKGEIEILELDNMNTIYT 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAK------------LLALPPLDPPRLEPMMDVEIKELPPRRVAYL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 161 RYTGSYGNLTSTFpkllERLFTYASEQNLLGlENTQILAIYHDNPQFTQEHQLRTSICMTIPDNIVVKENdnLGNMIIPS 240
Cdd:COG3449  149 RHRGPYEEIGEAF----ERLIAWAKARGLLP-PDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGG--VEVKTIPG 221

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489529555 241 GKYLVGHFDISKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNRHLVDIYLPIEP 305
Cdd:COG3449  222 GRYAVLRHKGPYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-305 2.23e-63

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


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 201.62  E-value: 2.23e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   1 MTNAKSKKEYLNRICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLIHRTDMT 80
Cdd:COG3449    1 MMKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  81 VTDIAHYFGFTDSAVFSRAFKNYYKISPIKYRNNYSKnckepykisqynRSISKPKCKNTREVKGEIEILELDNMNTIYT 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAK------------LLALPPLDPPRLEPMMDVEIKELPPRRVAYL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 161 RYTGSYGNLTSTFpkllERLFTYASEQNLLGlENTQILAIYHDNPQFTQEHQLRTSICMTIPDNIVVKENdnLGNMIIPS 240
Cdd:COG3449  149 RHRGPYEEIGEAF----ERLIAWAKARGLLP-PDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGG--VEVKTIPG 221

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489529555 241 GKYLVGHFDISKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNRHLVDIYLPIEP 305
Cdd:COG3449  222 GRYAVLRHKGPYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 146-304 5.36e-32

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: 116.42  E-value: 5.36e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   146 EIEILELDNMNTIYTRYTGSYGNltSTFPKLLERLFTYASEQNLLGLENT-QILAIYHDNPQFTQEHQLRTSICMTIPDN 224
Cdd:smart00871   1 EVRIVELPAFKVAGLRHRGPNED--EKIPELWQRLIQWAKELGLLPVGNSgEPYGVYYDDPDDTPDGEFRYDAGVEVSDE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   225 ivVKENDNLGNMIIPSGKYLVG-HFDISKSEYSDAWDFMYNEWLSNGNYKLRASFP-FEVYLNNPHNHPQNRHLVDIYLP 302
Cdd:smart00871  79 --VEAPEGVETKTIPAGKYAVFtHKGGSYDEIQEAWEAIYGEWLPNSGYELRDAGPdFEVYLNDPPDTDPEELVTEIYIP 156


                   ..
gi 489529555   303 IE 304
Cdd:smart00871 157 VK 158
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 146-303 8.07e-29

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: 107.88  E-value: 8.07e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  146 EIEILELDNMNTIYTRYTGSYGNltSTFPKLLERLFTYASEQNLLgLENTQILAIYHDNPQFTQEHQLRTSICMTIPDNi 225
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNE--EGIGALWEELCAWASENGLS-PAPSPLIGVSYDDPEVTEDEELRYDAGVAVPIP- 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489529555  226 vVKENDNLGNMIIPSGKYLVGHFDISKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNRHLVDIYLPI 303
Cdd:pfam06445  77 -VEGPEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWLPESGYERRDGPSFEIYLNDPREVPEEELKTEIYIPV 153
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
19-113 7.37e-17

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 74.58  E-value: 7.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  19 DYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTDSAVFSR 98
Cdd:PRK10219  12 AWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLA-AVELRTTERPIFDIAMDLGYVSQQTFSR 90

                         90
                 ....*....|....*
gi 489529555  99 AFKNYYKISPIKYRN 113
Cdd:PRK10219  91 VFRRQFDRTPSDYRH 105
 
Name Accession Description Interval E-value
SbmC COG3449
DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair];
1-305 2.23e-63

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


Pssm-ID: 442672 [Multi-domain]  Cd Length: 286  Bit Score: 201.62  E-value: 2.23e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   1 MTNAKSKKEYLNRICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLIHRTDMT 80
Cdd:COG3449    1 MMKLRTREADQRRRILLVLIALHDDLDLLLLALLLAFAFHFFFFHRRRRFRALIGRRARLLLRRRLLAALALLLLSSSAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  81 VTDIAHYFGFTDSAVFSRAFKNYYKISPIKYRNNYSKnckepykisqynRSISKPKCKNTREVKGEIEILELDNMNTIYT 160
Cdd:COG3449   81 IAAAAAASGYSSSASFRRFFRAFGGSSRSRRRRAKAK------------LLALPPLDPPRLEPMMDVEIKELPPRRVAYL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 161 RYTGSYGNLTSTFpkllERLFTYASEQNLLGlENTQILAIYHDNPQFTQEHQLRTSICMTIPDNIVVKENdnLGNMIIPS 240
Cdd:COG3449  149 RHRGPYEEIGEAF----ERLIAWAKARGLLP-PDSRTIGIYYDDPDITPPEKLRYDACVTVPEDVALPGG--VEVKTIPG 221

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489529555 241 GKYLVGHFDISKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNRHLVDIYLPIEP 305
Cdd:COG3449  222 GRYAVLRHKGPYEDLGAAWDWLYGEWLPASGYELRDRPCFEIYLNDPRETPEGELITDIYLPLKP 286
AraC_E_bind smart00871
Bacterial transcription activator, effector binding domain; This domain is found in the ...
 146-304 5.36e-32

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: 116.42  E-value: 5.36e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   146 EIEILELDNMNTIYTRYTGSYGNltSTFPKLLERLFTYASEQNLLGLENT-QILAIYHDNPQFTQEHQLRTSICMTIPDN 224
Cdd:smart00871   1 EVRIVELPAFKVAGLRHRGPNED--EKIPELWQRLIQWAKELGLLPVGNSgEPYGVYYDDPDDTPDGEFRYDAGVEVSDE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   225 ivVKENDNLGNMIIPSGKYLVG-HFDISKSEYSDAWDFMYNEWLSNGNYKLRASFP-FEVYLNNPHNHPQNRHLVDIYLP 302
Cdd:smart00871  79 --VEAPEGVETKTIPAGKYAVFtHKGGSYDEIQEAWEAIYGEWLPNSGYELRDAGPdFEVYLNDPPDTDPEELVTEIYIP 156


                   ..
gi 489529555   303 IE 304
Cdd:smart00871 157 VK 158
GyrI-like pfam06445
GyrI-like small molecule binding domain; This family contains the small molecule binding ...
 146-303 8.07e-29

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: 107.88  E-value: 8.07e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  146 EIEILELDNMNTIYTRYTGSYGNltSTFPKLLERLFTYASEQNLLgLENTQILAIYHDNPQFTQEHQLRTSICMTIPDNi 225
Cdd:pfam06445   1 EVEIVELPAFRVAGLRHRGPYNE--EGIGALWEELCAWASENGLS-PAPSPLIGVSYDDPEVTEDEELRYDAGVAVPIP- 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489529555  226 vVKENDNLGNMIIPSGKYLVGHFDISKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNRHLVDIYLPI 303
Cdd:pfam06445  77 -VEGPEGVEELELPGGEYAVFRHKGPYDDLQETYAKIYGEWLPESGYERRDGPSFEIYLNDPREVPEEELKTEIYIPV 153
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 13-116 2.18e-25

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: 102.93  E-value: 2.18e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  13 RICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTD 92
Cdd:COG4977  211 RLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERA-RRLLETTDLSIEEIAAACGFGS 289

                         90       100
                 ....*....|....*....|....
gi 489529555  93 SAVFSRAFKNYYKISPIKYRNNYS 116
Cdd:COG4977  290 ASHFRRAFRRRFGVSPSAYRRRFR 313
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
21-118 5.82e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 98.31  E-value: 5.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  21 IEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTDSAVFSRAF 100
Cdd:COG2207  161 LLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERA-KRLLAETDLSISEIAYELGFSSQSHFSRAF 239

                         90
                 ....*....|....*...
gi 489529555 101 KNYYKISPIKYRNNYSKN 118
Cdd:COG2207  240 KKRFGVTPSEYRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
28-112 1.00e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 92.23  E-value: 1.00e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555    28 PLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTDSAVFSRAFKNYYKIS 107
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERA-RRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVT 79


                   ....*
gi 489529555   108 PIKYR 112
Cdd:smart00342  80 PSEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
34-114 2.60e-21

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 85.72  E-value: 2.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555   34 LSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLIHRTDMTVTDIAHYFGFTDSAVFSRAFKNYYKISPIKYRN 113
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 489529555  114 N 114
Cdd:pfam12833  81 R 81
Cass2 pfam14526
Integron-associated effector binding protein; This family contains Cass2 from Vibrio cholerae, ...
 148-303 9.99e-18

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: 78.17  E-value: 9.99e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  148 EILELDNMNTIYTRYTGSYGNLTstFPKLLERLFTYASEQNLLG--LENTQILAIYHDNPQFTQEhqLRTSICMTIPDNI 225
Cdd:pfam14526   1 EIVELPSFTVAGIRYEGPNEYED--HNKEIGKFWEEFNEDGRLPniKKDDKSYGIYVDYEDEENE--FDYYAGVEVPSFS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489529555  226 VVKENdnLGNMIIPSGKYLVGHFDISKSE-YSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQnrhlVDIYLPI 303
Cdd:pfam14526  77 ELPEG--LVVIEIPGGKYAVFTIEGDFPDaIAEAWTRIYGWLLPNSGYERAGGPDFEVYKENGDENMK----IELYIPV 149
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
19-113 7.37e-17

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 74.58  E-value: 7.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  19 DYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTDSAVFSR 98
Cdd:PRK10219  12 AWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLA-AVELRTTERPIFDIAMDLGYVSQQTFSR 90

                         90
                 ....*....|....*
gi 489529555  99 AFKNYYKISPIKYRN 113
Cdd:PRK10219  91 VFRRQFDRTPSDYRH 105
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
14-112 5.42e-15

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 70.13  E-value: 5.42e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  14 ICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLeNATAFLIHRTDMTVTDIAHYFGFTDS 93
Cdd:PRK11511  11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKM-TEIAQKLKESNEPILYLAERYGFESQ 89

                         90
                 ....*....|....*....
gi 489529555  94 AVFSRAFKNYYKISPIKYR 112
Cdd:PRK11511  90 QTLTRTFKNYFDVPPHKYR 108
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 13-113 6.54e-15

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: 74.32  E-value: 6.54e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  13 RICkvqDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLihRTDMTVTDIAHYFGFTD 92
Cdd:COG2169   88 RAC---RLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLL--QTGLSVTDAAYAAGFGS 162

                         90       100
                 ....*....|....*....|.
gi 489529555  93 SAVFSRAFKNYYKISPIKYRN 113
Cdd:COG2169  163 LSRFYEAFKKLLGMTPSAYRR 183
PRK10016 PRK10016
DNA gyrase inhibitor SbmC;
172-305 1.31e-14

DNA gyrase inhibitor SbmC;


Pssm-ID: 182195  Cd Length: 156  Bit Score: 70.09  E-value: 1.31e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 172 TFPKLLERLFTYASEQNLLGLEntqILAIYHDNPQFTQEHQLRTSICMTIPDNIVVKEN-DNLGNMIIPSGKYLVGHFDI 250
Cdd:PRK10016  25 TVKQGFEQLMMWVDSHNIVPKE---WVAVYYDNPDEVPAEKLRCDTVVTVPDDFVLPENsEGVILTEIPGGQYAVAVARV 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489529555 251 SKSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNphnhpqNRHL----VDIYLPIEP 305
Cdd:PRK10016 102 VDDDFAKPWYQFFNSLLQDSAYQMAPKPCFEVYLND------GAEDgywdIEMYVPVQK 154
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 16-116 5.04e-13

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 68.13  E-value: 5.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  16 KVQDYIEEHLHEP-LSLDELSNIAGFSKFHFHRIFkAIEKETLAQYVNRLKLE-NATAFLIHRTDMTVTDIAHYFGFTDS 93
Cdd:PRK09685 201 KVVALIDQSIQEEiLRPEWIAGELGISVRSLYRLF-AEQGLVVAQYIRNRRLDrCADDLRPAADDEKITSIAYKWGFSDS 279

                         90       100
                 ....*....|....*....|...
gi 489529555  94 AVFSRAFKNYYKISPIKYRNNYS 116
Cdd:PRK09685 280 SHFSTAFKQRFGVSPGEYRRKFR 302
YdeE COG3708
Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription] ...
 146-304 2.03e-11

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


Pssm-ID: 442922  Cd Length: 157  Bit Score: 61.19  E-value: 2.03e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 146 EIEILELDNMNTI--YTRYTGSYGNLTSTFPKLLERLFTYASEQnLLGLENTQ-ILAIYH----DNPQFTQEHQLRTSIC 218
Cdd:COG3708    2 EYRIVEKPAFKLVglSARTSNSDEEANEEIPALWQRFLPEGLAE-IPNLSNPGgLYGVCTdyesDEGEFDYLAGVEVSSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 219 MTIPDNIVVKEndnlgnmiIPSGKYLV----GHFDiskSEYSDAWDFMYNEWLSNGNYKLRASFPFEVYLNNPHNHPQNR 294
Cdd:COG3708   81 DEVPEGLETLE--------IPAGTYAVfthkGPMP---EALQETWQYIYSEWLPSSGYERADGPDFEVYDERDDPSPDSE 149

                        170
                 ....*....|
gi 489529555 295 hlVDIYLPIE 304
Cdd:COG3708  150 --VEIWIPIK 157
BltR2 COG4978
GyrI-like small molecule binding domain [Signal transduction mechanisms];
147-299 4.76e-11

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


Pssm-ID: 444003  Cd Length: 144  Bit Score: 59.63  E-value: 4.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555 147 IEILELDNMNTIYTRYTGSYGNLTSTFPKLLERLFTYASEQNLLGLENtqILAIYHDNPqftqEHQLRTSICMTIPDNiv 226
Cdd:COG4978    1 VEVKELPAQPVASIRATVPMDELGELIGEAFGELFAYLAENGIEPAGP--PFAIYHDTD----EDDVDVEVGVPVAGP-- 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489529555 227 VKENDNLGNMIIPSGKYLV----GHFDisksEYSDAWDFMYnEWLSNGNYKLRASfPFEVYLNNPHNHP-QNRHLVDI 299
Cdd:COG4978   73 LPGTGDIKVGTLPAGKAATathrGPYD----TLDEAYEALL-AWIEENGLEVAGP-PREVYLTDPGNEPdPEEWVTEI 144
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
20-112 5.11e-11

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 61.95  E-value: 5.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  20 YIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENAtAFLIHRTDMTVTDIAHYFGFTDSAVFSRA 99
Cdd:PRK15121  13 WLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKA-AVALRLTSRPILDIALQYRFDSQQTFTRA 91

                         90
                 ....*....|...
gi 489529555 100 FKNYYKISPIKYR 112
Cdd:PRK15121  92 FKKQFAQTPALYR 104
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
19-108 2.19e-10

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 60.08  E-value: 2.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  19 DYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLIHrTDMTVTDIAHYFGFTDSAVFSR 98
Cdd:PRK13503 178 AWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRH-SDASVTDIAYRCGFGDSNHFST 256

                         90
                 ....*....|
gi 489529555  99 AFKNYYKISP 108
Cdd:PRK13503 257 LFRREFSWSP 266
PRK10371 PRK10371
transcriptional regulator MelR;
19-112 1.84e-09

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 57.52  E-value: 1.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  19 DYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAfLIHRTDMTVTDIAHYFGFTDSAVFSR 98
Cdd:PRK10371 198 GFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRA-LLSDTDKSILDIALTAGFRSSSRFYS 276

                         90
                 ....*....|....
gi 489529555  99 AFKNYYKISPIKYR 112
Cdd:PRK10371 277 TFGKYVGMSPQQYR 290
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
12-116 1.14e-08

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 54.98  E-value: 1.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  12 NRICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKaiekETLA---------QYVNRLKLenatafLIHRTDMTVT 82
Cdd:PRK10572 183 PRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR----QQLGisvlrwredQRISRAKL------LLQTTRMPIA 252

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489529555  83 DIAHYFGFTDSAVFSRAFKNYYKISPIKYRNNYS 116
Cdd:PRK10572 253 TIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
ftrA PRK09393
transcriptional activator FtrA; Provisional
 13-116 7.43e-08

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 53.04  E-value: 7.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  13 RICKVQDYIEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAfLIHRTDMTVTDIAHYFGFTD 92
Cdd:PRK09393 219 RLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARD-LLESSALSIDQIAERAGFGS 297

                         90       100
                 ....*....|....*....|....
gi 489529555  93 SAVFSRAFKNYYKISPIKYRNNYS 116
Cdd:PRK09393 298 EESLRHHFRRRAATSPAAYRKRFG 321
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 21-62 7.96e-07

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: 44.84  E-value: 7.96e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489529555   21 IEEHLHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVN 62
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
27-113 2.78e-05

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


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 45.17  E-value: 2.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  27 EPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATAFLihRTDMTVTDIAHYFGFTDSAVFSRAFKNYYKI 106
Cdd:PRK15435  98 TPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREAL--AKGESVTTSILNAGFPDSSSYYRKADETLGM 175


                 ....*..
gi 489529555 107 SPIKYRN 113
Cdd:PRK15435 176 TAKQFRH 182
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 77-113 8.66e-05

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: 39.06  E-value: 8.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489529555   77 TDMTVTDIAHYFGFtDSAVFSRAFKNYYKISPIKYRN 113
Cdd:pfam00165   7 TNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
25-113 9.87e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 40.09  E-value: 9.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529555  25 LHEPLSLDELSNIAGFSKFHFHRIFKAIEKETLAQYVNRLKLENATaFLIHRTDMTVTDIAHYFGFTDSAVFSRAFKNYY 104
Cdd:PRK13500 219 LKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQ-YLLQHSRLLISDISTECGFEDSNYFSVVFTRET 297


                 ....*....
gi 489529555 105 KISPIKYRN 113
Cdd:PRK13500 298 GMTPSQWRH 306
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH