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Conserved domains on  [gi|496035687|ref|WP_008760194|]
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MULTISPECIES: AraC family transcriptional regulator [Bacteroides]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11454391)

helix-turn-helix (HTH) domain-containing protein with an AraC family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.60
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  10473770|15808743|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
194-281 2.00e-21

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.61  E-value: 2.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*...
gi 496035687 274 WREQMKNN 281
Cdd:COG2207  250 YRKRLRAR 257
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
194-281 2.00e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.61  E-value: 2.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*...
gi 496035687 274 WREQMKNN 281
Cdd:COG2207  250 YRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-275 9.37e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 78.75  E-value: 9.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687   194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   ..
gi 496035687   274 WR 275
Cdd:smart00342  83 YR 84
HTH_18 pfam12833
Helix-turn-helix domain;
198-277 3.53e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 74.55  E-value: 3.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687  198 LASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKL-SITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKEWRE 276
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 496035687  277 Q 277
Cdd:pfam12833  81 R 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 194-278 1.15e-07

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 51.89  E-value: 1.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:PRK09393 236 TVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAA 315


                 ....*
gi 496035687 274 WREQM 278
Cdd:PRK09393 316 YRKRF 320
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 186-275 2.97e-06

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: 48.13  E-value: 2.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687  186 LNNYKKCKtVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSItDLPLGSIVYELNFSSLAHFSRFCKR 265
Cdd:TIGR04094 296 LNLYDPLK-VEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKK 373

                          90
                  ....*....|
gi 496035687  266 CLGCSPKEWR 275
Cdd:TIGR04094 374 HTGVSPKQYQ 383
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
194-281 2.00e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.61  E-value: 2.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*...
gi 496035687 274 WREQMKNN 281
Cdd:COG2207  250 YRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
194-275 9.37e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 78.75  E-value: 9.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687   194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   ..
gi 496035687   274 WR 275
Cdd:smart00342  83 YR 84
HTH_18 pfam12833
Helix-turn-helix domain;
198-277 3.53e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 74.55  E-value: 3.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687  198 LASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKL-SITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKEWRE 276
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 496035687  277 Q 277
Cdd:pfam12833  81 R 81
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 194-277 1.76e-13

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: 69.42  E-value: 1.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:COG4977  228 SVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSA 307


                 ....
gi 496035687 274 WREQ 277
Cdd:COG4977  308 YRRR 311
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 194-277 3.47e-10

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: 59.68  E-value: 3.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSiTDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:COG2169  102 SLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSLSRFYEAFKKLLGMTPSA 180


                 ....
gi 496035687 274 WREQ 277
Cdd:COG2169  181 YRRG 184
ftrA PRK09393
transcriptional activator FtrA; Provisional
 194-278 1.15e-07

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 51.89  E-value: 1.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPKE 273
Cdd:PRK09393 236 TVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAA 315


                 ....*
gi 496035687 274 WREQM 278
Cdd:PRK09393 316 YRKRF 320
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 186-275 2.97e-06

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: 48.13  E-value: 2.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687  186 LNNYKKCKtVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSItDLPLGSIVYELNFSSLAHFSRFCKR 265
Cdd:TIGR04094 296 LNLYDPLK-VEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKK 373

                          90
                  ....*....|
gi 496035687  266 CLGCSPKEWR 275
Cdd:TIGR04094 374 HTGVSPKQYQ 383
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 198-277 2.40e-05

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 45.02  E-value: 2.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 198 LASVCGISISSFKRQFAAEfgetptGWMQKQLVREIKYKLSITDL-------PLGSIVYELNFSSLAHFSRFCKRCLGCS 270
Cdd:PRK09685 220 IAGELGISVRSLYRLFAEQ------GLVVAQYIRNRRLDRCADDLrpaaddeKITSIAYKWGFSDSSHFSTAFKQRFGVS 293


                 ....*..
gi 496035687 271 PKEWREQ 277
Cdd:PRK09685 294 PGEYRRK 300
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
194-277 4.19e-05

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 44.19  E-value: 4.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 194 TVKELAS-VCgISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRCLGCSPK 272
Cdd:PRK10572 201 DIESVAQhVC-LSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPS 279


                 ....*
gi 496035687 273 EWREQ 277
Cdd:PRK10572 280 EFRAR 284
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 185-226 1.68e-04

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: 38.29  E-value: 1.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 496035687  185 VLNNYKKCKTVKELASVCGISISSFKRQFAAEFGETPTGWMQ 226
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
187-278 7.77e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 40.05  E-value: 7.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496035687 187 NNYKKCKTVKELASVCGISISSFKRQFAAEFGETPTGWMQKQLVREIKYKLSITDLPLGSIVYELNFSSLAHFSRFCKRC 266
Cdd:PRK13503 182 DHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRRE 261

                         90
                 ....*....|..
gi 496035687 267 LGCSPKEWREQM 278
Cdd:PRK13503 262 FSWSPRDIRQGR 273
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 240-275 6.45e-03

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: 34.05  E-value: 6.45e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 496035687  240 TDLPLGSIVYELNFSSlAHFSRFCKRCLGCSPKEWR 275
Cdd:pfam00165   7 TNLTIADIADELGFSR-SYFSRLFKKYTGVTPSQYR 41
 
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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