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Conserved domains on  [gi|1040072017|ref|WP_065082467|]
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AraC family transcriptional regulator [Elizabethkingia miricola]

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];
173-256 4.82e-14

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 70.19  E-value: 4.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017 173 MSIEEIAEKNQISRQYFNKMFRKYIGKSPSEFRKVNKFRNSISQ-KNKNTNLIELSLDADFYDQSHFIRNFKELTKVNPG 251
Cdd:COG2207   169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLlAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*
gi 1040072017 252 SFFNN 256
Cdd:COG2207   249 EYRKR 253
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
173-256 4.82e-14

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 70.19  E-value: 4.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017 173 MSIEEIAEKNQISRQYFNKMFRKYIGKSPSEFRKVNKFRNSISQ-KNKNTNLIELSLDADFYDQSHFIRNFKELTKVNPG 251
Cdd:COG2207   169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLlAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*
gi 1040072017 252 SFFNN 256
Cdd:COG2207   249 EYRKR 253
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
174-253 5.78e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 60.26  E-value: 5.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017  174 SIEEIAEKNQISRQYFNKMFRKYIGKSPSEF---RKVNKFRNSISQKNKNtnLIELSLDADFYDQSHFIRNFKELTKVNP 250
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYlrdRRLERARRLLRDTDLS--VTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 1040072017  251 GSF 253
Cdd:smart00342  81 SEY 83
HTH_18 pfam12833
Helix-turn-helix domain;
178-256 2.82e-10

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 55.29  E-value: 2.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017 178 IAEKNQISRQYFNKMFRKYIGKSPSEF---RKVNKFRNSISQkNKNTNLIELSLDADFYDQSHFIRNFKELTKVNPGSFF 254
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYlrrLRLERARRLLLE-DTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79


                  ..
gi 1040072017 255 NN 256
Cdd:pfam12833  80 RR 81
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
188-206 2.56e-03

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 38.42  E-value: 2.56e-03
                          10
                  ....*....|....*....
gi 1040072017 188 YFNKMFRKYIGKSPSEFRK 206
Cdd:PRK10572  265 YFSRVFKKCTGASPSEFRA 283
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
173-256 4.82e-14

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 70.19  E-value: 4.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017 173 MSIEEIAEKNQISRQYFNKMFRKYIGKSPSEFRKVNKFRNSISQ-KNKNTNLIELSLDADFYDQSHFIRNFKELTKVNPG 251
Cdd:COG2207   169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLlAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*
gi 1040072017 252 SFFNN 256
Cdd:COG2207   249 EYRKR 253
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
174-253 5.78e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 60.26  E-value: 5.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017  174 SIEEIAEKNQISRQYFNKMFRKYIGKSPSEF---RKVNKFRNSISQKNKNtnLIELSLDADFYDQSHFIRNFKELTKVNP 250
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYlrdRRLERARRLLRDTDLS--VTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 1040072017  251 GSF 253
Cdd:smart00342  81 SEY 83
HTH_18 pfam12833
Helix-turn-helix domain;
178-256 2.82e-10

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 55.29  E-value: 2.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1040072017 178 IAEKNQISRQYFNKMFRKYIGKSPSEF---RKVNKFRNSISQkNKNTNLIELSLDADFYDQSHFIRNFKELTKVNPGSFF 254
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYlrrLRLERARRLLLE-DTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79


                  ..
gi 1040072017 255 NN 256
Cdd:pfam12833  80 RR 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
170-205 7.19e-06

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 43.31  E-value: 7.19e-06
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1040072017  170 NSTMSIEEIAEKNQI-SRQYFNKMFRKYIGKSPSEFR 205
Cdd:smart00342  48 DTDLSVTEIALRVGFsSQSYFSRAFKKLFGVTPSEYR 84
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 166-206 1.39e-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: 41.37  E-value: 1.39e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1040072017 166 ISDVNSTMSIEEIAEKNQISRQYFNKMFRKYIGKSPSEFRK 206
Cdd:pfam00165   2 RENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
188-206 2.56e-03

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 38.42  E-value: 2.56e-03
                          10
                  ....*....|....*....
gi 1040072017 188 YFNKMFRKYIGKSPSEFRK 206
Cdd:PRK10572  265 YFSRVFKKCTGASPSEFRA 283
 
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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