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Conserved domains on  [gi|2316063006|ref|WP_263059491|]
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helix-turn-helix transcriptional regulator [Pectobacterium sp. F1-1]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 11454547)

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

CATH:  1.10.10.1310
Gene Ontology:  GO:0003700|GO:0043565|GO:0006355
PubMed:  9409145|8831795|15808743|2644244
SCOP:  4000332

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
207-288 6.98e-17

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 73.74  E-value: 6.98e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  207 WTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYKSSARFSERFKTRFGCSPT 285
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 2316063006  286 KIR 288
Cdd:smart00342  82 EYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
97-288 1.57e-11

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 63.26  E-value: 1.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  97 GGHDAVFRSLFLTFSSTLLAQFYHRYPEKLAPVHPSAPFTHLLLDDDLTHTLQYLVEGMTSNTLTESRLELRLMDMLLVL 176
Cdd:COG2207    59 LLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 177 SERGYHFGAPPQPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSW 255
Cdd:COG2207   139 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDL 218

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2316063006 256 SMQRLAEACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:COG2207   219 SISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
207-288 6.98e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 73.74  E-value: 6.98e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  207 WTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYKSSARFSERFKTRFGCSPT 285
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 2316063006  286 KIR 288
Cdd:smart00342  82 EYR 84
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 188-286 4.72e-15

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 73.42  E-value: 4.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 188 QPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYK 267
Cdd:PRK09978  140 QPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYH 219

                          90
                  ....*....|....*....
gi 2316063006 268 SSARFSERFKTRFGCSPTK 286
Cdd:PRK09978  220 SVSYFIYVFRNYYGMTPTE 238
HTH_18 pfam12833
Helix-turn-helix domain;
214-288 9.29e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 62.61  E-value: 9.29e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2316063006 214 RQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAM-MLVQTTSWSMQRLAEACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:pfam12833   3 AALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARrLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
97-288 1.57e-11

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 63.26  E-value: 1.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  97 GGHDAVFRSLFLTFSSTLLAQFYHRYPEKLAPVHPSAPFTHLLLDDDLTHTLQYLVEGMTSNTLTESRLELRLMDMLLVL 176
Cdd:COG2207    59 LLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 177 SERGYHFGAPPQPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSW 255
Cdd:COG2207   139 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDL 218

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2316063006 256 SMQRLAEACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:COG2207   219 SISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 193-288 4.34e-11

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: 62.48  E-value: 4.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 193 AQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE--QT--RFevlLLETRMQHAMMLVQTTSWSMQRLAEACGYKS 268
Cdd:COG4977   213 ARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAAtgTTpaRY---LQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                          90       100
                  ....*....|....*....|
gi 2316063006 269 SARFSERFKTRFGCSPTKIR 288
Cdd:COG4977   290 ASHFRRAFRRRFGVSPSAYR 309
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
207-288 6.98e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 73.74  E-value: 6.98e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  207 WTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYKSSARFSERFKTRFGCSPT 285
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKEtGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 2316063006  286 KIR 288
Cdd:smart00342  82 EYR 84
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 188-286 4.72e-15

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 73.42  E-value: 4.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 188 QPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYK 267
Cdd:PRK09978  140 QPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYH 219

                          90
                  ....*....|....*....
gi 2316063006 268 SSARFSERFKTRFGCSPTK 286
Cdd:PRK09978  220 SVSYFIYVFRNYYGMTPTE 238
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 191-287 4.87e-13

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 67.42  E-value: 4.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 191 ITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSwSMQRLAEACGYKSSA 270
Cdd:PRK09940  135 VSGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTS 213

                          90
                  ....*....|....*..
gi 2316063006 271 RFSERFKTRFGCSPTKI 287
Cdd:PRK09940  214 YFIYAFRKHFGNSPKRV 230
HTH_18 pfam12833
Helix-turn-helix domain;
214-288 9.29e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 62.61  E-value: 9.29e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2316063006 214 RQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAM-MLVQTTSWSMQRLAEACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:pfam12833   3 AALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARrLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 198-285 2.15e-12

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 66.17  E-value: 2.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 198 LISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYKSSARFSERFK 277
Cdd:PRK15185  214 IISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFK 293


                  ....*...
gi 2316063006 278 TRFGCSPT 285
Cdd:PRK15185  294 KYFKTTPS 301
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
97-288 1.57e-11

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 63.26  E-value: 1.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006  97 GGHDAVFRSLFLTFSSTLLAQFYHRYPEKLAPVHPSAPFTHLLLDDDLTHTLQYLVEGMTSNTLTESRLELRLMDMLLVL 176
Cdd:COG2207    59 LLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLL 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 177 SERGYHFGAPPQPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTTSW 255
Cdd:COG2207   139 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEEtGTSPKQYLRELRLERAKRLLAETDL 218

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2316063006 256 SMQRLAEACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:COG2207   219 SISEIAYELGFSSQSHFSRAFKKRFGVTPSEYR 251
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 193-288 4.34e-11

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: 62.48  E-value: 4.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 193 AQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE--QT--RFevlLLETRMQHAMMLVQTTSWSMQRLAEACGYKS 268
Cdd:COG4977   213 ARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAAtgTTpaRY---LQRLRLERARRLLETTDLSIEEIAAACGFGS 289

                          90       100
                  ....*....|....*....|
gi 2316063006 269 SARFSERFKTRFGCSPTKIR 288
Cdd:COG4977   290 ASHFRRAFRRRFGVSPSAYR 309
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 188-286 4.35e-11

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 62.01  E-value: 4.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 188 QPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYK 267
Cdd:PRK15186  179 QNTLAENIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYD 258

                          90
                  ....*....|....*....
gi 2316063006 268 SSARFSERFKTRFGCSPTK 286
Cdd:PRK15186  259 SASYFTCVFKKHFKTTPSE 277
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 184-288 2.24e-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: 60.45  E-value: 2.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 184 GAPPQPGITAQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE-QTRFEVLLLETRMQHAMMLVQTtSWSMQRLAE 262
Cdd:COG2169    78 GSPPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHtGVTPKAYARARRLLRARQLLQT-GLSVTDAAY 156

                          90       100
                  ....*....|....*....|....*.
gi 2316063006 263 ACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:COG2169   157 AAGFGSLSRFYEAFKKLLGMTPSAYR 182
ftrA PRK09393
transcriptional activator FtrA; Provisional
 186-288 3.66e-09

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 56.51  E-value: 3.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 186 PPQPGIT-AQLRALISEEPERHWTAQSAGRQLAMSEATLRRRLSAE--QTRFEVLLLEtRMQHAMMLVQTTSWSMQRLAE 262
Cdd:PRK09393  213 ASRESDRlGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAtgMTPAEWLLRE-RLARARDLLESSALSIDQIAE 291

                          90       100
                  ....*....|....*....|....*.
gi 2316063006 263 ACGYKSSARFSERFKTRFGCSPTKIR 288
Cdd:PRK09393  292 RAGFGSEESLRHHFRRRAATSPAAYR 317
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 198-284 9.29e-09

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 55.42  E-value: 9.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2316063006 198 LISEEPERHWTAQSAGRQLAMSEATLRRRLSAEQTRFEVLLLETRMQHAMMLVQTTSWSMQRLAEACGYKSSARFSERFK 277
Cdd:PRK15044  200 IIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFK 279


                  ....*..
gi 2316063006 278 TRFGCSP 284
Cdd:PRK15044  280 RHFKITP 286
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 252-288 3.97e-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: 37.13  E-value: 3.97e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2316063006 252 TTSWSMQRLAEACGYkSSARFSERFKTRFGCSPTKIR 288
Cdd:pfam00165   6 STNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYR 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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