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Conserved domains on  [gi|499485120|ref|WP_011171760|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Yersinia pseudotuberculosis complex]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12122938)

helix-turn-helix (HTH) domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
154-231 8.56e-23

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 8.56e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499485120  154 YANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLL-STRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMR 231
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
154-231 8.56e-23

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 8.56e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499485120  154 YANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLL-STRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMR 231
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
148-231 1.24e-22

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 87.99  E-value: 1.24e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120   148 PWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCP 227
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 499485120   228 SHMR 231
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-231 1.21e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 1.21e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 150 SVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSH 229
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ..
gi 499485120 230 MR 231
Cdd:COG2207  250 YR 251
ftrA PRK09393
transcriptional activator FtrA; Provisional
 137-231 3.33e-14

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 70.38  E-value: 3.33e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 137 LLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFS 216
Cdd:PRK09393 223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLR 302

                         90
                 ....*....|....*
gi 499485120 217 DSFRRRFQQCPSHMR 231
Cdd:PRK09393 303 HHFRRRAATSPAAYR 317
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
154-231 8.56e-23

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 88.03  E-value: 8.56e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499485120  154 YANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLL-STRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMR 231
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
148-231 1.24e-22

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 87.99  E-value: 1.24e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120   148 PWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCP 227
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 499485120   228 SHMR 231
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-231 1.21e-21

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.22  E-value: 1.21e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 150 SVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSH 229
Cdd:COG2207  170 TLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ..
gi 499485120 230 MR 231
Cdd:COG2207  250 YR 251
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 136-231 2.33e-21

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: 90.22  E-value: 2.33e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 136 ELLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHF 215
Cdd:COG4977  214 RAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHF 293

                         90
                 ....*....|....*.
gi 499485120 216 SDSFRRRFQQCPSHMR 231
Cdd:COG4977  294 RRAFRRRFGVSPSAYR 309
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 136-231 7.25e-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: 78.17  E-value: 7.25e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 136 ELLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLlSTRLRVADIAMECGFSNHAHF 215
Cdd:COG2169   88 RACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLL-QTGLSVTDAAYAAGFGSLSRF 166

                         90
                 ....*....|....*.
gi 499485120 216 SDSFRRRFQQCPSHMR 231
Cdd:COG2169  167 YEAFKKLLGMTPSAYR 182
ftrA PRK09393
transcriptional activator FtrA; Provisional
 137-231 3.33e-14

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 70.38  E-value: 3.33e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 137 LLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFS 216
Cdd:PRK09393 223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLR 302

                         90
                 ....*....|....*
gi 499485120 217 DSFRRRFQQCPSHMR 231
Cdd:PRK09393 303 HHFRRRAATSPAAYR 317
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 155-232 8.67e-13

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 66.21  E-value: 8.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 155 ANELGISTRKLNFLFYEKfGMSAKQWLLDQRLKKGCELL--LSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMRS 232
Cdd:PRK09685 221 AGELGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRCADDLrpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRR 299
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
147-233 5.03e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 55.49  E-value: 5.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 147 NPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQC 226
Cdd:PRK13500 221 SPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMT 300


                 ....*..
gi 499485120 227 PSHMRSL 233
Cdd:PRK13500 301 PSQWRHL 307
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
90-235 9.30e-09

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 54.59  E-value: 9.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120  90 VEIIQA-------AEEL-INIervasLRFLYLYCLGIDNVYFSKLLDSIVgtnNELLEFFEKNRLNPWSVSRYANELGIS 161
Cdd:PRK10572 141 GQIEQAgqsegrySELLaMNL-----LERLLLRCMEAIPESLHPPMDPRV---REACQYISDHLASEFDIESVAQHVCLS 212

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499485120 162 TRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMRSLIE 235
Cdd:PRK10572 213 PSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCE 286
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
148-233 1.75e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 53.52  E-value: 1.75e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 148 PWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCP 227
Cdd:PRK13502 192 PFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTP 271


                 ....*.
gi 499485120 228 SHMRSL 233
Cdd:PRK13502 272 SQWRHL 277
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
124-229 6.76e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 51.83  E-value: 6.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 124 SKLLDSIvGTNNELLEFFEKNRLnpwsvsryanelgiSTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADI 203
Cdd:PRK13501 183 SALQQSL-GAYFDMADFCHKNQL--------------VERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDI 247

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499485120 204 AMECGFSNHAHFS-----------DSFRRRFQQCPSH 229
Cdd:PRK13501 248 AARCGFEDSNYFSavftreagmtpRDYRQRFIRSPVL 284
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
90-232 8.65e-08

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 51.60  E-value: 8.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120  90 VEIIQAAEELINIERVASLRFLYLYCLGIdnVYFSKLLDSivGTNNELleffEKNRLNPWSVSRYANEL---------GI 160
Cdd:PRK13503 128 VAQMEQQEESNDLEAIASREILFMQLLVL--LRKSSLQEN--GENSDA----RLNQLLAWLEDHFAEEVnwealadqfSL 199

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499485120 161 STRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPSHMRS 232
Cdd:PRK13503 200 SLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQ 271
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
135-231 1.29e-07

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 48.38  E-value: 1.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 135 NELLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAH 214
Cdd:PRK10219   8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQT 87

                         90
                 ....*....|....*..
gi 499485120 215 FSDSFRRRFQQCPSHMR 231
Cdd:PRK10219  88 FSRVFRRQFDRTPSDYR 104
PRK10371 PRK10371
transcriptional regulator MelR;
136-233 4.90e-04

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 40.57  E-value: 4.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 136 ELLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLSTRLRVADIAMECGFSNHAHF 215
Cdd:PRK10371 195 QMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRF 274

                         90
                 ....*....|....*...
gi 499485120 216 SDSFRRRFQQCPSHMRSL 233
Cdd:PRK10371 275 YSTFGKYVGMSPQQYRKL 292
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 194-231 6.06e-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: 36.36  E-value: 6.06e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 499485120  194 LSTRLRVADIAMECGFSNHaHFSDSFRRRFQQCPSHMR 231
Cdd:pfam00165   5 LSTNLTIADIADELGFSRS-YFSRLFKKYTGVTPSQYR 41
PRK10130 PRK10130
HTH-type transcriptional regulator EutR;
139-228 4.03e-03

HTH-type transcriptional regulator EutR;


Pssm-ID: 182258 [Multi-domain]  Cd Length: 350  Bit Score: 37.59  E-value: 4.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 139 EFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKFGMSAKQWLLDQRLKKGCELLLS---TRLRVADIAMECGFSNHAHF 215
Cdd:PRK10130 247 EYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPNAWLKRIRLNAVRRELISpwsQSTTVKDAAMQWGFWHLGQF 326

                         90
                 ....*....|...
gi 499485120 216 SDSFRRRFQQCPS 228
Cdd:PRK10130 327 ATDYQQLFAEKPS 339
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 111-228 8.93e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 36.44  E-value: 8.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499485120 111 LYLYCLGIDNVYFSKLLDSIVGTN--NELLEFFEKNRLNPWSVSRYANELGISTRKLNFLFYEKfGMSAKQWLLDQRLKK 188
Cdd:PRK09978 119 FALLSVFLEDEHFIPLLLNVLQPNmrTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQR 197

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 499485120 189 GCELLLSTRLRVADIAMECGFSNHAHFSDSFRRRFQQCPS 228
Cdd:PRK09978 198 ALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPT 237
 
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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