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Conserved domains on  [gi|492445087|ref|WP_005846596|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Bacteroidaceae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 13303781)

helix-turn-helix domain-containing protein such as an AraC family transcriptional regulator, which controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
196-275 3.83e-22

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 87.26  E-value: 3.83e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087  196 YAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLH-TSHSIKEISVILGFESVGTFSRFFKNMTGENTSAYRK 274
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 492445087  275 R 275
Cdd:pfam12833  81 R 81
PRK13502 super family cl32883
HTH-type transcriptional activator RhaR;
103-273 8.18e-04

HTH-type transcriptional activator RhaR;


The actual alignment was detected with superfamily member PRK13502:

Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 40.04  E-value: 8.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 103 FNGTSGIVHLRLPIADSELLHEVVDRMVTEYILRDNLQGEMLRLLLKRFIILCTRlARKQLSGFPVNEKGfDIIQRYYVL 182
Cdd:PRK13502 107 FQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKR-HRYATDDLPATSRE-TLLDKLITA 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 183 VDNHFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMPSPLKIIQERVVtEAKRLLLHTSHSIKEISVILGFESVGTFSRFF 261
Cdd:PRK13502 185 LANSLECPFALDAFCQQEQCSERVLRQQFrAQTGMTINQYLRQVRIC-HAQYLLQHSPLMISEISMQCGFEDSNYFSVVF 263

                        170
                 ....*....|..
gi 492445087 262 KNMTGENTSAYR 273
Cdd:PRK13502 264 TRETGMTPSQWR 275
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
196-275 3.83e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 87.26  E-value: 3.83e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087  196 YAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLH-TSHSIKEISVILGFESVGTFSRFFKNMTGENTSAYRK 274
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 492445087  275 R 275
Cdd:pfam12833  81 R 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
193-277 2.41e-19

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 84.83  E-value: 2.41e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 193 VQAYAALLHRSPKTLSNLF-AAYGMpSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNMTGENTSA 271
Cdd:COG2207  171 LEELARELGLSPRTLSRLFkEETGT-SPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 492445087 272 YRKRLQ 277
Cdd:COG2207  250 YRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
193-273 1.89e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.28  E-value: 1.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087   193 VQAYAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNMTGENTSAY 272
Cdd:smart00342   4 LEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83


                   .
gi 492445087   273 R 273
Cdd:smart00342  84 R 84
ftrA PRK09393
transcriptional activator FtrA; Provisional
 186-275 5.91e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 46.88  E-value: 5.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 186 HFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMPSPLKIIQERVvTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNM 264
Cdd:PRK09393 230 HLAEPHTVASLAARAAMSPRTFLRRFeAATGMTPAEWLLRERL-ARARDLLESSALSIDQIAERAGFGSEESLRHHFRRR 308

                         90
                 ....*....|.
gi 492445087 265 TGENTSAYRKR 275
Cdd:PRK09393 309 AATSPAAYRKR 319
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
103-273 8.18e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 40.04  E-value: 8.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 103 FNGTSGIVHLRLPIADSELLHEVVDRMVTEYILRDNLQGEMLRLLLKRFIILCTRlARKQLSGFPVNEKGfDIIQRYYVL 182
Cdd:PRK13502 107 FQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKR-HRYATDDLPATSRE-TLLDKLITA 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 183 VDNHFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMPSPLKIIQERVVtEAKRLLLHTSHSIKEISVILGFESVGTFSRFF 261
Cdd:PRK13502 185 LANSLECPFALDAFCQQEQCSERVLRQQFrAQTGMTINQYLRQVRIC-HAQYLLQHSPLMISEISMQCGFEDSNYFSVVF 263

                        170
                 ....*....|..
gi 492445087 262 KNMTGENTSAYR 273
Cdd:PRK13502 264 TRETGMTPSQWR 275
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 183-273 3.45e-03

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: 38.50  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087  183 VDNHFKEKKQVQAYAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKrLLLHTSHSIKEISVILGFESVGTFSRFFK 262
Cdd:TIGR04094 294 INLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAK-YLLRSQIPVSEVSNELGFYDLSHFSRTFK 372

                          90
                  ....*....|.
gi 492445087  263 NMTGENTSAYR 273
Cdd:TIGR04094 373 KHTGVSPKQYQ 383
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
196-275 3.83e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 87.26  E-value: 3.83e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087  196 YAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLH-TSHSIKEISVILGFESVGTFSRFFKNMTGENTSAYRK 274
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 492445087  275 R 275
Cdd:pfam12833  81 R 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
193-277 2.41e-19

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 84.83  E-value: 2.41e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 193 VQAYAALLHRSPKTLSNLF-AAYGMpSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNMTGENTSA 271
Cdd:COG2207  171 LEELARELGLSPRTLSRLFkEETGT-SPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249


                 ....*.
gi 492445087 272 YRKRLQ 277
Cdd:COG2207  250 YRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
193-273 1.89e-17

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.28  E-value: 1.89e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087   193 VQAYAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNMTGENTSAY 272
Cdd:smart00342   4 LEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83


                   .
gi 492445087   273 R 273
Cdd:smart00342  84 R 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 182-275 1.58e-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: 1.58e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 182 LVDNHFKEKKQVQAYAALLHRSPKTLSNLFAAY-GMpSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRF 260
Cdd:COG4977  218 WMEANLEEPLSVDELARRAGMSPRTLERRFRAAtGT-TPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRA 296

                         90
                 ....*....|....*
gi 492445087 261 FKNMTGENTSAYRKR 275
Cdd:COG4977  297 FRRRFGVSPSAYRRR 311
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 182-275 9.32e-08

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: 52.36  E-value: 9.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 182 LVDNHFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMpSPLKIIQERVVTEAKRLLlHTSHSIKEISVILGFESVGTFSRF 260
Cdd:COG2169   92 LIEAGAEDRPSLEDLAARLGLSPRHLRRLFkAHTGV-TPKAYARARRLLRARQLL-QTGLSVTDAAYAAGFGSLSRFYEA 169

                         90
                 ....*....|....*
gi 492445087 261 FKNMTGENTSAYRKR 275
Cdd:COG2169  170 FKKLLGMTPSAYRRG 184
ftrA PRK09393
transcriptional activator FtrA; Provisional
 186-275 5.91e-06

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 46.88  E-value: 5.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 186 HFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMPSPLKIIQERVvTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNM 264
Cdd:PRK09393 230 HLAEPHTVASLAARAAMSPRTFLRRFeAATGMTPAEWLLRERL-ARARDLLESSALSIDQIAERAGFGSEESLRHHFRRR 308

                         90
                 ....*....|.
gi 492445087 265 TGENTSAYRKR 275
Cdd:PRK09393 309 AATSPAAYRKR 319
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
182-275 7.83e-05

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 43.42  E-value: 7.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 182 LVDNHFKEKKQVQAYAALLHRSPKTLSNLFA-AYGMpSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRF 260
Cdd:PRK10572 191 YISDHLASEFDIESVAQHVCLSPSRLAHLFRqQLGI-SVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRV 269

                         90
                 ....*....|....*
gi 492445087 261 FKNMTGENTSAYRKR 275
Cdd:PRK10572 270 FKKCTGASPSEFRAR 284
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
174-276 1.13e-04

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 40.68  E-value: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 174 DIIQRYYVLVDNHFKEKKQVQAYAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFES 253
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|...
gi 492445087 254 VGTFSRFFKNMTGENTSAYRKRL 276
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYRHRL 107
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 148-276 1.52e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 42.44  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 148 LKRFIILCTRLARKQLSGFPVNEKGFDIIQRYYVLVDN-HFKEKKQVQAYAALLHRSPKTLSNLFAA---YGMPSPLKII 223
Cdd:PRK10296 142 LDEFVELVTFYVINRLRHYREEQVIDDIPQWLKATVEKmHDKEQFSESALENMVRLSGKSQEYLTRAtrrYYGKTPMQII 221

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492445087 224 QERVVTEAKRLLLHTSHSIKEISVILGFESVGTFSRFFKNMTGENTSAYRKRL 276
Cdd:PRK10296 222 NEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKKL 274
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
103-273 8.18e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 40.04  E-value: 8.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 103 FNGTSGIVHLRLPIADSELLHEVVDRMVTEYILRDNLQGEMLRLLLKRFIILCTRlARKQLSGFPVNEKGfDIIQRYYVL 182
Cdd:PRK13502 107 FQGAQWHPHWRLGSMGMNQARQVINQLEHESNGRDPLANEMAELLFGQLVMTLKR-HRYATDDLPATSRE-TLLDKLITA 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 183 VDNHFKEKKQVQAYAALLHRSPKTLSNLF-AAYGMPSPLKIIQERVVtEAKRLLLHTSHSIKEISVILGFESVGTFSRFF 261
Cdd:PRK13502 185 LANSLECPFALDAFCQQEQCSERVLRQQFrAQTGMTINQYLRQVRIC-HAQYLLQHSPLMISEISMQCGFEDSNYFSVVF 263

                        170
                 ....*....|..
gi 492445087 262 KNMTGENTSAYR 273
Cdd:PRK13502 264 TRETGMTPSQWR 275
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
176-276 1.49e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 39.50  E-value: 1.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087 176 IQRYYVLVdnHFKEKKQVqayaallhrSPKTLSNLFAAYGMPSPLKIIQERVVTEAKRLLLHTSHSIKEISVILGFESVG 255
Cdd:PRK13501 189 LGAYFDMA--DFCHKNQL---------VERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSN 257

                         90       100
                 ....*....|....*....|.
gi 492445087 256 TFSRFFKNMTGENTSAYRKRL 276
Cdd:PRK13501 258 YFSAVFTREAGMTPRDYRQRF 278
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 183-273 3.45e-03

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: 38.50  E-value: 3.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492445087  183 VDNHFKEKKQVQAYAALLHRSPKTLSNLFAAYGMPSPLKIIQERVVTEAKrLLLHTSHSIKEISVILGFESVGTFSRFFK 262
Cdd:TIGR04094 294 INLNLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAK-YLLRSQIPVSEVSNELGFYDLSHFSRTFK 372

                          90
                  ....*....|.
gi 492445087  263 NMTGENTSAYR 273
Cdd:TIGR04094 373 KHTGVSPKQYQ 383
 
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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