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Conserved domains on  [gi|1391526017|gb|PWN00668|]
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MAG: hypothetical protein DBX37_00665, partial [Massilioclostridium sp.]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 12204063)

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:0006355|GO:0043565|GO:0003700
PubMed:  2644244|15808743|8831795
SCOP:  4000332

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
43-126 4.01e-23

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 86.07  E-value: 4.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   43 EVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSV 122
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1391526017  123 TKFR 126
Cdd:smart00342  81 SEYR 84
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
43-126 4.01e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 86.07  E-value: 4.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   43 EVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSV 122
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1391526017  123 TKFR 126
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
44-127 5.16e-22

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 87.91  E-value: 5.16e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  44 VTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVT 123
Cdd:COG2207   169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....
gi 1391526017 124 KFRQ 127
Cdd:COG2207   249 EYRK 252
HTH_18 pfam12833
Helix-turn-helix domain;
49-127 9.46e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 77.24  E-value: 9.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  49 MANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYL-KNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQ 127
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
7-126 7.81e-14

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 66.15  E-value: 7.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   7 LSRIEAVNPLPKPegktdPKQQKIYDILSYMKDHY-SEVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAG 85
Cdd:PRK10572  167 LRCMEAIPESLHP-----PMDPRVREACQYISDHLaSEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAK 241

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1391526017  86 IYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFR 126
Cdd:PRK10572  242 LLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
43-126 4.01e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 86.07  E-value: 4.01e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   43 EVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSV 122
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1391526017  123 TKFR 126
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
44-127 5.16e-22

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 87.91  E-value: 5.16e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  44 VTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVT 123
Cdd:COG2207   169 LTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....
gi 1391526017 124 KFRQ 127
Cdd:COG2207   249 EYRK 252
HTH_18 pfam12833
Helix-turn-helix domain;
49-127 9.46e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 77.24  E-value: 9.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  49 MANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYL-KNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQ 127
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 15-128 2.28e-17

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: 75.96  E-value: 2.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  15 PLPKPEGKTDPKqqkIYDILSYMKDHYSE-VTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNF 93
Cdd:COG4977   200 PLLVPLGHRDPR---LARAQAWMEANLEEpLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDL 276

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1391526017  94 SVEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQT 128
Cdd:COG4977   277 SIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRR 311
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
7-126 7.81e-14

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 66.15  E-value: 7.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   7 LSRIEAVNPLPKPegktdPKQQKIYDILSYMKDHY-SEVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAG 85
Cdd:PRK10572  167 LRCMEAIPESLHP-----PMDPRVREACQYISDHLaSEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAK 241

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1391526017  86 IYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFR 126
Cdd:PRK10572  242 LLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 18-133 5.97e-13

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: 64.30  E-value: 5.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  18 KPEGK--TDPKQQKIYDILSYMKDHYSE-VTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKnSNFS 94
Cdd:COG2169    72 RPDLApgSPPRADLVARACRLIEAGAEDrPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLS 150

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1391526017  95 VEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQTALNEK 133
Cdd:COG2169   151 VTDAAYAAGFGSLSRFYEAFKKLLGMTPSAYRRGGAGAA 189
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
29-127 4.02e-09

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 53.14  E-value: 4.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  29 KIYDILSYMKDHYS-EVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDT 107
Cdd:PRK13503  172 RLNQLLAWLEDHFAeEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDS 251

                          90       100
                  ....*....|....*....|
gi 1391526017 108 SYFYRLFKRITGVSVTKFRQ 127
Cdd:PRK13503  252 NHFSTLFRREFSWSPRDIRQ 271
PRK10371 PRK10371
transcriptional regulator MelR;
26-133 8.26e-09

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 52.13  E-value: 8.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  26 KQQKIYDILSYMKDHYSE-VTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGF 104
Cdd:PRK10371  189 AQFYVSQMLGFIAENYDQaLTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGF 268

                          90       100
                  ....*....|....*....|....*....
gi 1391526017 105 HDTSYFYRLFKRITGVSVTKFRQTALNEK 133
Cdd:PRK10371  269 RSSSRFYSTFGKYVGMSPQQYRKLSQQRR 297
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
46-127 5.03e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 44.27  E-value: 5.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  46 LESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKF 125
Cdd:PRK13502  195 LDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQW 274


                  ..
gi 1391526017 126 RQ 127
Cdd:PRK13502  275 RH 276
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
30-128 6.14e-06

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 42.78  E-value: 6.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  30 IYDILSYMKDHY-SEVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTS 108
Cdd:PRK11511   11 IHSILDWIEDNLeSPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQ 90

                          90       100
                  ....*....|....*....|
gi 1391526017 109 YFYRLFKRITGVSVTKFRQT 128
Cdd:PRK11511   91 TLTRTFKNYFDVPPHKYRMT 110
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
58-127 7.41e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 43.74  E-value: 7.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  58 RHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQ 127
Cdd:PRK13501  207 RSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQ 276
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
42-135 7.45e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 43.94  E-value: 7.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  42 SEVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQYKIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVS 121
Cdd:PRK13500  221 SPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMT 300

                          90
                  ....*....|....
gi 1391526017 122 VTKFRQtaLNEKKN 135
Cdd:PRK13500  301 PSQWRH--LNSQKD 312
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 4-127 3.35e-05

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 42.05  E-value: 3.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017   4 FVELSRIEAVNPLP--KPEGKTDPKQQKIYDILSYMKD--HYSEVTLESMANHFHYTPRHISRLIKENSGKTFIQLVNQY 79
Cdd:PRK10296  145 FVELVTFYVINRLRhyREEQVIDDIPQWLKATVEKMHDkeQFSESALENMVRLSGKSQEYLTRATRRYYGKTPMQIINEI 224

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1391526017  80 KIANAGIYLKNSNFSVEEIMQITGFHDTSYFYRLFKRITGVSVTKFRQ 127
Cdd:PRK10296  225 RINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRK 272
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 91-127 3.21e-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: 35.98  E-value: 3.21e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1391526017  91 SNFSVEEIMQITGFhDTSYFYRLFKRITGVSVTKFRQ 127
Cdd:pfam00165   7 TNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
22-131 2.45e-03

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 36.69  E-value: 2.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1391526017  22 KTDPKQQKIYDILSYMK--DHYSEVTLESMANHFHYTPRHISRLIKENSG---KTFIQLVNQYKIANAgiyLKNSNfSVE 96
Cdd:PRK15435   76 KANPQQHRLDKITHACRllEQETPVTLEALADQVAMSPFHLHRLFKATTGmtpKAWQQAWRARRLREA---LAKGE-SVT 151

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1391526017  97 EIMQITGFHDTSYFYRLFKRITGVSVTKFRQTALN 131
Cdd:PRK15435  152 TSILNAGFPDSSSYYRKADETLGMTAKQFRHGGEN 186
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 103-130 5.22e-03

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 35.39  E-value: 5.22e-03
                          10        20
                  ....*....|....*....|....*...
gi 1391526017 103 GFHDTSYFYRLFKRITGVSVTKFRQTAL 130
Cdd:PRK09685  275 GFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
 
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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