NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|516727857|ref|WP_018068920|]
View 

MULTISPECIES: helix-turn-helix domain-containing protein [Rhizobium]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-80 2.38e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 2.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516727857   1 MTPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIiwdEAEELFLLARSSDPRVVID 80
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRN-PSLETLLKLAKALGV---SLDELLGGADEELPEALLS 80
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-80 2.38e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 2.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516727857   1 MTPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIiwdEAEELFLLARSSDPRVVID 80
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRN-PSLETLLKLAKALGV---SLDELLGGADEELPEALLS 80
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 2.31e-13

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.87  E-value: 2.31e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516727857   5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIIWDE 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-58 2.57e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.14  E-value: 2.57e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 516727857     8 VRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNI 58
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGV 51
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-58 2.26e-10

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 52.16  E-value: 2.26e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 516727857    8 VRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRgLPTFDLLQRIAGYFNI 58
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGV 50
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 5-54 7.01e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 43.40  E-value: 7.01e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 516727857   5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKrGLPTFDLLQRIAG 54
Cdd:PRK08154  30 GERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQ-GNVSILLLRRVAR 78
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-57 9.37e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 32.97  E-value: 9.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 516727857   16 GVSQKEMAEALNVSPAYLSALEHGKRGLpTFDLLQRIAGYFN 57
Cdd:TIGR02607  18 GLSVRALAKALGVSRSTLSRIVNGRAAI-TADMALRLAKALG 58
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-80 2.38e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.48  E-value: 2.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516727857   1 MTPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIiwdEAEELFLLARSSDPRVVID 80
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRN-PSLETLLKLAKALGV---SLDELLGGADEELPEALLS 80
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-69 4.19e-15

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 64.48  E-value: 4.19e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516727857   4 FGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRgLPTFDLLQRIAGYFNIiwdEAEELFLL 69
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGV---SLEELFSL 66
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 1.96e-13

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 60.34  E-value: 1.96e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 516727857   4 FGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRgLPTFDLLQRIAGYFNI 58
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEA-TPSLDTLRKLEKALGI 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 2.31e-13

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.87  E-value: 2.31e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516727857   5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIIWDE 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-58 2.57e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.14  E-value: 2.57e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 516727857     8 VRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNI 58
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGV 51
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-58 2.26e-10

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 52.16  E-value: 2.26e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 516727857    8 VRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRgLPTFDLLQRIAGYFNI 58
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGV 50
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-53 3.13e-10

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 52.15  E-value: 3.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 516727857    4 FGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGLPTFDLLQRIA 53
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLA 51
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-57 5.13e-08

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 47.32  E-value: 5.13e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516727857   2 TPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFN 57
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRD-PTVSTLEKIAEALG 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-70 5.69e-08

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 46.13  E-value: 5.69e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516727857    5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGlPTFDLLQRIAGYFNIiwdEAEELFLLA 70
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSV-PPAETLYKIAELLGV---PANWLLQGE 62
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 2-58 1.08e-07

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 45.96  E-value: 1.08e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516727857   2 TPFGEAVRR-LRARKGVSQKEMAEALNVSPAYLSALEHGKRGLpTFDLLQRIAGYFNI 58
Cdd:COG3093    7 IHPGEILREeFLEPLGLSQTELAKALGVSRQRISEILNGKRAI-TADTALRLARAFGT 63
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-67 2.42e-07

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 44.80  E-value: 2.42e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516727857   1 MTPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGL---PTF--DLLQRIAGYFNIiwdEAEELF 67
Cdd:COG1426    3 LETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDAlpgPVYvrGFLRSYARALGL---DPEELL 71
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
2-53 7.40e-07

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 43.38  E-value: 7.40e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516727857   2 TPFGEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKR--GLPTFDLLQRIA 53
Cdd:COG2944    5 PLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRkpSGAALKLLRLLE 58
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 5-54 7.01e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 43.40  E-value: 7.01e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 516727857   5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKrGLPTFDLLQRIAG 54
Cdd:PRK08154  30 GERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQ-GNVSILLLRRVAR 78
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 9-58 1.04e-05

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 40.22  E-value: 1.04e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 516727857    9 RRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGLPTFDLLQRIAGYFNI 58
Cdd:pfam13443   3 RKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGC 52
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
5-52 1.51e-03

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 36.69  E-value: 1.51e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 516727857   5 GEAVRRLRARKGVSQKEMAEALNVSPAYLSALEHGKRGLPTFDLLQRI 52
Cdd:COG1709   24 GETLRKWREDFGISQTELARELGVSPSVISDYESGRRKSPGIAFVKKF 71
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
18-44 3.77e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 33.73  E-value: 3.77e-03
                         10        20
                 ....*....|....*....|....*..
gi 516727857  18 SQKEMAEALNVSPAYLSALEHGKRGLP 44
Cdd:COG4197   10 SQSALARALGVSQQAVSQWLNGKRRVP 36
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 8-53 7.24e-03

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 33.96  E-value: 7.24e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 516727857   8 VRRLRARKGVSQKEMAEALNVSPAYLSALEHGKrGLPTFDLLQRIA 53
Cdd:PRK13890  10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGK-ANPSLKVMEAIA 54
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-57 9.37e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 32.97  E-value: 9.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 516727857   16 GVSQKEMAEALNVSPAYLSALEHGKRGLpTFDLLQRIAGYFN 57
Cdd:TIGR02607  18 GLSVRALAKALGVSRSTLSRIVNGRAAI-TADMALRLAKALG 58
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH