NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|667705093|gb|KFA57942|]
View 

hypothetical protein HMPREF1632_00100 [Mageeibacillus indolicus 0009-5]

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];
7-72 2.27e-15

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.87  E-value: 2.27e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667705093   7 PDISPIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLL 72
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-72 2.27e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.87  E-value: 2.27e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667705093   7 PDISPIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLL 72
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-71 1.70e-12

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: 60.64  E-value: 1.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 667705093  14 GDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-71 3.56e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 3.56e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 667705093    16 NIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 17-71 8.98e-11

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: 55.62  E-value: 8.98e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 667705093   17 IRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 12-51 6.82e-08

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 49.94  E-value: 6.82e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 667705093   12 IIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQII 51
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVR 104
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 13-64 3.65e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 42.53  E-value: 3.65e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 667705093  13 IGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARAL 64
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL 57
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-72 2.27e-15

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.87  E-value: 2.27e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 667705093   7 PDISPIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLL 72
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
13-73 1.31e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 61.02  E-value: 1.31e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 667705093  13 IGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLLY 73
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFS 65
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-71 1.70e-12

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: 60.64  E-value: 1.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 667705093  14 GDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-71 3.56e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.45  E-value: 3.56e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 667705093    16 NIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-70 1.78e-11

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: 58.03  E-value: 1.78e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 667705093   1 MNLGANPDISPIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQ 70
Cdd:COG1813    1 MAKESTGELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 17-71 8.98e-11

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: 55.62  E-value: 8.98e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 667705093   17 IRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQL 71
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 12-51 6.82e-08

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 49.94  E-value: 6.82e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 667705093   12 IIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQII 51
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVR 104
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 14-72 2.53e-07

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: 46.51  E-value: 2.53e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 667705093   14 GDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLL 72
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 11-68 2.76e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 46.50  E-value: 2.76e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 667705093   11 PIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNL 68
Cdd:TIGR03070   1 KQIGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 13-72 2.88e-07

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: 2.88e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 667705093  13 IGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARALGVNLEQLL 72
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
8-49 5.00e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 45.70  E-value: 5.00e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 667705093   8 DISPIIGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQ 49
Cdd:COG2944    2 TKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGR 43
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 13-64 3.65e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 42.53  E-value: 3.65e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 667705093  13 IGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIILDVQTLYEIARAL 64
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL 57
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 13-66 7.14e-04

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: 37.12  E-value: 7.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 667705093   13 IGDNIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQIIL-DVQTLYEIARALGV 66
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRpSPAVVERLARALGV 56
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 16-75 2.90e-03

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: 35.21  E-value: 2.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 667705093   16 NIRFFRKRLKLTQSDLGSLINKGKATVAKYESGQI-ILDVQTLYEIARALGVNLEQLL-YVP 75
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLeYVP 62
 
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