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Conserved domains on  [gi|392690448|gb|EIY83715|]
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hypothetical protein HMPREF1058_00039 [Phocaeicola vulgatus CL09T03C04]

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

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
44-96 5.91e-14

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 5.91e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGI 96
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
44-96 5.91e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 5.91e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGI 96
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
47-99 1.25e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.14  E-value: 1.25e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 392690448    47 LRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 44-99 1.85e-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: 56.79  E-value: 1.85e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 47-99 2.20e-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: 54.08  E-value: 2.20e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392690448   47 LRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 44-97 2.70e-10

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: 51.51  E-value: 2.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392690448   44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIE 97
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLE 57
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 44-103 3.35e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 39.84  E-value: 3.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALgiEFTPTFV 103
Cdd:PRK09706   7 GQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL--QCSPTWL 64
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
44-96 5.91e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.55  E-value: 5.91e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGI 96
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 44-98 7.25e-14

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: 61.57  E-value: 7.25e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEF 98
Cdd:COG3620   19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKEL 73
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 43-99 1.53e-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: 59.95  E-value: 1.53e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392690448  43 YGDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
39-98 3.86e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 58.71  E-value: 3.86e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392690448  39 MAWYYGDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEF 98
Cdd:COG1476    1 MKKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
47-99 1.25e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.14  E-value: 1.25e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 392690448    47 LRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 44-99 1.85e-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: 56.79  E-value: 1.85e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 47-99 2.20e-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: 54.08  E-value: 2.20e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392690448   47 LRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 44-97 2.70e-10

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: 51.51  E-value: 2.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392690448   44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIE 97
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLE 57
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 44-97 4.32e-08

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: 45.95  E-value: 4.32e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFF------RIARALGIE 97
Cdd:COG1426    7 GELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYvrgflrSYARALGLD 66
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 44-96 4.51e-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: 45.74  E-value: 4.51e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392690448   44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGI 96
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGV 53
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 44-96 2.35e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.10  E-value: 2.35e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392690448  44 GDILRERR-KELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGI 96
Cdd:COG3093   10 GEILREEFlEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGT 63
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 44-95 6.79e-06

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: 40.20  E-value: 6.79e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392690448   44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDI-QLSSFFRIARALG 95
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRpSPAVVERLARALG 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 44-103 3.35e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 39.84  E-value: 3.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALgiEFTPTFV 103
Cdd:PRK09706   7 GQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL--QCSPTWL 64
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
34-99 4.13e-05

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 38.81  E-value: 4.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392690448  34 FNEKSMAWYygdiLRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFT 99
Cdd:PRK09726   8 YSPTQLANA----MKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 44-95 6.08e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 37.24  E-value: 6.08e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 392690448  44 GDILRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVDIQLSSFFRIARALG 95
Cdd:PRK08154  30 GERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALG 81
Thioredoxin_4 pfam13462
Thioredoxin;
41-103 1.79e-03

Thioredoxin;


Pssm-ID: 433227 [Multi-domain]  Cd Length: 164  Bit Score: 35.39  E-value: 1.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392690448   41 WYYGDILRERRKELKLTqKQLAQ-KIGKEQSYIARVEKGEVDIQLSSFFRIARALGIEFTPTFV 103
Cdd:pfam13462  81 LVIDKLLYSQQEEWAQD-LELAAlAGLKDEEFEACLEEEDFLALVMADVKEARAAGINFTPTFI 143
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 27-95 5.27e-03

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 32.97  E-value: 5.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392690448   27 GTDTREKFNEKSMAWYYgdiLRERRKELKLTQKQLAQKIGKEQSYIARVEKGEVD-IQLSSFFRIARALG 95
Cdd:pfam13744   6 GFEDAEELQAKAQLARA---IARLIEGRGLSQQEAAALLGIAQPKVSALLKGKLSrFSLDKLLDFLTALG 72
 
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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