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Conserved domains on  [gi|503577570|ref|WP_013811646|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Serratia]

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];
16-73 2.82e-11

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.46  E-value: 2.82e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 503577570 16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAVMKR 73
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-73 2.82e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.46  E-value: 2.82e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 503577570 16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAVMKR 73
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-66 1.11e-10

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: 51.40  E-value: 1.11e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 503577570 14 KILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-66 7.06e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.44  E-value: 7.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 503577570   16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-66 3.65e-09

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: 47.54  E-value: 3.65e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 503577570  16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 15-63 4.09e-06

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: 39.95  E-value: 4.09e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 503577570  15 ILRDARIEKGITQAKLAEALGRPQSFIAKVENGErklDVVEFAVMARLL 63
Cdd:TIGR03070  6 LVRARRKALGLTQADLADLAGVGLRFIRDLENGK---PTVRLDKVLRVL 51
PRK02866 PRK02866
cyanate hydratase; Validated
 10-70 1.65e-05

cyanate hydratase; Validated


Pssm-ID: 235079 [Multi-domain]  Cd Length: 147  Bit Score: 39.80  E-value: 1.65e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503577570  10 QLVIKILrDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAV 70
Cdd:PRK02866   5 ELTEKIL-AAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAV 64
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-73 2.82e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.46  E-value: 2.82e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 503577570 16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAVMKR 73
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 14-66 1.10e-10

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: 51.86  E-value: 1.10e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 503577570 14 KILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:COG1813  15 ERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-66 1.11e-10

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: 51.40  E-value: 1.11e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 503577570 14 KILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-66 7.06e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.44  E-value: 7.06e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 503577570   16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
16-66 1.30e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.08  E-value: 1.30e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 503577570 16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVS 59
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-66 3.65e-09

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: 47.54  E-value: 3.65e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 503577570  16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVD 66
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 14-75 6.17e-09

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: 47.28  E-value: 6.17e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503577570  14 KILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAVMKRIG 75
Cdd:pfam12844  2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEG 63
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 14-71 1.82e-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: 43.64  E-value: 1.82e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503577570 14 KILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAV------MARLLGVDAGAVM 71
Cdd:COG1426   8 ELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVrgflrsYARALGLDPEELL 71
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 16-66 3.88e-07

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: 42.52  E-value: 3.88e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503577570  16 LRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEF-AVMARLLGVD 66
Cdd:pfam13560  6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVvERLARALGVD 57
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 12-70 3.95e-06

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: 40.77  E-value: 3.95e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 503577570 12 VIKILRDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAV 70
Cdd:COG3620  18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 15-63 4.09e-06

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: 39.95  E-value: 4.09e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 503577570  15 ILRDARIEKGITQAKLAEALGRPQSFIAKVENGErklDVVEFAVMARLL 63
Cdd:TIGR03070  6 LVRARRKALGLTQADLADLAGVGLRFIRDLENGK---PTVRLDKVLRVL 51
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 15-68 6.44e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.18  E-value: 6.44e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 503577570 15 ILRDARIE-KGITQAKLAEALGRPQSFIAKVENGERKLDvVEFAV-MARLLGVDAG 68
Cdd:COG3093  12 ILREEFLEpLGLSQTELAKALGVSRQRISEILNGKRAIT-ADTALrLARAFGTSAE 66
PRK02866 PRK02866
cyanate hydratase; Validated
 10-70 1.65e-05

cyanate hydratase; Validated


Pssm-ID: 235079 [Multi-domain]  Cd Length: 147  Bit Score: 39.80  E-value: 1.65e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503577570  10 QLVIKILrDARIEKGITQAKLAEALGRPQSFIAKVENGERKLDVVEFAVMARLLGVDAGAV 70
Cdd:PRK02866   5 ELTEKIL-AAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAV 64
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 15-70 1.93e-03

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


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 33.24  E-value: 1.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503577570  15 ILRDARIEKGITQAKLAEALGRPQSFIAKVENGE-RKLDVVEFAV-----MARLLGVDAGAV 70
Cdd:pfam13413  1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDfDALPEPVYARgflrsYARALGLDPEEL 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.
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