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Conserved domains on  [gi|491993334|ref|WP_005710405|]
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DNA-binding transcriptional regulator [Glaesserella parasuis]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11459264)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
38-96 2.74e-23

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


:

Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 84.60  E-value: 2.74e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491993334  38 ITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTF 96
Cdd:COG2944    6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
 
Name Accession Description Interval E-value
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
38-96 2.74e-23

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 84.60  E-value: 2.74e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491993334  38 ITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTF 96
Cdd:COG2944    6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 37-100 5.69e-13

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: 59.95  E-value: 5.69e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491993334   37 VITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTFEQIA 100
Cdd:TIGR03830  64 LLTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
NadS NF041265
NadS family protein;
4-102 6.42e-12

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 56.34  E-value: 6.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491993334   4 LFNELMEGMQ-ALELHLQGKITLKTTVVEVPDpivitpeeVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQA 82
Cdd:NF041265   3 FFDELKASLEeAVEIKNGVKAPARVTRYEVAD--------VKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLA 74

                         90       100
                 ....*....|....*....|
gi 491993334  83 VLLLKMVEKSPKTFEQIASI 102
Cdd:NF041265  75 AKVLATIQDNPAFFKELAAH 94
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
42-86 2.59e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 2.59e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 491993334    42 EVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKL 45
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 41-86 4.84e-08

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: 45.62  E-value: 4.84e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491993334  41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKL 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 43-86 1.88e-07

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: 44.07  E-value: 1.88e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 491993334   43 VKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKL 44
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
43-89 1.30e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 40.51  E-value: 1.30e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 491993334  43 VKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMV 89
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGKVPMPYCAFKLERRL 47
PRK10072 PRK10072
HTH-type transcriptional regulator;
42-99 5.77e-04

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 35.92  E-value: 5.77e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491993334  42 EVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTFEQI 99
Cdd:PRK10072  37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANPALSKQL 94
 
Name Accession Description Interval E-value
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
38-96 2.74e-23

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 84.60  E-value: 2.74e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491993334  38 ITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTF 96
Cdd:COG2944    6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPELL 64
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 37-100 5.69e-13

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: 59.95  E-value: 5.69e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491993334   37 VITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTFEQIA 100
Cdd:TIGR03830  64 LLTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
NadS NF041265
NadS family protein;
4-102 6.42e-12

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 56.34  E-value: 6.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491993334   4 LFNELMEGMQ-ALELHLQGKITLKTTVVEVPDpivitpeeVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQA 82
Cdd:NF041265   3 FFDELKASLEeAVEIKNGVKAPARVTRYEVAD--------VKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLA 74

                         90       100
                 ....*....|....*....|
gi 491993334  83 VLLLKMVEKSPKTFEQIASI 102
Cdd:NF041265  75 AKVLATIQDNPAFFKELAAH 94
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 40-91 1.11e-08

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: 47.63  E-value: 1.11e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491993334  40 PEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQavlLLKMVEK 91
Cdd:COG1813   14 GERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLD---TLRKLEK 62
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
42-86 2.59e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 2.59e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 491993334    42 EVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKL 45
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 41-86 4.84e-08

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: 45.62  E-value: 4.84e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491993334  41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKL 47
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
41-86 9.35e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 45.37  E-value: 9.35e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491993334  41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKL 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 43-86 1.88e-07

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: 44.07  E-value: 1.88e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 491993334   43 VKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKL 44
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
41-86 6.85e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 42.91  E-value: 6.85e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 491993334  41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLL 86
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKI 52
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 37-99 8.23e-07

Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.


Pssm-ID: 292359 [Multi-domain]  Cd Length: 131  Bit Score: 43.91  E-value: 8.23e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491993334   37 VITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTFEQI 99
Cdd:pfam15731  68 LIDPAFIARVRKKLGLDQREAAEIFGGGVNAFSRYENGKTRPPLALVKLLRLLDRHPELLEEI 130
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
43-89 1.30e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 40.51  E-value: 1.30e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 491993334  43 VKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMV 89
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGKVPMPYCAFKLERRL 47
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 41-86 1.15e-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: 1.15e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 491993334   41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRT-KPNPQAVLLL 86
Cdd:pfam13560   4 ARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRgRPSPAVVERL 50
PRK10072 PRK10072
HTH-type transcriptional regulator;
42-99 5.77e-04

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 35.92  E-value: 5.77e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491993334  42 EVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMVEKSPKTFEQI 99
Cdd:PRK10072  37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELKLMRLIQANPALSKQL 94
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 25-78 2.16e-03

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: 34.23  E-value: 2.16e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491993334  25 LKTTVVEVpDPIVITPEEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKP 78
Cdd:COG3620    5 MSRDVVTV-SPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDP 57
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 41-89 3.26e-03

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: 33.24  E-value: 3.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 491993334  41 EEVKAIRQKLNLSQAVFARKLHTSVRTYQGWEQGRTKPNPQAVLLLKMV 89
Cdd:COG1426    8 ELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFL 56
 
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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