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Conserved domains on  [gi|488432424|ref|WP_002501809|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Staphylococcus]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 18527876)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator similar to cytoskeleton protein RodZ, an inner membrane protein which functions in cell-shape control through regulation of the length of the long axis; also contains a DUF4115 domain

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];
5-72 2.59e-14

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 65.40  E-value: 2.59e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488432424   5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNELFESISSSDKEEEI 72
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRrNPSLETLLKLAKALGVSLDELLGGADEELPEALL 79
Voltage_gated_ClC super family cl02915
CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of ...
 72-200 6.42e-03

CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family. The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria. They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating. Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry. Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge. In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function.


The actual alignment was detected with superfamily member PRK05277:

Pssm-ID: 445960 [Multi-domain]  Cd Length: 438  Bit Score: 36.79  E-value: 6.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488432424  72 IMEISKEQQKQFNYRkneLFTIKLITFSFIFVFLgLFGIFVGELEGLEQNIY-----RIIWIFALF-LSLAIMYYFLNVF 145
Cdd:PRK05277 162 ILFVIEEMRPQFRYS---LISIKAVFIGVIMATI-VFRLFNGEQAVIEVGKFsapplNTLWLFLLLgIIFGIFGVLFNKL 237

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488432424 146 ISKKLDkkypmtigMKNRNRKNEpvkngwdfMARYWWIVFPIG---GFLSWLIPELTG 200
Cdd:PRK05277 238 LLRTQD--------LFDRLHGGN--------KKRWVLMGGAVGglcGLLGLLAPAAVG 279
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-72 2.59e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 65.40  E-value: 2.59e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488432424   5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNELFESISSSDKEEEI 72
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRrNPSLETLLKLAKALGVSLDELLGGADEELPEALL 79
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-59 2.73e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.98  E-value: 2.73e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488432424     5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKrKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-59 7.23e-09

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: 50.24  E-value: 7.23e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488432424   4 SKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKrNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-59 7.62e-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: 49.85  E-value: 7.62e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488432424    6 VAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKrEPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-54 1.78e-03

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: 35.33  E-value: 1.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 488432424   10 RKQKSLTQENLAEKAYVTVRTIQRMEAGEEvsSETLKSVSNALDV 54
Cdd:TIGR03070  11 RKALGLTQADLADLAGVGLRFIRDLENGKP--TVRLDKVLRVLDA 53
PRK05277 PRK05277
H(+)/Cl(-) exchange transporter ClcA;
72-200 6.42e-03

H(+)/Cl(-) exchange transporter ClcA;


Pssm-ID: 235385 [Multi-domain]  Cd Length: 438  Bit Score: 36.79  E-value: 6.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488432424  72 IMEISKEQQKQFNYRkneLFTIKLITFSFIFVFLgLFGIFVGELEGLEQNIY-----RIIWIFALF-LSLAIMYYFLNVF 145
Cdd:PRK05277 162 ILFVIEEMRPQFRYS---LISIKAVFIGVIMATI-VFRLFNGEQAVIEVGKFsapplNTLWLFLLLgIIFGIFGVLFNKL 237

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488432424 146 ISKKLDkkypmtigMKNRNRKNEpvkngwdfMARYWWIVFPIG---GFLSWLIPELTG 200
Cdd:PRK05277 238 LLRTQD--------LFDRLHGGN--------KKRWVLMGGAVGglcGLLGLLAPAAVG 279
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-72 2.59e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 65.40  E-value: 2.59e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488432424   5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNELFESISSSDKEEEI 72
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRrNPSLETLLKLAKALGVSLDELLGGADEELPEALL 79
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-61 2.34e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.17  E-value: 2.34e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488432424   3 KSKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNELFE 61
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKyNPSLELALKIARALGVSLEELFS 65
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-59 2.73e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.98  E-value: 2.73e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488432424     5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKrKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-59 7.23e-09

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: 50.24  E-value: 7.23e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488432424   4 SKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKrNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-59 7.62e-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: 49.85  E-value: 7.62e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 488432424    6 VAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKrEPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 7.35e-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: 7.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488432424   4 SKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNE 58
Cdd:COG1813   15 ERIREAREARGLSQEELAEKLGVSESTIRRIERGEaTPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-59 5.10e-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: 43.47  E-value: 5.10e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488432424   6 VAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE-EVSSETLKSVSNALDVTVNEL 59
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKrDPTVSTLEKIAEALGKELSAV 76
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-67 4.80e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 40.13  E-value: 4.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488432424   1 MNKSKVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE--EVSSETLKSVSNALDVTVNELFESISSSD 67
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKakAVRLDTLEKICKALDCQPGDLLEYVPDEE 69
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 8-60 5.04e-04

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: 37.09  E-value: 5.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488432424   8 EIRKQKSLTQENLAEKAYVTVRTIQRMEAG--EEVSSET-----LKSVSNALDVTVNELF 60
Cdd:COG1426   12 QAREAKGLSLEDVAERTKISVSYLEAIEEGdfDALPGPVyvrgfLRSYARALGLDPEELL 71
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-61 8.26e-04

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: 36.36  E-value: 8.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488432424    5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE--EVSSETLKSVSNALDVTVNELFE 61
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKpkRVSLDTLDKICDALGCQPGDLLE 59
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-38 1.37e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.07  E-value: 1.37e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 488432424   6 VAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGE 38
Cdd:COG2944   11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGR 43
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-54 1.78e-03

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: 35.33  E-value: 1.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 488432424   10 RKQKSLTQENLAEKAYVTVRTIQRMEAGEEvsSETLKSVSNALDV 54
Cdd:TIGR03070  11 RKALGLTQADLADLAGVGLRFIRDLENGKP--TVRLDKVLRVLDA 53
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-60 4.51e-03

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: 34.57  E-value: 4.51e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 488432424    5 KVAEIRKQKSLTQENLAEKAYVTVRTIQRMEAGEEV-SSETLKSVSNALDVTVNELF 60
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVpPAETLYKIAELLGVPANWLL 59
PRK05277 PRK05277
H(+)/Cl(-) exchange transporter ClcA;
72-200 6.42e-03

H(+)/Cl(-) exchange transporter ClcA;


Pssm-ID: 235385 [Multi-domain]  Cd Length: 438  Bit Score: 36.79  E-value: 6.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488432424  72 IMEISKEQQKQFNYRkneLFTIKLITFSFIFVFLgLFGIFVGELEGLEQNIY-----RIIWIFALF-LSLAIMYYFLNVF 145
Cdd:PRK05277 162 ILFVIEEMRPQFRYS---LISIKAVFIGVIMATI-VFRLFNGEQAVIEVGKFsapplNTLWLFLLLgIIFGIFGVLFNKL 237

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488432424 146 ISKKLDkkypmtigMKNRNRKNEpvkngwdfMARYWWIVFPIG---GFLSWLIPELTG 200
Cdd:PRK05277 238 LLRTQD--------LFDRLHGGN--------KKRWVLMGGAVGglcGLLGLLAPAAVG 279
 
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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