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Conserved domains on  [gi|490298487|ref|WP_004193926|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Burkholderia]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12807598)

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; also contains a DUF4115 domain; similar to cytoskeleton protein RodZ, an inner membrane protein which functions in cell-shape control through regulation of the length of the long axis

CATH:  1.10.260.40
Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 7-72 3.39e-21

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: 85.63  E-value: 3.39e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490298487   7 VGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPGTTFALGLVRSYAKMLGVDPEPFA 72
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 261-329 1.27e-17

Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.


:

Pssm-ID: 433229 [Multi-domain]  Cd Length: 67  Bit Score: 76.07  E-value: 1.27e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490298487  261 LKVAQDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPVDPAKYstARGN 329
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVE-VSVNGKPVDLLGY--ARGN 67
PRK10856 super family cl35960
cytoskeleton protein RodZ;
159-336 4.67e-11

cytoskeleton protein RodZ;


The actual alignment was detected with superfamily member PRK10856:

Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 63.12  E-value: 4.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 159 QQEGAASDLPASAAVSGTVMQAGALAASATQSVGGASAGDTAAASVPAAGAAPVVASAAAALSASAPVAAAQPAQGAQQP 238
Cdd:PRK10856 156 QNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAA 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 239 AASAADGASAAVTAAPGQSVVALKVaqDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPV 318
Cdd:PRK10856 236 PLPTDQAGVSTPAADPNALVMNFTA--DCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPAAVQ-IQYQGKPV 312

                        170
                 ....*....|....*...
gi 490298487 319 DPAKYSTArGNVARFALP 336
Cdd:PRK10856 313 DLSRFIRT-NQVARLTLN 329
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 7-72 3.39e-21

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: 85.63  E-value: 3.39e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490298487   7 VGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPGTTFALGLVRSYAKMLGVDPEPFA 72
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 10-71 7.06e-21

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: 84.47  E-value: 7.06e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490298487   10 RLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPGTTFALGLVRSYAKMLGVDPEPF 71
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 261-329 1.27e-17

Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.


Pssm-ID: 433229 [Multi-domain]  Cd Length: 67  Bit Score: 76.07  E-value: 1.27e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490298487  261 LKVAQDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPVDPAKYstARGN 329
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVE-VSVNGKPVDLLGY--ARGN 67
PRK10856 PRK10856
cytoskeleton protein RodZ;
159-336 4.67e-11

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 63.12  E-value: 4.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 159 QQEGAASDLPASAAVSGTVMQAGALAASATQSVGGASAGDTAAASVPAAGAAPVVASAAAALSASAPVAAAQPAQGAQQP 238
Cdd:PRK10856 156 QNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAA 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 239 AASAADGASAAVTAAPGQSVVALKVaqDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPV 318
Cdd:PRK10856 236 PLPTDQAGVSTPAADPNALVMNFTA--DCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPAAVQ-IQYQGKPV 312

                        170
                 ....*....|....*...
gi 490298487 319 DPAKYSTArGNVARFALP 336
Cdd:PRK10856 313 DLSRFIRT-NQVARLTLN 329
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-69 4.35e-05

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: 40.61  E-value: 4.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490298487   8 GARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSqlpgttFALGLVRSYAKMLGVDPE 69
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN------PSLETLEKLAKALGVSLD 56
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-69 2.52e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.27  E-value: 2.52e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487    10 RLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSqlpgttFALGLVRSYAKMLGVDPE 69
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK------PSLETLKKLAKALGVSLD 54
 
Name Accession Description Interval E-value
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 7-72 3.39e-21

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: 85.63  E-value: 3.39e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490298487   7 VGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPGTTFALGLVRSYAKMLGVDPEPFA 72
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGFLRSYARALGLDPEELL 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 10-71 7.06e-21

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: 84.47  E-value: 7.06e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490298487   10 RLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPGTTFALGLVRSYAKMLGVDPEPF 71
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDDFDALPEPVYARGFLRSYARALGLDPEEL 62
DUF4115 pfam13464
Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of ...
 261-329 1.27e-17

Domain of unknown function (DUF4115); This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.


Pssm-ID: 433229 [Multi-domain]  Cd Length: 67  Bit Score: 76.07  E-value: 1.27e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490298487  261 LKVAQDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPVDPAKYstARGN 329
Cdd:pfam13464   2 LTFTGDSWVEVRDADGKVLFEGLLKAGETRTVTGKPPLTLVLGNAGAVE-VSVNGKPVDLLGY--ARGN 67
PRK10856 PRK10856
cytoskeleton protein RodZ;
159-336 4.67e-11

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 63.12  E-value: 4.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 159 QQEGAASDLPASAAVSGTVMQAGALAASATQSVGGASAGDTAAASVPAAGAAPVVASAAAALSASAPVAAAQPAQGAQQP 238
Cdd:PRK10856 156 QNSGQSVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAA 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487 239 AASAADGASAAVTAAPGQSVVALKVaqDCWFSVRDKNGKELFSALVRAGETRQVAGDAPLKVTIGNKAGLEsVAFDGKPV 318
Cdd:PRK10856 236 PLPTDQAGVSTPAADPNALVMNFTA--DCWLEVTDATGKKLFSGMQRKGGNLNLTGQAPYKLKIGAPAAVQ-IQYQGKPV 312

                        170
                 ....*....|....*...
gi 490298487 319 DPAKYSTArGNVARFALP 336
Cdd:PRK10856 313 DLSRFIRT-NQVARLTLN 329
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-69 3.94e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 41.52  E-value: 3.94e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487   1 MASVA-AVGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSqlPGttfaLGLVRSYAKMLGVDPE 69
Cdd:COG1396    1 MSTLKkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRN--PS----LETLLKLAKALGVSLD 64
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-69 4.35e-05

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: 40.61  E-value: 4.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490298487   8 GARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSqlpgttFALGLVRSYAKMLGVDPE 69
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN------PSLETLEKLAKALGVSLD 56
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-69 1.41e-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: 39.43  E-value: 1.41e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490298487    6 AVGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSQLPgttfaLGLVRSYAKMLGVDPE 69
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPS-----PAVVERLARALGVDGA 59
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 8-73 1.96e-04

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: 38.81  E-value: 1.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490298487    8 GARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDtsqlpgTTFALGLVRSYAKMLGVDPEPFAQ 73
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGK------SVPPAETLYKIAELLGVPANWLLQ 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-69 2.52e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.27  E-value: 2.52e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490298487    10 RLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTSqlpgttFALGLVRSYAKMLGVDPE 69
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK------PSLETLKKLAKALGVSLD 54
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-67 3.81e-04

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: 38.38  E-value: 3.81e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490298487   4 VAAVGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDTsqLPGttfaLGLVRSYAKMLGVD 67
Cdd:COG1813   10 VEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEA--TPS----LDTLRKLEKALGIS 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
7-69 6.19e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.82  E-value: 6.19e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490298487   7 VGARLAELRRTKGWSVDDVSARLKVAAPKLQALEAGDtsqlpgTTFALGLVRSYAKMLGVDPE 69
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGK------YNPSLELALKIARALGVSLE 61
 
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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