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Conserved domains on  [gi|1436568793|emb|STO00135|]
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Uncharacterised protein [Slackia exigua]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 1000092)

helix-turn-helix domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CitB super family cl34424
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 39-75 4.02e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


The actual alignment was detected with superfamily member COG2197:

Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 41.42  E-value: 4.02e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQEL 75
Cdd:COG2197    84 GLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTEL 120
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 39-75 4.02e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 41.42  E-value: 4.02e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQEL 75
Cdd:COG2197    84 GLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTEL 120
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 46-78 3.17e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 37.90  E-value: 3.17e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1436568793 46 AENLRIADNTVKYHCKSICRKPGVRSRQELFDL 78
Cdd:cd06170   22 ADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 39-79 6.09e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 37.12  E-value: 6.09e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQELFDLL 79
Cdd:smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE pfam00196
Bacterial regulatory proteins, luxR family;
46-78 1.91e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 35.64  E-value: 1.91e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1436568793 46 AENLRIADNTVKYHCKSICRKPGVRSRQELFDL 78
Cdd:pfam00196 24 ADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 10-74 2.03e-03

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 35.00  E-value: 2.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1436568793  10 AKTQQTDRSDRHATRRmrgEAEGGTLQRGGCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQE 74
Cdd:PRK10651  144 ANRATTERDVNQLTPR---ERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 39-75 4.02e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 41.42  E-value: 4.02e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQEL 75
Cdd:COG2197    84 GLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTEL 120
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
39-79 9.01e-06

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 41.28  E-value: 9.01e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQELFDLL 79
Cdd:COG2771   142 GLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALA 182
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
39-79 1.03e-05

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 41.23  E-value: 1.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQELFDLL 79
Cdd:COG2909   137 GLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARA 177
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 46-75 2.22e-05

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 38.40  E-value: 2.22e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 1436568793 46 AENLRIADNTVKYHCKSICRKPGVRSRQEL 75
Cdd:COG5905   34 ARQLFISEKTVKNHVSNILRKLGVRNRVQA 63
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 46-78 3.17e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 37.90  E-value: 3.17e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1436568793 46 AENLRIADNTVKYHCKSICRKPGVRSRQELFDL 78
Cdd:cd06170   22 ADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 39-79 6.09e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 37.12  E-value: 6.09e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1436568793  39 GCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQELFDLL 79
Cdd:smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE pfam00196
Bacterial regulatory proteins, luxR family;
46-78 1.91e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 35.64  E-value: 1.91e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1436568793 46 AENLRIADNTVKYHCKSICRKPGVRSRQELFDL 78
Cdd:pfam00196 24 ADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 10-74 2.03e-03

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 35.00  E-value: 2.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1436568793  10 AKTQQTDRSDRHATRRmrgEAEGGTLQRGGCSVPYAAENLRIADNTVKYHCKSICRKPGVRSRQE 74
Cdd:PRK10651  144 ANRATTERDVNQLTPR---ERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
 
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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