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Conserved domains on  [gi|2197122857|ref|WP_239041072|]
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Trp family transcriptional regulator [Marinobacterium sediminicola]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 229396)

helix-turn-helix domain-containing protein may bind DNA and be involved in the regulation of gene expression

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARSR super family cl46857
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 5-76 5.49e-19

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


The actual alignment was detected with superfamily member pfam01371:

Pssm-ID: 481197  Cd Length: 86  Bit Score: 73.44  E-value: 5.49e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2197122857  5 HLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRM-LEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:pfam01371  2 AWDALFEAILKLENQEECYAFLDDLLTPDEREALAQRLQVAKMlLRGELTQREIAQELGASIATITRGSRCLK 74
 
Name Accession Description Interval E-value
Trp_repressor pfam01371
Trp repressor protein; This protein binds to tryptophan and represses transcription of the Trp ...
 5-76 5.49e-19

Trp repressor protein; This protein binds to tryptophan and represses transcription of the Trp operon.


Pssm-ID: 426227  Cd Length: 86  Bit Score: 73.44  E-value: 5.49e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2197122857  5 HLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRM-LEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:pfam01371  2 AWDALFEAILKLENQEECYAFLDDLLTPDEREALAQRLQVAKMlLRGELTQREIAQELGASIATITRGSRCLK 74
YerC COG4496
Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General ...
 2-76 4.00e-18

Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General function prediction only];


Pssm-ID: 443584  Cd Length: 92  Bit Score: 71.34  E-value: 4.00e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2197122857  2 NTTHLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRMLEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:COG4496    6 KDEALDQLFEAILSLKDPEECYAFLEDLCTPAELKALAQRLEVARLLREGKTYREIAEETGASTATISRVKRCLN 80
TrpR TIGR01321
trp operon repressor, proteobacterial; This model represents TrpR, the repressor of the trp ...
 7-76 4.31e-11

trp operon repressor, proteobacterial; This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis. [Amino acid biosynthesis, Aromatic amino acid family, Regulatory functions, DNA interactions]


Pssm-ID: 130388  Cd Length: 94  Bit Score: 53.67  E-value: 4.31e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2197122857  7 NELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILR-MLEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:TIGR01321 10 EAFLKLLKKADSEDDMQLLLELILTRSEREDLGDRIRIVNeLLNGNMSQREIASKLGVSIATITRGSNNLK 80
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 30-70 9.19e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 36.15  E-value: 9.19e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 2197122857 30 LTPAELTEvcnrlqILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:cd00569    6 LTPEQIAE------ARRLLAAGESVAEIARELGVSRSTLYR 40
transpos_IS630 NF033545
IS630 family transposase;
41-70 9.20e-05

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 38.78  E-value: 9.20e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 2197122857  41 RLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:NF033545    2 RARILLLAAEGLSITEIAERLGVSRSTVYR 31
 
Name Accession Description Interval E-value
Trp_repressor pfam01371
Trp repressor protein; This protein binds to tryptophan and represses transcription of the Trp ...
 5-76 5.49e-19

Trp repressor protein; This protein binds to tryptophan and represses transcription of the Trp operon.


Pssm-ID: 426227  Cd Length: 86  Bit Score: 73.44  E-value: 5.49e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2197122857  5 HLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRM-LEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:pfam01371  2 AWDALFEAILKLENQEECYAFLDDLLTPDEREALAQRLQVAKMlLRGELTQREIAQELGASIATITRGSRCLK 74
YerC COG4496
Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General ...
 2-76 4.00e-18

Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General function prediction only];


Pssm-ID: 443584  Cd Length: 92  Bit Score: 71.34  E-value: 4.00e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2197122857  2 NTTHLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRMLEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:COG4496    6 KDEALDQLFEAILSLKDPEECYAFLEDLCTPAELKALAQRLEVARLLREGKTYREIAEETGASTATISRVKRCLN 80
TrpR COG2973
Trp operon repressor [Transcription];
1-78 7.22e-18

Trp operon repressor [Transcription];


Pssm-ID: 442212  Cd Length: 99  Bit Score: 71.04  E-value: 7.22e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2197122857  1 MNTTHLNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRMLEAG-VPQREIAKQLGVGIATVTRGARALKIK 78
Cdd:COG2973    5 REEEDWQQFVELLQQAFDEDDLQPLLQLLLTPDEREALGTRVRIVKELLRGeMSQREIAQELGVSIATITRGSNSLKTA 83
TrpR TIGR01321
trp operon repressor, proteobacterial; This model represents TrpR, the repressor of the trp ...
 7-76 4.31e-11

trp operon repressor, proteobacterial; This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis. [Amino acid biosynthesis, Aromatic amino acid family, Regulatory functions, DNA interactions]


Pssm-ID: 130388  Cd Length: 94  Bit Score: 53.67  E-value: 4.31e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2197122857  7 NELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILR-MLEAGVPQREIAKQLGVGIATVTRGARALK 76
Cdd:TIGR01321 10 EAFLKLLKKADSEDDMQLLLELILTRSEREDLGDRIRIVNeLLNGNMSQREIASKLGVSIATITRGSNNLK 80
yecD_yerC TIGR02531
TrpR-related protein YerC/YecD; This model represents a protein subfamily found mostly in the ...
 6-75 2.85e-06

TrpR-related protein YerC/YecD; This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence. [Unknown function, General]


Pssm-ID: 188231  Cd Length: 87  Bit Score: 41.26  E-value: 2.85e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2197122857  6 LNELLDHLLEMQNRDSLEEALRDLLTPAELTEVCNRLQILRMLEAGVPQREIAKQLGVGIATVTRGARAL 75
Cdd:TIGR02531  5 LDELFDAILTLKNREECYRFFDDICTINEIQSLAQRLQVAKMLKQGKTYSDIEAETGASTATISRVKRCL 74
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 20-70 2.37e-05

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 40.61  E-value: 2.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2197122857  20 DSLEEALRDLLTPAELTEVCNRLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:COG3415     7 EEERRDLEKLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYR 57
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 30-70 9.19e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 36.15  E-value: 9.19e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 2197122857 30 LTPAELTEvcnrlqILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:cd00569    6 LTPEQIAE------ARRLLAAGESVAEIARELGVSRSTLYR 40
transpos_IS630 NF033545
IS630 family transposase;
41-70 9.20e-05

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 38.78  E-value: 9.20e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 2197122857  41 RLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:NF033545    2 RARILLLAAEGLSITEIAERLGVSRSTVYR 31
HTH_23 pfam13384
Homeodomain-like domain;
41-70 2.48e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.32  E-value: 2.48e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 2197122857 41 RLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:pfam13384  7 RARALLLLAEGLSVKEIAELLGVSRRTVYR 36
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 9-68 3.20e-04

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: 36.41  E-value: 3.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2197122857   9 LLDhlLEMQNRDSLEeALRDLLTPAELtevcnrlQILRMLEAGVPQREIAKQLGVGIATV 68
Cdd:COG2197    52 LLD--IRMPGMDGLE-ALRRLLTPRER-------EVLRLLAEGLSNKEIAERLGISERTV 101
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
43-70 4.85e-04

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 36.74  E-value: 4.85e-04
                          10        20
                  ....*....|....*....|....*...
gi 2197122857  43 QILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:COG4584     9 EIRRLLREGLSIREIARELGISRNTVRK 36
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
41-70 1.67e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 35.23  E-value: 1.67e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 2197122857  41 RLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:COG3677    65 WLQAIRLLLNGISLRQIARVLGVSYKTVWR 94
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 30-70 2.76e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 32.48  E-value: 2.76e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 2197122857 30 LTPAEltevcnRLQILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:pfam13936  5 LSLEE------REEIARLLAEGLSLREIARRLGRSPSTISR 39
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 41-75 3.77e-03

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 34.31  E-value: 3.77e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2197122857  41 RLQILRMLEaGVPQREIAKQLGVGIATVTRGARAL 75
Cdd:pfam15978 190 RLKILVEDE-GLSLREIAKELGVDIKTVKRYARKL 223
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
43-70 5.45e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 31.94  E-value: 5.45e-03
                         10        20
                 ....*....|....*....|....*...
gi 2197122857 43 QILRMLEAGVPQREIAKQLGVGIATVTR 70
Cdd:pfam02796 13 EVITLLEEGISIKQIAKIFGISRSTVYR 40
 
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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