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Conserved domains on  [gi|1277125595|gb|PIR27587|]
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hypothetical protein COV40_00060 [Candidatus Berkelbacteria bacterium CG11_big_fil_rev_8_21_14_0_20_42_15]

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_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 14-81 1.77e-04

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member TIGR02531:

Pssm-ID: 481199  Cd Length: 87  Bit Score: 37.02  E-value: 1.77e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277125595 14 DQESKKLFLETLNKITGDEFADLFESLLSSSEFKDISRRLMAAKLLHQKVTYEEAQEIMGMGSNTVNK 81
Cdd:TIGR02531  2 GELLDELFDAILTLKNREECYRFFDDICTINEIQSLAQRLQVAKMLKQGKTYSDIEAETGASTATISR 69
 
Name Accession Description Interval E-value
yecD_yerC TIGR02531
TrpR-related protein YerC/YecD; This model represents a protein subfamily found mostly in the ...
 14-81 1.77e-04

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: 37.02  E-value: 1.77e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277125595 14 DQESKKLFLETLNKITGDEFADLFESLLSSSEFKDISRRLMAAKLLHQKVTYEEAQEIMGMGSNTVNK 81
Cdd:TIGR02531  2 GELLDELFDAILTLKNREECYRFFDDICTINEIQSLAQRLQVAKMLKQGKTYSDIEAETGASTATISR 69
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 28-81 2.50e-03

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: 35.21  E-value: 2.50e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277125595  28 ITGDEFADLfESLLSSSEFKDISRRLMAAKLLHQKVTYEEAQEIMGMGSNTVNK 81
Cdd:COG3415     5 LTEEERRDL-EKLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYR 57
 
Name Accession Description Interval E-value
yecD_yerC TIGR02531
TrpR-related protein YerC/YecD; This model represents a protein subfamily found mostly in the ...
 14-81 1.77e-04

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: 37.02  E-value: 1.77e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277125595 14 DQESKKLFLETLNKITGDEFADLFESLLSSSEFKDISRRLMAAKLLHQKVTYEEAQEIMGMGSNTVNK 81
Cdd:TIGR02531  2 GELLDELFDAILTLKNREECYRFFDDICTINEIQSLAQRLQVAKMLKQGKTYSDIEAETGASTATISR 69
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 28-81 2.50e-03

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: 35.21  E-value: 2.50e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1277125595  28 ITGDEFADLfESLLSSSEFKDISRRLMAAKLLHQKVTYEEAQEIMGMGSNTVNK 81
Cdd:COG3415     5 LTEEERRDL-EKLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYR 57
 
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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