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Conserved domains on  [gi|1241130375|gb|ASZ73081|]
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hypothetical protein SEA_GERALT_87 [Mycobacterium phage Geralt]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10578545)

helix-turn-helix (HTH) domain-containing protein may function in DNA binding; similar to excisionase

CATH:  1.10.1660.10
Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 15-48 9.53e-06

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


:

Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 38.60  E-value: 9.53e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 1241130375 15 LVTAAEAAALCGVTTSTIYVWVNRGTLAPSGKNR 48
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGR 34
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 15-48 9.53e-06

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 38.60  E-value: 9.53e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 1241130375 15 LVTAAEAAALCGVTTSTIYVWVNRGTLAPSGKNR 48
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGR 34
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
20-61 2.81e-05

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 38.35  E-value: 2.81e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1241130375  20 EAAALCGVTTSTIYVWVNRGTLAPSGKNRTGHNVYRVLDVAK 61
Cdd:COG0789     3 EVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVER 44
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 17-65 8.64e-04

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 34.65  E-value: 8.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1241130375  17 TAAEAAALCGVTTSTIYVWVNRGTLAPSGKNRTGHNVYRVLDVAKAEYA 65
Cdd:cd04773     2 TIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLI 50
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 15-48 9.53e-06

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 38.60  E-value: 9.53e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 1241130375 15 LVTAAEAAALCGVTTSTIYVWVNRGTLAPSGKNR 48
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGR 34
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
20-61 2.81e-05

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 38.35  E-value: 2.81e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1241130375  20 EAAALCGVTTSTIYVWVNRGTLAPSGKNRTGHNVYRVLDVAK 61
Cdd:COG0789     3 EVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVER 44
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
13-41 8.44e-05

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 36.45  E-value: 8.44e-05
                         10        20
                 ....*....|....*....|....*....
gi 1241130375 13 DTLVTAAEAAALCGVTTSTIYVWVNRGTL 41
Cdd:COG3311    6 DRLLRLKEVAELLGVSRSTIYRLIKKGEF 34
MerR_1 pfam13411
MerR HTH family regulatory protein;
17-60 1.86e-04

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 35.61  E-value: 1.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 1241130375 17 TAAEAAALCGVTTSTIYVWVNRGTLAPSgKNRTGHNVYRVLDVA 60
Cdd:pfam13411  2 TISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVE 44
MerR pfam00376
MerR family regulatory protein;
17-54 2.99e-04

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 34.32  E-value: 2.99e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1241130375 17 TAAEAAALCGVTTSTIYVWVNRGTLAPSGKNRTGHNVY 54
Cdd:pfam00376  1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
HTH_TioE_rpt2 cd04773
Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative ...
 17-65 8.64e-04

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.


Pssm-ID: 133400  Cd Length: 108  Bit Score: 34.65  E-value: 8.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1241130375  17 TAAEAAALCGVTTSTIYVWVNRGTLAPSGKNRTGHNVYRVLDVAKAEYA 65
Cdd:cd04773     2 TIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLI 50
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 16-61 5.64e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 31.40  E-value: 5.64e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1241130375 16 VTAAEAAALCGVTTSTIYVWVNRGTLaPSGKNRTGHNVYRVLDVAK 61
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKL-KAIRTPGGHRRFPEEDLER 45
 
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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