Summary: Ribbon-helix-helix domain
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Ribbon-helix-helix domain Provide feedback
This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding.
Internal database links
|Similarity to PfamA using HHSearch:||RHH_1 CcdA|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This superfamily contains the MetJ and Arc repressors that feature a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA .
The clan contains the following 21 members:Arc CcdA DUF1662 DUF1778 DUF2191 DUF2610 DUF3423 DUF3924 HicB MetJ Omega_Repress ParD ParG PSK_trans_fac RelB RepB-RCR_reg RHH_1 RHH_2 RHH_3 RHH_4 TraY
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||28|
|Number in full:||354|
|Average length of the domain:||42.50 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||41.58 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
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The tree shows the occurrence of this domain across different species. More...
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