Summary: Rv0623-like transcription factor
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Rv0623-like transcription factor Provide feedback
Anantharaman V, Aravind L; , Genome Biol 2003;4:R81.: New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. PUBMED:14659018 EPMC:14659018
External database links
- 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:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Author:||Anantharaman V, Aravind L, Studholme DJ|
|Number in seed:||29|
|Number in full:||347|
|Average length of the domain:||81.60 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||96.75 %|
|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:||6|
|Download:||download the raw HMM for this family|
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