Summary: ECF-type riboflavin transporter, S component
ECF-type riboflavin transporter, S component Provide feedback
This family is the substrate-binding component (S component) of the energy coupling-factor (ECF)-type riboflavin transporter. It is a transmembrane protein which binds riboflavin, and is responsible for riboflavin-uptake by cells [1,2].
Vogl C, Grill S, Schilling O, Stulke J, Mack M, Stolz J;, J Bacteriol. 2007;189:7367-7375.: Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. PUBMED:17693491 EPMC:17693491
Internal database links
|SCOOP:||Hpre_diP_synt_I 5TM-5TMR_LYT ThiW Thia_YuaJ DUF3816 DUF4257|
|Similarity to PfamA using HHSearch:||CbiM QueT ThiW Thia_YuaJ DUF3816|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR009825
This family consists of several bacterial proteins of around 180 residues in length that appear to be multi-pass membrane proteins. Many family members are functionally uncharacterised. Others appear to be substrate specific components of an energy-coupling factor (ECF) type transport system.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
- 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
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This superfamily includes a wide range of transporters that contain many conserved glycine residues in the presumed transmembrane regions.
The clan contains the following 11 members:5TM-5TMR_LYT BioY CbiM DUF3816 ECF-ribofla_trS Hpre_diP_synt_I MreD QueT Thia_YuaJ ThiW TrpP
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
|Seed source:||Pfam-B_16301 (release 10.0)|
|Author:||Moxon SJ, Eberhardt R|
|Number in seed:||49|
|Number in full:||10204|
|Average length of the domain:||163.70 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||89.99 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ECF-ribofla_trS domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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