Summary: Siderophore-interacting FAD-binding domain
Siderophore-interacting FAD-binding domain Provide feedback
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Butterton JR, Calderwood SB; , J Bacteriol 1994;176:5631-5638.: Identification, cloning, and sequencing of a gene required for ferric vibriobactin utilization by Vibrio cholerae. PUBMED:8083157 EPMC:8083157
Internal database links
|Similarity to PfamA using HHSearch:||FAD_binding_6|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013113
Proteins in this entry are siderophore-interacting FAD-binding proteins.
This entry includes the vibriobactin utilization protein ViuB, which is involved in the removal of iron from iron-vibriobactin complexes, as well as several hypothetical proteins.
- 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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Riboflavin nucleotide coenzymes and flavin adenine dinucleotide (FAD) are essential cofactors for a large number of flavoproteins involved in a diverse set of redox reactions. There are thought to be four different FAD-binding folds .The FAD-binding fold of this clan is a cylindrical beta-fold. More specifically, the domain forms a flattened six-stranded antiparallel beta-barrel organised into two orthogonal sheets (1-2-5 and 4-3-6) separated by one alpha-helix. The cylinder is open between strands strand 4 and 5. This opening of the cylinder makes space for the isoalloxazine and ribityl moieties of the FAD, to which hydrogen bonds are formed from the open edges of the strands. The other end of the cylinder is covered by the only helix of the domain, which is essential for the binding of the pyrophosphate groups of the FAD .The structural differences in the FAD-binding domain are manifested mainly as loops of different length and extra extending structural elements, which may be important for interactions with their redox partners . The structural core of all clan members is highly conserved.
The clan contains the following 5 members:FAD_binding_1 FAD_binding_6 FAD_binding_8 FAD_binding_9 Lum_binding
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||40|
|Number in full:||1962|
|Average length of the domain:||109.60 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||37.53 %|
|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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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 FAD_binding_9 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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