The eight amino acids lining the putative binding pocket of EntF are: DVWHFSLV
Hint: The Glycine highlighted in blue is highly conserved, and can be used to confirmed the alignment. Often two Glycine residues are present and the second one is the conserved one, the first one being the sixth residue lining the binding pocket.
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There are two databases
to choose from:
The "Assigned
Database" consist of the eight amino acids lining the binding pocket
of 198 adenylation domains where the substrate has been proven experimentally.
The "Unassigned Database" consist of the eight amino acids lining the binding pocket of 88 adenylation domains where the substrate has NOT been proven experimentally.
In the definition line, you'll find the gi and genbank number followed by the name of the gene-the module number in the gene-the amino acid activated (represented by the three-letter code).
Example: >gi|4481934|emb|CAB38518.1|Cda1-M5-Asp|CDA peptide synthetase I
CDA peptide synthetase I, Module 5 in the gene, and activated Aspartate (Asp)
The gene name codes are as follows:
Abbreviations for the protein names are as follows: Acm, actinomycin synthetase; Acv, ACV synthetase (Aspergillus nidulans); AngR, anguibactin synthetase; Bac, bacitracin synthetases; Cda, calcium-dependent anitbiotic; Cep, chloroeremomycin synthetases; Cpps, Claviceps purpurea peptide synthetase; CssA, cyclosporin synthetase; Dhb, 2,-3-dihydroxy-benzoylglycine synthetase; DltA, D-alanine-teichoic acid synthetase (B. subtilis); DaeA, D-alanine-teichoic acid synthetase (Lactobacillus casei); Epo, epothilone synthetase; Esyn1; enniatin synthetase; EntF, enterobactin synthetase; Fxb, exochelin synthetases; Glg1, D-alanine-teichoic acid synthetase (Streptococcus mutans); Grs, gramicidin synthetases; Irp2, yersiniabactin synthetase; Lmb, lyncomycin synthetase; Nos, Nostopeptolide synthetase; Pps and Fen, fengycin synthetases; FkbP, FK506 synthetase; Hts1, HC-toxin synthetase; LchA, lichenysin A synthetases; Lic, lichenysin D synthetases; Mcy, microcystin synthetase, Mbt, mycobactin synthetases; Myc, mycosubtilin synthetase; PcbAB, ACV synthetase (Nocardia lactamdurans); Pch; pyochelin synthetases; PvdD, pyoverdin synthetase; RapP, rapamycin synthetase; Saf, saframycin synthetases; Snb, pristinamycin/virginiamycin synthetase; SrfA, surfactin A synthetases; Syr, synringomycin synthetases; Tyc, tyrocidine synthetases;
Activated amino acids are represented by the three-letter amino acid code. Modified amino acids are indicated by the use of prefixes: Me: N-methylation; D: D-configuration; xh: hydroxylation at position x relative to the a-carbon atom, xf(a): formylation (acylation) at position x relative to the a-carbon atom. Bmt: (4R)-4-[(E)-2-butenyl]-4-methyl-L-threonine, 3h4mPhe: 3-hydroxy-4-methoxy-L-phenylalanine, Pip: L-pipecolic acid, 4pPro: 4 propyl-L-proline, Orn: L-Ornithine, PGly: L-phenylglycine, HPG: 4-hydroxy-L-phenylglycine, DHPG: 3,5-hydroxy-L-phenylglycine.