GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Pseudomonas fluorescens FW300-N1B4

Best path

prs?, hisG, hisI, hisE, hisA, hisF, hisH, hisB, hisC, hisN, hisD

Also see fitness data for the top candidates

Rules

Overview: Histidine biosynthesis in GapMind is based on the MetaCyc pathway (link).

11 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
prs? ribose-phosphate diphosphokinase spurious
hisG ATP phosphoribosyltransferase Pf1N1B4_1067  
hisI phosphoribosyl-ATP pyrophosphatase Pf1N1B4_1566 Pf1N1B4_1066  
hisE phosphoribosyl-AMP cyclohydrolase Pf1N1B4_1565 Pf1N1B4_1066  
hisA isomerase HisA Pf1N1B4_1624 Pf1N1B4_1623  
hisF IGP synthase, cyclase subunit Pf1N1B4_1623 Pf1N1B4_1624  
hisH IGP synthase, amidotransferase subunit Pf1N1B4_1626  
hisB IGP dehydratase Pf1N1B4_1627  
hisC histidinol-phosphate aminotransferase Pf1N1B4_1065 Pf1N1B4_349  
hisN histidinol-phosphate phosphatase Pf1N1B4_2282 Pf1N1B4_3743  
hisD histidinol dehydrogenase Pf1N1B4_1066  

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory