GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Phaeobacter inhibens BS107

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
prs ribose-phosphate diphosphokinase PGA1_c25050
hisG ATP phosphoribosyltransferase PGA1_c29870
hisI phosphoribosyl-ATP pyrophosphatase PGA1_c09230 PGA1_c31190
hisE phosphoribosyl-AMP cyclohydrolase PGA1_c14400 PGA1_c31190
hisA isomerase HisA PGA1_c09270 PGA1_c17910
hisF IGP synthase, cyclase subunit PGA1_c09240 PGA1_c09270
hisH IGP synthase, amidotransferase subunit PGA1_c09320
hisB IGP dehydratase PGA1_c09330
hisC histidinol-phosphate aminotransferase PGA1_c25240 PGA1_c23930
hisN histidinol-phosphate phosphatase PGA1_c21860 PGA1_c23320
hisD histidinol dehydrogenase PGA1_c31190 PGA1_c07750

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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, the preprint on GapMind for carbon sources, 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