GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Dinoroseobacter shibae DFL-12

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 Dshi_2931
hisG ATP phosphoribosyltransferase Dshi_2953
hisI phosphoribosyl-ATP pyrophosphatase Dshi_2575 Dshi_0979
hisE phosphoribosyl-AMP cyclohydrolase Dshi_1515 Dshi_0979
hisA isomerase HisA Dshi_2578 Dshi_2576
hisF IGP synthase, cyclase subunit Dshi_2576 Dshi_2578
hisH IGP synthase, amidotransferase subunit Dshi_0795
hisB IGP dehydratase Dshi_0794
hisC histidinol-phosphate aminotransferase Dshi_2946 Dshi_2088
hisN histidinol-phosphate phosphatase Dshi_2774 Dshi_0794
hisD histidinol dehydrogenase Dshi_0979 Dshi_2034

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