L-histidine biosynthesis in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

L-histidine biosynthesis in Azospirillum brasilense Sp245

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).

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

11 steps (10 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate	Class of gap
prs	ribose-phosphate diphosphokinase	AZOBR_RS31185	AZOBR_RS06995
hisG	ATP phosphoribosyltransferase	AZOBR_RS19500
hisI	phosphoribosyl-ATP pyrophosphatase	AZOBR_RS01690	AZOBR_RS14500
hisE	phosphoribosyl-AMP cyclohydrolase	AZOBR_RS08645
hisA	isomerase HisA	AZOBR_RS01680	AZOBR_RS01685
hisF	IGP synthase, cyclase subunit	AZOBR_RS01685	AZOBR_RS01680
hisH	IGP synthase, amidotransferase subunit	AZOBR_RS01670
hisB	IGP dehydratase	AZOBR_RS01665
hisC	histidinol-phosphate aminotransferase	AZOBR_RS20485	AZOBR_RS08675
hisN	histidinol-phosphate phosphatase	AZOBR_RS03845	AZOBR_RS01665
hisD ?	histidinol dehydrogenase			spurious

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis