GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis in Desulfovibrio vulgaris Hildenborough

Best path

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

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 Class of gap
prs ribose-phosphate diphosphokinase DVU1575  
hisG ATP phosphoribosyltransferase DVU0114  
hisI phosphoribosyl-ATP pyrophosphatase DVU1186 DVU0796  
hisE phosphoribosyl-AMP cyclohydrolase DVU0113 DVU0796  
hisA isomerase HisA DVU1038  
hisF IGP synthase, cyclase subunit DVU0286  
hisH IGP synthase, amidotransferase subunit DVU0285  
hisB IGP dehydratase DVU1040  
hisC histidinol-phosphate aminotransferase DVU1029 DVU0392  
hisN? histidinol-phosphate phosphatase DVU2490 DVU1040 diverged
hisD histidinol dehydrogenase DVU0796  

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 Mar 30 2021. The underlying query database was built on Mar 30 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