GapMind for Amino acid biosynthesis

 

L-proline biosynthesis in Tistlia consotensis USBA 355

Best path

proB, proA, proC

Rules

Overview: Proline biosynthesis in GapMind is based on MetaCyc pathways L-proline biosynthesis I from L-glutamate (link) and III via L-ornithine aminotransferase (link). GapMind also describes proline synthesis via ornithine cyclodeaminase (PMID:11489875). Pathway II from arginine (link) should perhaps be included, but is not; it is reported in nitrogen-fixing cyanobacteria and the bacteria it was reported in also have pathway I. Pathway IV is not included because it is not reported in prokaryotes (link). Also, pathway III is described in MetaCyc as occuring only in plants, but it has been reported in the archaeon Thermococcus kodakarensis (PMC5846162).

17 steps (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
proB glutamate 5-kinase B9O00_RS07355 B9O00_RS07360
proA gamma-glutamylphosphate reductase B9O00_RS07360
proC pyrroline-5-carboxylate reductase B9O00_RS18410
Alternative steps:
argA N-acylglutamate synthase B9O00_RS15030 B9O00_RS02295
argB N-acylglutamate kinase B9O00_RS02295
argC N-acylglutamylphosphate reductase B9O00_RS07225
argD N-acetylornithine aminotransferase B9O00_RS06850 B9O00_RS09970
argE N-acetylornithine deacetylase B9O00_RS00345 B9O00_RS06895
argJ ornithine acetyltransferase B9O00_RS15030
argX glutamate--LysW ligase
cyclodeaminase ornithine cyclodeaminase B9O00_RS02510 B9O00_RS15675
lysJ [LysW]-glutamate-semialdehyde aminotransferase B9O00_RS06850 B9O00_RS09970
lysK [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-glutamate-6-phosphate reductase
lysZ [LysW]-glutamate kinase B9O00_RS02295
OAT L-ornithine 5-aminotransferase B9O00_RS06850 B9O00_RS09970

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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