GapMind for Amino acid biosynthesis

 

L-proline biosynthesis in Pseudomonas fluorescens FW300-N2E3

Best path

argA, argB, argC, argD, argE, cyclodeaminase

Also see fitness data for the top candidates

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 also is reported in the archaeon Thermococcus kodakarensis (PMC5846162).

17 steps (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
argA N-acylglutamate synthase AO353_08685 AO353_03670
argB N-acylglutamate kinase AO353_09240 AO353_08685
argC N-acylglutamylphosphate reductase AO353_07155
argD N-acetylornithine aminotransferase AO353_03025 AO353_10500
argE N-acetylornithine deacetylase AO353_08690 AO353_29125
cyclodeaminase ornithine cyclodeaminase AO353_25185
Alternative steps:
argJ ornithine acetyltransferase AO353_03670
argX glutamate--LysW ligase AO353_11755
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase AO353_03025 AO353_15640
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysW 2-aminoadipate/glutamate carrier protein
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase AO353_07155
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase AO353_09240
OAT L-ornithine 5-aminotransferase AO353_15640 AO353_10500
proA gamma-glutamylphosphate reductase AO353_06495
proB glutamate 5-kinase AO353_14115 AO353_06495
proC pyrroline-5-carboxylate reductase AO353_08165

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:

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