L-arginine biosynthesis

GapMind for Amino acid biosynthesis

L-arginine biosynthesis

Analysis of pathway arg in 35 genomes

Genome	Best path
Acidovorax sp. GW101-3H11	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Azospirillum brasilense Sp245	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Bacteroides thetaiotaomicron VPI-5482	argA, argB, argC, argD'B, argF'B, argE'B, argG, argH
Burkholderia phytofirmans PsJN	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Caulobacter crescentus NA1000	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Cupriavidus basilensis 4G11	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Dechlorosoma suillum PS	argJ, argB, argC, argD, carA, carB, argI, argG, argH
Desulfovibrio vulgaris Hildenborough	argJ, argB, argC, argD, carA, carB, argI, argG, argH
Desulfovibrio vulgaris Miyazaki F	argJ, argB, argC, argD, carA, carB, argI, argG, argH
Dinoroseobacter shibae DFL-12	argJ, argB, argC, argD, carA, carB, argI, argG, argH
Dyella japonica UNC79MFTsu3.2	argA, argB, argC, argD, carA, carB, argF', argE, argG, argH
Echinicola vietnamensis KMM 6221, DSM 17526	argA, argB, argC, argD'B, argF'B, argE'B, argG, argH
Escherichia coli BW25113	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Herbaspirillum seropedicae SmR1	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Klebsiella michiganensis M5al	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Magnetospirillum magneticum AMB-1	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Marinobacter adhaerens HP15	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Paraburkholderia bryophila 376MFSha3.1	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pedobacter sp. GW460-11-11-14-LB5	argA, argB, argC, argD'B, argF'B, argE'B, argG, argH
Phaeobacter inhibens BS107	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas fluorescens FW300-N1B4	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas fluorescens FW300-N2C3	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas fluorescens FW300-N2E2	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas fluorescens FW300-N2E3	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas fluorescens GW456-L13	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas putida KT2440	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas simiae WCS417	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Pseudomonas stutzeri RCH2	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Shewanella amazonensis SB2B	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Shewanella loihica PV-4	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Shewanella oneidensis MR-1	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Shewanella sp. ANA-3	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Sinorhizobium meliloti 1021	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Sphingomonas koreensis DSMZ 15582	argA, argB, argC, argD, argE, carA, carB, argI, argG, argH
Synechococcus elongatus PCC 7942	argJ, argB, argC, argD, carA, carB, argI, argG, argH

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

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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:

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
the source code
instructions for running GapMind on your computer
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