GapMind for catabolism of small carbon sources


L-alanine catabolism

Analysis of pathway alanine in 35 genomes

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

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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