GapMind for catabolism of small carbon sources

 

D-alanine catabolism

Analysis of pathway D-alanine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 cycA, dadA
Azospirillum brasilense Sp245 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Bacteroides thetaiotaomicron VPI-5482 cycA, dadA
Burkholderia phytofirmans PsJN mctP, dadA
Caulobacter crescentus NA1000 cycA, dadA
Cupriavidus basilensis 4G11 cycA, dadA
Dechlorosoma suillum PS cycA, dadA
Desulfovibrio vulgaris Hildenborough cycA, dadA
Desulfovibrio vulgaris Miyazaki F cycA, dadA
Dinoroseobacter shibae DFL-12 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Dyella japonica UNC79MFTsu3.2 cycA, dadA
Echinicola vietnamensis KMM 6221, DSM 17526 cycA, dadA
Escherichia coli BW25113 cycA, dadA
Herbaspirillum seropedicae SmR1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Klebsiella michiganensis M5al cycA, dadA
Magnetospirillum magneticum AMB-1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Marinobacter adhaerens HP15 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Paraburkholderia bryophila 376MFSha3.1 mctP, dadA
Pedobacter sp. GW460-11-11-14-LB5 cycA, dadA
Phaeobacter inhibens BS107 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas fluorescens FW300-N1B4 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas fluorescens FW300-N2C3 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas fluorescens FW300-N2E2 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas fluorescens FW300-N2E3 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas fluorescens GW456-L13 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas putida KT2440 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas simiae WCS417 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Pseudomonas stutzeri RCH2 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA
Shewanella amazonensis SB2B cycA, dadA
Shewanella loihica PV-4 cycA, dadA
Shewanella oneidensis MR-1 cycA, dadA
Shewanella sp. ANA-3 cycA, dadA
Sinorhizobium meliloti 1021 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, dadA
Sphingomonas koreensis DSMZ 15582 cycA, dadA
Synechococcus elongatus PCC 7942 Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA

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 May 21 2021. The underlying query database was built on May 21 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.

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