GapMind for catabolism of small carbon sources

 

D-serine catabolism

Analysis of pathway D-serine in 35 genomes

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

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