GapMind for catabolism of small carbon sources

 

L-threonine catabolism

Analysis of pathway threonine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Azospirillum brasilense Sp245 braC, braD, braE, braF, braG, tdcB, tdcE, pccA, pccB, epi, mcm-large, mcm-small
Bacteroides thetaiotaomicron VPI-5482 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Burkholderia phytofirmans PsJN snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Caulobacter crescentus NA1000 snatA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Cupriavidus basilensis 4G11 RR42_RS28305, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dechlorosoma suillum PS phtA, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Desulfovibrio vulgaris Hildenborough braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Desulfovibrio vulgaris Miyazaki F braC, braD, braE, braF, braG, ltaE, ald-dh-CoA, gcvP, gcvT, gcvH, lpd
Dinoroseobacter shibae DFL-12 snatA, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Dyella japonica UNC79MFTsu3.2 RR42_RS28305, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Echinicola vietnamensis KMM 6221, DSM 17526 tdcC, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Escherichia coli BW25113 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Herbaspirillum seropedicae SmR1 braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Klebsiella michiganensis M5al sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Magnetospirillum magneticum AMB-1 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Marinobacter adhaerens HP15 braC, braD, braE, braF, braG, tdcB, tdcE, prpC, acnD, prpF, acn, prpB
Paraburkholderia bryophila 376MFSha3.1 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd
Pedobacter sp. GW460-11-11-14-LB5 tdcC, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Phaeobacter inhibens BS107 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N1B4 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2C3 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2E2 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens FW300-N2E3 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas fluorescens GW456-L13 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas putida KT2440 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas simiae WCS417 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Pseudomonas stutzeri RCH2 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella amazonensis SB2B sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella loihica PV-4 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella oneidensis MR-1 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Shewanella sp. ANA-3 sstT, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sinorhizobium meliloti 1021 braC, braD, braE, braF, braG, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
Sphingomonas koreensis DSMZ 15582 snatA, tdh, kbl, gcvP, gcvT, gcvH, lpd
Synechococcus elongatus PCC 7942 braC, braD, braE, braF, braG, ltaE, adh, acs, gcvP, gcvT, gcvH, lpd

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 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