GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism

Analysis of pathway 4-hydroxybenzoate in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Azospirillum brasilense Sp245 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Bacteroides thetaiotaomicron VPI-5482 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Burkholderia phytofirmans PsJN pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Caulobacter crescentus NA1000 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Cupriavidus basilensis 4G11 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Dechlorosoma suillum PS pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Desulfovibrio vulgaris Hildenborough pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfovibrio vulgaris Miyazaki F pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Dinoroseobacter shibae DFL-12 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Dyella japonica UNC79MFTsu3.2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Echinicola vietnamensis KMM 6221, DSM 17526 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Escherichia coli BW25113 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Herbaspirillum seropedicae SmR1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Klebsiella michiganensis M5al pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Magnetospirillum magneticum AMB-1 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Marinobacter adhaerens HP15 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Paraburkholderia bryophila 376MFSha3.1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pedobacter sp. GW460-11-11-14-LB5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Phaeobacter inhibens BS107 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas fluorescens FW300-N1B4 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2C3 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2E2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2E3 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens GW456-L13 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas putida KT2440 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas simiae WCS417 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas stutzeri RCH2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Shewanella amazonensis SB2B pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella loihica PV-4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella oneidensis MR-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella sp. ANA-3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sinorhizobium meliloti 1021 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Sphingomonas koreensis DSMZ 15582 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Synechococcus elongatus PCC 7942 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs

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