GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism

Analysis of pathway rhamnose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Azospirillum brasilense Sp245 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Bacteroides thetaiotaomicron VPI-5482 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Burkholderia phytofirmans PsJN BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, LRA1, LRA2, LRA3, LRA5, LRA6
Caulobacter crescentus NA1000 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Cupriavidus basilensis 4G11 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Dechlorosoma suillum PS rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Desulfovibrio vulgaris Hildenborough rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Desulfovibrio vulgaris Miyazaki F rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Dinoroseobacter shibae DFL-12 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dyella japonica UNC79MFTsu3.2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Echinicola vietnamensis KMM 6221, DSM 17526 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Escherichia coli BW25113 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Herbaspirillum seropedicae SmR1 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Klebsiella michiganensis M5al rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Magnetospirillum magneticum AMB-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Marinobacter adhaerens HP15 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Paraburkholderia bryophila 376MFSha3.1 rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
Pedobacter sp. GW460-11-11-14-LB5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Phaeobacter inhibens BS107 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas fluorescens FW300-N1B4 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas fluorescens FW300-N2C3 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas fluorescens FW300-N2E2 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas fluorescens FW300-N2E3 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Pseudomonas fluorescens GW456-L13 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas putida KT2440 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas simiae WCS417 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudomonas stutzeri RCH2 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Shewanella amazonensis SB2B rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Shewanella loihica PV-4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Shewanella oneidensis MR-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Shewanella sp. ANA-3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sinorhizobium meliloti 1021 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingomonas koreensis DSMZ 15582 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Synechococcus elongatus PCC 7942 rhaT, LRA1, LRA2, LRA3, LRA4, aldA

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