GapMind for catabolism of small carbon sources

 

L-proline catabolism

Analysis of pathway proline in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Azospirillum brasilense Sp245 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Bacteroides thetaiotaomicron VPI-5482 proY, put1, putA
Burkholderia phytofirmans PsJN HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Caulobacter crescentus NA1000 CCNA_00435, put1, putA
Cupriavidus basilensis 4G11 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Dechlorosoma suillum PS HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Desulfovibrio vulgaris Hildenborough proY, put1, putA
Desulfovibrio vulgaris Miyazaki F proY, put1, putA
Dinoroseobacter shibae DFL-12 aapJ, aapQ, aapM, aapP, put1, putA
Dyella japonica UNC79MFTsu3.2 N515DRAFT_2924, put1, putA
Echinicola vietnamensis KMM 6221, DSM 17526 ectP, put1, putA
Escherichia coli BW25113 proV, proW, proX, put1, putA
Herbaspirillum seropedicae SmR1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Klebsiella michiganensis M5al HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Magnetospirillum magneticum AMB-1 AZOBR_RS08235, AZOBR_RS08240, AZOBR_RS08245, AZOBR_RS08250, AZOBR_RS08260, put1, putA
Marinobacter adhaerens HP15 putP, put1, putA
Paraburkholderia bryophila 376MFSha3.1 HSERO_RS00870, HSERO_RS00885, HSERO_RS00890, HSERO_RS00895, HSERO_RS00900, put1, putA
Pedobacter sp. GW460-11-11-14-LB5 N515DRAFT_2924, put1, putA
Phaeobacter inhibens BS107 ectP, put1, putA
Pseudomonas fluorescens FW300-N1B4 putP, put1, putA
Pseudomonas fluorescens FW300-N2C3 putP, put1, putA
Pseudomonas fluorescens FW300-N2E2 putP, put1, putA
Pseudomonas fluorescens FW300-N2E3 putP, put1, putA
Pseudomonas fluorescens GW456-L13 putP, put1, putA
Pseudomonas putida KT2440 putP, put1, putA
Pseudomonas simiae WCS417 putP, put1, putA
Pseudomonas stutzeri RCH2 putP, put1, putA
Shewanella amazonensis SB2B putP, put1, putA
Shewanella loihica PV-4 putP, put1, putA
Shewanella oneidensis MR-1 putP*, put1, putA
Shewanella sp. ANA-3 putP, put1, putA
Sinorhizobium meliloti 1021 aapJ, aapQ, aapM, aapP, put1, putA
Sphingomonas koreensis DSMZ 15582 CCNA_00435, put1, putA
Synechococcus elongatus PCC 7942 natA, natB, natC, natD, natE, put1, putA

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