GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Sinorhizobium meliloti 1021

Best path

rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA

Also see fitness data for the top candidates

Rules

Overview: Rhamnose utilization in GapMind is based on MetaCyc pathway I via L-rhamnulose 1-phosphate aldolase (link), pathway II via 2-keto-3-deoxy-L-rhamnonate aldolase (link), and pathway III via 2,4-diketo-3-deoxyrhamnonate hydrolase (link).

22 steps (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) SMc03000 SM_b21375
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) SMc03001 SM_b21017
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS SMc02324 SM_b21016
rhaT' L-rhamnose ABC transporter, ATPase component RhaT SMc02325 SM_b20713
rhaM L-rhamnose mutarotase SMc03002 SM_b21108
rhaA L-rhamnose isomerase SMc02321
rhaB L-rhamnulokinase SMc03003 SM_b20489
rhaD rhamnulose 1-phosphate aldolase SMc02322 SM_b21015
tpi triose-phosphate isomerase SMc01023 SMc01614
aldA lactaldehyde dehydrogenase SMc02322 SMa2213
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component SM_b20352 SM_b21375
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component SM_b21344 SM_b20673
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase SMc01582 SMa0263
LRA1 L-rhamnofuranose dehydrogenase SMa0335 SMc02037
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase SMc02776 SMa1351
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase SMc02778
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase SMc01214 SMc01698
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase SM_b21112 SMc04240
rhaT L-rhamnose:H+ symporter RhaT

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, the preprint on GapMind for carbon sources, 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