GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Sinorhizobium fredii NGR234

Best path

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

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) NGR_RS12590 NGR_RS27965
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) NGR_RS12595 NGR_RS00530
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS NGR_RS12580 NGR_RS05490
rhaT' L-rhamnose ABC transporter, ATPase component RhaT NGR_RS12585 NGR_RS09875
rhaM L-rhamnose mutarotase NGR_RS12600
rhaA L-rhamnose isomerase NGR_RS12565
rhaB L-rhamnulokinase NGR_RS12605 NGR_RS05515
rhaD rhamnulose 1-phosphate aldolase NGR_RS12570
tpi triose-phosphate isomerase NGR_RS17645 NGR_RS14620
aldA lactaldehyde dehydrogenase NGR_RS12570 NGR_RS30435
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component NGR_RS00535 NGR_RS00530
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component NGR_RS19930 NGR_RS07170
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase NGR_RS21905 NGR_RS14365
LRA1 L-rhamnofuranose dehydrogenase NGR_RS14530 NGR_RS02170
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase NGR_RS27945 NGR_RS06830
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase NGR_RS27935 NGR_RS09675
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase NGR_RS19205 NGR_RS26075
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase NGR_RS05215 NGR_RS02045
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 Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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