GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Amantichitinum ursilacus IGB-41

Best path

rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) WG78_RS08790 WG78_RS19015
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) WG78_RS08785 WG78_RS19935
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS WG78_RS08780
rhaT' L-rhamnose ABC transporter, ATPase component RhaT WG78_RS08795 WG78_RS19930
LRA1 L-rhamnofuranose dehydrogenase WG78_RS08810 WG78_RS04575
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase WG78_RS08815 WG78_RS01020
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase WG78_RS08820 WG78_RS16965
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase WG78_RS08825 WG78_RS02700
Alternative steps:
aldA lactaldehyde dehydrogenase WG78_RS14820 WG78_RS16670
BPHYT_RS34240 L-rhamnose ABC transporter, permease component WG78_RS19935 WG78_RS08790
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component WG78_RS15685 WG78_RS19930
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component WG78_RS21610
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase WG78_RS06220 WG78_RS03390
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase
rhaM L-rhamnose mutarotase WG78_RS08805
rhaT L-rhamnose:H+ symporter RhaT
tpi triose-phosphate isomerase WG78_RS15400 WG78_RS03140

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 24 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 (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