GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Streptacidiphilus oryzae TH49

Best path

BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, 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
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component BS73_RS15640
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component BS73_RS15635 BS73_RS32735
BPHYT_RS34240 L-rhamnose ABC transporter, permease component BS73_RS15630 BS73_RS01760
rhaM L-rhamnose mutarotase BS73_RS29745
rhaA L-rhamnose isomerase BS73_RS10615
rhaB L-rhamnulokinase BS73_RS10625
rhaD rhamnulose 1-phosphate aldolase BS73_RS10620
tpi triose-phosphate isomerase BS73_RS12430 BS73_RS16890
aldA lactaldehyde dehydrogenase BS73_RS10620 BS73_RS23595
Alternative steps:
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase BS73_RS30995 BS73_RS27570
LRA1 L-rhamnofuranose dehydrogenase BS73_RS30360 BS73_RS31355
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase BS73_RS29945 BS73_RS04805
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BS73_RS04585 BS73_RS07230
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase BS73_RS30775 BS73_RS00400
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) BS73_RS32740 BS73_RS01760
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) BS73_RS32745 BS73_RS01760
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS BS73_RS32750
rhaT L-rhamnose:H+ symporter RhaT
rhaT' L-rhamnose ABC transporter, ATPase component RhaT BS73_RS32735 BS73_RS01755

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