L-rhamnose catabolism in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

L-rhamnose catabolism in Dinoroseobacter shibae DFL-12

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).

all:

rhamnose-transport, rhaM, rhaA, rhaB, rhaD, tpi and lactaldehyde-conversion
or rhamnose-transport, LRA1, LRA2, LRA3, LRA4 and lactaldehyde-conversion
or rhamnose-transport, LRA1, LRA2, LRA3, LRA5 and LRA6
Comment: In pathway I, the mutarotase rhaM forms beta-rhamnopyranose, isomerase rhaA forms rhamnulofuranose, kinase rhaB forms rhamnulose 1-phosphate, aldolase rhaD forms (S)-lactaldehyde and glycerone phosphate, and tpi converts glycerone phosphate to glyceraldehyde 3-phosphate. In pathway II, the 1-dehydrogenase LRA1 forms L-rhamnono-1,4-lactone, the lactonase LRA2 forms L-rhamnonate, the dehydratase LRA3 forms 2-dehydro-3-deoxy-L-rhamnonate, and the aldolase LRA4 forms pyruvate and lactaldehyde. In pathway III, rhamnose is also oxidized and dehydrated to 2-dehydro-3-deoxy-L-rhamnonate, but then, dehydrogenase LRA5 forms 2,4-didehydro-3-deoxy-L-rhamnonate and hydrolase LRA6 forms L-lactate and pyruvate.

lactaldehyde-conversion:

aldA
or fucO
Comment: Lactaldehyde might be oxidized to lactate and secreted (or oxidized to pyruvate); or, it might be reduced to propane-1,2-diol and secreted.

rhamnose-transport:

rhaT
or rhaP, rhaQ, rhaS and rhaT'
or Echvi_1617
or BPHYT_RS34250, BPHYT_RS34245 and BPHYT_RS34240
Comment: Transporters were identified usiung: query: transporter:L-rhamnose:rhamnose:L-rhamnofuranose:L-rhamnopyranose:CPD-16564:CPD-16565:CPD0-1112:CPD-15405

22 steps (17 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
rhaP	L-rhamnose ABC transporter, permease component 1 (RhaP)	Dshi_2432	Dshi_0529
rhaQ	L-rhamnose ABC transporter, permease component 2 (RhaQ)	Dshi_2431	Dshi_2432
rhaS	L-rhamnose ABC transporter, substrate-binding component RhaS	Dshi_2434
rhaT'	L-rhamnose ABC transporter, ATPase component RhaT	Dshi_2433	Dshi_0530
rhaM	L-rhamnose mutarotase	Dshi_2430
rhaA	L-rhamnose isomerase	Dshi_2437
rhaB	L-rhamnulokinase	Dshi_2429
rhaD	rhamnulose 1-phosphate aldolase	Dshi_2436
tpi	triose-phosphate isomerase	Dshi_2078	Dshi_2155
aldA	lactaldehyde dehydrogenase	Dshi_2436	Dshi_1095
Alternative steps:
BPHYT_RS34240	L-rhamnose ABC transporter, permease component	Dshi_2432	Dshi_1424
BPHYT_RS34245	L-rhamnose ABC transporter, ATPase component	Dshi_2433	Dshi_0530
BPHYT_RS34250	L-rhamnose ABC transporter, substrate-binding component
Echvi_1617	L-rhamnose transporter
fucO	L-lactaldehyde reductase
LRA1	L-rhamnofuranose dehydrogenase	Dshi_0553	Dshi_2182
LRA2	L-rhamnono-gamma-lactonase
LRA3	L-rhamnonate dehydratase	Dshi_2447	Dshi_2038
LRA4	2-keto-3-deoxy-L-rhamnonate aldolase	Dshi_1647	Dshi_2586
LRA5	2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase	Dshi_2036	Dshi_2182
LRA6	2,4-diketo-3-deoxyrhamnonate hydrolase	Dshi_2542	Dshi_0967
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources