Definition of L-rhamnose catabolism
As rules and steps, or see full text
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:
Steps
rhaT: L-rhamnose:H+ symporter RhaT
- Curated sequence P27125: L-rhamnose-proton symporter; L-rhamnose-H(+) transport protein. Rhamnose:H+ symporter, RhaT. rhamnose/lyxose:H+ symporter. rhamnose/lyxose:H+ symporter
- UniProt sequence Q8A1A1: SubName: Full=L-rhamnose/H+ symporter {ECO:0000313|EMBL:AAO78870.1};
- Comment: Fitness data shows that the (distant) homolog in Bacteroides thetaiotaomicron (BT3765, Q8A1A1) is also a rhamnose transporter
- Total: 2 characterized proteins
rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP)
- Curated sequence Q7BSH3: RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!)
- Comment: 4-part ABC transporter rhaPQST. In TCDB, the rhamnose transporter of Rhizobium leguminosarum is described as rhaSTP but rhaQ (Q7BSH2_RHILT) is also probably part of this system. The comment in TCDB also speculates about group translocation, because the R. leguminosarum system requires the rhamnose/rhamnulose kinase rhaK for activity; but in Sinorhizobium meliloti, which has a similar system, the rhaK protein has rhamnulokinase activity only (Rivers 2015, link).
- Total: 1 characterized proteins
rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ)
rhaS: L-rhamnose ABC transporter, substrate-binding component RhaS
- Curated sequence Q7BSH5: RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!)
- Total: 1 characterized proteins
rhaT': L-rhamnose ABC transporter, ATPase component RhaT
- Curated sequence Q7BSH4: RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!)
- Comment: Because of the one-component transporter rhaT, the ATPase component is named rhaT' in GapMind.
- Total: 1 characterized proteins
Echvi_1617: L-rhamnose transporter
- UniProt sequence L0FX46: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:AGA77882.1};
- Comment: Fitness data suggests Echvi_1617 is the rhamnose transporter. It is probably Na+ dependent, but this is uncertain.
- Total: 1 characterized proteins
BPHYT_RS34250: L-rhamnose ABC transporter, substrate-binding component
- UniProt sequence B2T9W0: SubName: Full=Periplasmic binding protein/LacI transcriptional regulator {ECO:0000313|EMBL:ACD21212.1}; Flags: Precursor;
- Comment: In Burkholderia phytofirmans PsJN, a 3-part ABC transporter is involved in utilization of L-rhamnose, L-fucose, and xylitol
- Total: 1 characterized proteins
BPHYT_RS34245: L-rhamnose ABC transporter, ATPase component
BPHYT_RS34240: L-rhamnose ABC transporter, permease component
- UniProt sequence B2T9V8: SubName: Full=Monosaccharide-transporting ATPase {ECO:0000313|EMBL:ACD21210.1}; EC=3.6.3.17 {ECO:0000313|EMBL:ACD21210.1}; Flags: Precursor;
- Total: 1 characterized proteins
rhaM: L-rhamnose mutarotase
rhaA: L-rhamnose isomerase
rhaB: L-rhamnulokinase
rhaD: rhamnulose 1-phosphate aldolase
- Curated proteins or TIGRFams with EC 4.1.2.19
- UniProt sequence Q8A1A0: RecName: Full=Rhamnulose-1-phosphate aldolase {ECO:0000255|HAMAP-Rule:MF_00770}; EC=4.1.2.19 {ECO:0000255|HAMAP-Rule:MF_00770};
- Comment: BT3766 (Q8A1A0) was confirmed by fitness data
- Total: 1 HMMs and 9 characterized proteins
tpi: triose-phosphate isomerase
- Curated proteins or TIGRFams with EC 5.3.1.1
- Ignore hits to P85814 when looking for 'other' hits (Triosephosphate isomerase; TIM; Triose-phosphate isomerase; Allergen Pla o 4; EC 5.3.1.1)
- Comment: Ignore a fragmentary (allergen) sequence
- Total: 1 HMMs and 55 characterized proteins
aldA: lactaldehyde dehydrogenase
- Curated proteins or TIGRFams with EC 1.2.1.22
- Ignore hits to items matching lactaldehyde dehydrogenase when looking for 'other' hits
- Comment: The EC number is for the NAD dependent reaction. There's also a NADP dependent reaction, sometimes given this EC, sometimes not.
- Total: 10 characterized proteins
fucO: L-lactaldehyde reductase
LRA1: L-rhamnofuranose dehydrogenase
- Curated proteins or TIGRFams with EC 1.1.1.378
- Curated proteins or TIGRFams with EC 1.1.1.173
- Curated proteins or TIGRFams with EC 1.1.1.377
- Comment: The rhamnofuranose dehydrogenase may be either NADH or NADPH dependent, or use either
- Total: 5 characterized proteins
LRA2: L-rhamnono-gamma-lactonase
LRA3: L-rhamnonate dehydratase
- Curated proteins or TIGRFams with EC 4.2.1.90
- Ignore hits to BPHYT_RS34235 when looking for 'other' hits (putative accessory domain for L-fuconate/L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90))
- Comment: Ignore BPHYT_RS34235, a putative accessory domain
- Total: 6 characterized proteins
LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase
- Curated proteins or TIGRFams with EC 1.1.1.401
- Ignore hits to MONOMER-16233 when looking for 'other' hits (L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401))
- Comment: The enzyme from Sphingomonas strain SKA58 is Q1NEI6 not Q1NEI7; there is an error in MetaCyc. Q1NEI6 is annotated correctly in other resources
- Total: 2 characterized proteins
LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase
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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:
- 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, 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