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:
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