Definition of L-fucose catabolism
As rules and steps, or see full text
Rules
Overview: Fucose degradation in GapMind is based on the MetaCyc pathway via L-fuculose (link) or the oxidative pathway via 2,4-diketo-3-deoxy-L-fuconate (KDF) hydrolase (PMC6336799).
- all:
- fucose-transport, fucU, fucI, fucK, fucA, tpi and lactaldehyde-conversion
- or fucose-transport, fucU, fdh, fuconolactonase, fucD, fucDH and KDF-hydrolase
- Comment: In the L-fucuolose pathway, mutarotase fucU converts the beta-pyranose to the alpha-pyranose form, isomerase fucI produces L-fuculose, kinase fucK forms L-fuculose 1-phosphate, and aldolase fucA produces glycerone phosphate and (S)-lactaldehyde. Lactaldehyde might be oxidized to lactate and secreted (or oxidized to pyruvate), or, it might be reduced to propane-1,2-diol and secreted; tpi converts glycerone-phosphate to glyceraldehyde 3-phosphate. In the oxidative pathway, mutarotase fucU forms the beta-pyranose form, fucose dehydrogenase (fdh) forms L-fucono-1,5-lactone, a lactonase forms L-fuconate, dehydratase fucD forms 2-keto-3-deoxy-L-fuconate, dehydrogenase fucDH forms 2,4-diketo-3-deoxy-L-fuconate (KDF, also known as 2,4-diketo-3-deoxy-L-rhamnonate), and a hydrolase forms lactate and pyruvate. The lactate could be secreted or oxidized to pyruvate.
- lactaldehyde-conversion:
- aldA
- or fucO
- Comment: Lactaldehyde can be oxidized to lactate (aldA) or reduced to propanediol (fucO). Either of these can be excreted.
- fucose-transport:
Steps
fucP: L-fucose:H+ symporter FucP
- Curated sequence P11551: L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease. L-Fucose:H+ symporter. The x-ray structure (3.1Å resolution). L-fucose:H+ symporter. L-fucose:H+ symporter
- UniProt sequence G8JZT2: SubName: Full=L-fucose permease {ECO:0000313|EMBL:AAO76384.1};
- Comment: BT1277 (G8JZT2) is distantly related and important for fucose utilization
- Total: 2 characterized proteins
SM_b21103: ABC transporter for L-fucose, substrate-binding component
SM_b21104: ABC transporter for L-fucose, permease component 1
SM_b21105: ABC transporter for L-fucose, permease component 2
SM_b21106: ABC transporter for L-fucose, ATPase component
BPHYT_RS34250: ABC transporter for L-fucose, substrate-binding component
- UniProt sequence B2T9W0: SubName: Full=Periplasmic binding protein/LacI transcriptional regulator {ECO:0000313|EMBL:ACD21212.1}; Flags: Precursor;
- Comment: A 3-part ABC transporter was identified in Burkholderia phytofirmans based on fitness data
- Total: 1 characterized proteins
BPHYT_RS34245: ABC transporter for L-fucose, ATPase component
BPHYT_RS34240: ABC transporter for L-fucose, 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
HSERO_RS05250: ABC transporter for L-fucose, ATPase component
- UniProt sequence D8J111: RecName: Full=Ribose import ATP-binding protein RbsA {ECO:0000256|HAMAP-Rule:MF_01716}; EC=7.5.2.7 {ECO:0000256|HAMAP-Rule:MF_01716};
- Comment: A 3-part ABC transporter was identified in Herbaspirillum seropedicae based on fitness data
- Total: 1 characterized proteins
HSERO_RS05255: ABC transporter for L-fucose, permease component
- UniProt sequence D8J112: SubName: Full=ABC-type sugar transport system, permease component protein {ECO:0000313|EMBL:ADJ62567.1};
- Total: 1 characterized proteins
HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
- UniProt sequence D8J113: SubName: Full=ABC-type sugar transport system, periplasmic component protein {ECO:0000313|EMBL:ADJ62568.1};
- Total: 1 characterized proteins
fucU: L-fucose mutarotase FucU
- Curated proteins or TIGRFams with EC 5.1.3.29
- UniProt sequence Q8A896: SubName: Full=Rhamnose mutarotase {ECO:0000313|EMBL:AAO76383.1};
- Comment: BT1276 (Q8A896) is important for fucose utilization
- Total: 6 characterized proteins
fucI: L-fucose isomerase FucI
fucK: L-fuculose kinase FucK
fucA: L-fuculose-phosphate aldolase FucA
- Curated proteins or TIGRFams with EC 4.1.2.17
- UniProt sequence G8JZT1: SubName: Full=L-fuculose-1-phosphate aldolase {ECO:0000313|EMBL:AAO76381.1};
- Comment: BT2174 (G8JZT1) is important for fucose utilization
- Total: 1 HMMs and 5 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
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
fdh: L-fucose 1-dehydrogenase
fuconolactonase: L-fucono-1,5-lactonase
- UniProt sequence A0A0H3KNC4: SubName: Full=Putative amidohydrolase {ECO:0000313|EMBL:BAG46761.1};
- Curated sequence SM_b21101: L-fucono-1,5-lactonase; D-arabinolactonase
- UniProt sequence A0A0H3KNC4: SubName: Full=Putative amidohydrolase {ECO:0000313|EMBL:BAG46761.1};
- UniProt sequence D8J114: SubName: Full=Metal-dependent hydrolase of the TIM-barrel fold protein {ECO:0000313|EMBL:ADJ62569.1};
- UniProt sequence B2T9V4: SubName: Full=Amidohydrolase 2 {ECO:0000313|EMBL:ACD21206.1};
- Comment: BmulJ_04915 (A0A0H3KNC4) is the biochemically characterized enzyme, see PMID:23214453. HSERO_RS05265 (D8J114) and BPHYT_RS34220 (B2T9V4) are important for fucose utilization
- Total: 4 characterized proteins
fucD: L-fuconate dehydratase
- Curated proteins or TIGRFams with EC 4.2.1.68
- UniProt sequence D8J108: RecName: Full=L-fuconate dehydratase {ECO:0000256|ARBA:ARBA00014265}; EC=4.2.1.68 {ECO:0000256|ARBA:ARBA00013142};
- 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: HSERO_RS05235 (D8J108) is important for fucose utilization. Ignore the putative accessory protein BPHYT_RS34235.
- Total: 5 characterized proteins
fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase
- Curated sequence Q8P3K4: 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.-
- UniProt sequence A0A4P7ABK7: SubName: Full=SDR family oxidoreductase {ECO:0000313|EMBL:QBP77113.1};
- UniProt sequence D8IS13: SubName: Full=Short-chain alcohol dehydrogenase protein {ECO:0000313|EMBL:ADJ65356.1};
- UniProt sequence B2T9V3: SubName: Full=Short-chain dehydrogenase/reductase SDR {ECO:0000313|EMBL:ACD21205.1};
- Comment: No EC number, but XCC4067 (Q8P3K4) is annotated in SwissProt based on PMID:17144652. C785_RS13675 (A0A4P7ABK7) was also shown to have this acivity (PMC6336799) HSERO_RS19365 (D8IS13) and BPHYT_RS34215 (B2T9V3) are important for fucose utilization (The substrate for EC 1.1.1.401 (2-dehydro-3-deoxy-L-rhamnonate 4-dehydrogenase) has the other stereochemistry at position 4.)
- Total: 4 characterized proteins
KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase
- UniProt sequence A0A2E7P912: SubName: Full=FAA hydrolase family protein {ECO:0000313|EMBL:MBO18215.1};
- Curated sequence BPHYT_RS34210: 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-)
- Curated sequence SM_b21112: L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase
- UniProt sequence D8INW0: SubName: Full=2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway) protein {ECO:0000313|EMBL:ADJ62780.1}; EC=4.2.1.80 {ECO:0000313|EMBL:ADJ62780.1};
- Ignore hits to Q39BA7 when looking for 'other' hits (Ureidoglycolate lyase; UGL; Ureidoglycolase; Ureidoglycolatase; Ureidoglycolate hydrolase; EC 4.3.2.3)
- Curated sequence MONOMER-16233: L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401)
- Comment: C785_RS20550 (A0A2E7P912) was shown to be a L-2-keto-3-deoxyfuconate (L-KDF) hydrolase by PMC6336799. HSERO_RS06355 (D8INW0) is important for fucose utilization. Q39BA7 is rather closely related but is reported to be a ureidoglycolate lyase. metacyc MONOMER-16233 is misannotated as a dehydrogenase in MetaCyc -- it is the hydrolase.
- Total: 5 characterized proteins
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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