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:
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