Definition of L-leucine biosynthesis
As rules and steps, or see full text
Rules
Overview: Leucine biosynthesis in GapMind is based on MetaCyc pathway L-leucine biosynthesis (link). This begins with the initial steps of valine biosynthesis (see link), up to 3-methyloxobutanoate.
Steps
ilvH: acetohydroxybutanoate synthase catalytic subunit
ilvI: acetohydroxybutanoate synthase regulatory subunit
ilvC: ketol-acid reductoisomerase
ilvD: (R)-2,3-dihydroxy-3-methylbutanoate dehydratase
- Curated proteins or TIGRFams with EC 4.2.1.9
- Ignore hits to MONOMER-15882 when looking for 'other' hits (dihydroxy-acid dehydratase)
- Comment: The ignored enzyme is involved in salinosporamide A biosynthesis but does a very similar reaction and is >50% identical to N515DRAFT_0569, which is confirmed by fitness data to be biosynthetic.
- Total: 1 HMMs and 6 characterized proteins
leuA: 2-isopropylmalate synthase
leuC: 3-isopropylmalate dehydratase, large subunit
- Curated proteins matching 3-isopropylmalate dehydratase large subunit
- Curated proteins matching 3-isopropylmalate dehydratase%LeuC
- HMM TIGR00170
- HMM TIGR02083
- HMM TIGR02086
- Ignore hits to Q0QLE2 when looking for 'other' hits (2,3-dimethylmalate dehydratase large subunit; EC 4.2.1.85)
- Ignore hits to items matching EC 4.2.1.33 when looking for 'other' hits
- Ignore hits to items matching EC 4.2.1.35 when looking for 'other' hits
- UniProt sequence LEUC_DESVH: RecName: Full=3-isopropylmalate dehydratase large subunit {ECO:0000255|HAMAP-Rule:MF_01027}; EC=4.2.1.33 {ECO:0000255|HAMAP-Rule:MF_01027}; AltName: Full=Alpha-IPM isomerase {ECO:0000255|HAMAP-Rule:MF_01027}; Short=IPMI {ECO:0000255|HAMAP-Rule:MF_01027}; AltName: Full=Isopropylmalate isomerase {ECO:0000255|HAMAP-Rule:MF_01027};
- Ignore hits to CH_122621 when looking for 'other' hits (alpha isopropylmalate isomerase (Eurofung))
- Comment: Ignore some BRENDA annotations without subunit information for LeuCD and ignore CharProtDB::CH_122621 (leuCD fusion) which is not actually characterized. Ignore a 2,3-methylmalate dehydratase (Q0QLE2,Q0QLE1) which is >50% identical to leuCD from DvH (DVU2982,DVU2983). And, DvH leuC (DVU2982) has similarity to both LeuC and to homoaconitase, and fitness data confirms its role in amino acid biosynthesis, so explicitly include it.
- Total: 3 HMMs and 7 characterized proteins
leuD: 3-isopropylmalate dehydaratase, small subunit
- Curated proteins matching 3-isopropylmalate dehydratase small subunit
- Curated proteins matching 3-isopropylmalate dehydratase%LeuD
- HMM TIGR00171
- HMM TIGR02084
- HMM TIGR02087
- Ignore hits to Q0QLE1 when looking for 'other' hits (2,3-dimethylmalate dehydratase small subunit; EC 4.2.1.85)
- Ignore hits to items matching EC 4.2.1.33 when looking for 'other' hits
- Ignore hits to items matching EC 4.2.1.35 when looking for 'other' hits
- UniProt sequence LEUD_DESVH: RecName: Full=3-isopropylmalate dehydratase small subunit {ECO:0000255|HAMAP-Rule:MF_01032}; EC=4.2.1.33 {ECO:0000255|HAMAP-Rule:MF_01032}; AltName: Full=Alpha-IPM isomerase {ECO:0000255|HAMAP-Rule:MF_01032}; Short=IPMI {ECO:0000255|HAMAP-Rule:MF_01032}; AltName: Full=Isopropylmalate isomerase {ECO:0000255|HAMAP-Rule:MF_01032};
- Ignore hits to CH_122621 when looking for 'other' hits (alpha isopropylmalate isomerase (Eurofung))
- Comment: DvH leuD (DVU2983) has similarity to both LeuD and to homoaconitase, and fitness data confirms its role in amino acid biosynthesis.
- Total: 3 HMMs and 8 characterized proteins
leuB: 3-isopropylmalate dehydrogenase
ilvE: leucine transaminase
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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, or see changes to Amino acid biosynthesis since the publication.
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