Finding step leuC for L-isoleucine biosynthesis in Paraburkholderia bryophila 376MFSha3.1
4 candidates for leuC: 3-isopropylmalate dehydratase / citramalate isomerase, large subunit
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Also see fitness data for the candidates
Definition of step leuC
- Curated proteins matching citramalate isomerase 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. dimethylmaleate hydratase subunit A (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))
- Ignore hits to S3E7P8 when looking for 'other' hits (3-isopropylmalate dehydratase large subunit gloJ; L-homotyrosine biosynthesis sub-cluster protein gloJ; Pneumocandin biosynthesis cluster protein J; EC 4.2.1.33)
- UniProt sequence A0A1X9Z7T5: RecName: Full=3-isopropylmalate dehydratase large subunit {ECO:0000256|HAMAP-Rule:MF_01026}; EC=4.2.1.33 {ECO:0000256|HAMAP-Rule:MF_01026}; AltName: Full=Alpha-IPM isomerase {ECO:0000256|HAMAP-Rule:MF_01026}; Short=IPMI {ECO:0000256|HAMAP-Rule:MF_01026}; AltName: Full=Isopropylmalate isomerase {ECO:0000256|HAMAP-Rule:MF_01026};
- Comment: In leucine synthesis, LeuCD allows the dehydration of 2-isopropylmalate and hydration to 3-isopropylmalate. Similarly, many of these enzymes allow the isomerization of citramalate to 3-methylmalate via citraconate. Citramalate isomerase is usually given as EC 4.2.1.35, as opposed to 4.2.1.33 for traditional leuCD. However, many the bacteria with the citramalate pathway appeared to have "typical" leuBCD (i.e., Desulfovibrio vulgaris Hildenborough, Desulfovibrio vulgaris Miyazaki F, Bacteroides thetaiotaomicron, Magnetospirillum magneticum AMB-1, and Synechococcus elongatus PCC 7942). So we do not try to distinguish between 3-isoprpylmalate dehydratase and citramalate isomerase. Ignore a 2,3-methylmalate dehydratase (Q0QLE2,Q0QLE1) which is >50% identical to leuCD from DvH (DVU2982,DVU2983). Ignore some BRENDA annotations without subunit information, and ignore CharProtDB::CH_122621 (leuCD fusion) which is not actually characterized. 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. CA265_RS15830 (A0A1X9Z7T5) from Pedobacter sp. GW460-11-11-14-LB5 is important for fitness unless amino acids are added. S3E7P8 is annotated as this in SwissProt but we did not find experimental evidence, so it is ignored.
Or cluster all characterized leuC proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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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