Finding step ilvH for L-isoleucine biosynthesis in Thioalkalivibrio halophilus HL17
1 candidates for ilvH: acetolactate/acetohydroxybutanoate synthase regulatory 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.
Definition of step ilvH
- HMM TIGR00119
- Curated proteins matching acetohydroxy-acid synthase%small
- Curated proteins matching acetohydroxybutanoate synthase, regulatory subunit
- Curated proteins matching small subunit of acetolactate synthase
- Curated sequence P0ADG1: acetolactate synthase (subunit 1/2) (EC 2.2.1.6). acetolactate synthase II subunit IlvM (EC 2.2.1.6)
- Ignore hits to items matching EC 2.2.1.6 when looking for 'other' hits
- UniProt sequence A0A154R0Y7: RecName: Full=Acetolactate synthase small subunit {ECO:0000256|RuleBase:RU368092}; Short=AHAS {ECO:0000256|RuleBase:RU368092}; Short=ALS {ECO:0000256|RuleBase:RU368092}; EC=2.2.1.6 {ECO:0000256|RuleBase:RU368092}; AltName: Full=Acetohydroxy-acid synthase small subunit {ECO:0000256|RuleBase:RU368092};
- Curated sequence Q93YZ7: Acetolactate synthase small subunit 1, chloroplastic; ALS-interacting protein 1; Acetohydroxyacid synthase small subunit 1
- UniProt sequence A0A0H2X4P1: SubName: Full=Acetolactate synthase isozyme II small subunit {ECO:0000313|EMBL:AAY47914.1};
- Predicted: UniProt sequence A0A7J3AYJ4: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:HGD33185.1};
- Predicted: UniProt sequence A0A161J739: SubName: Full=Acetolactate synthase 3 regulatory subunit domain protein {ECO:0000313|EMBL:ANC53960.1};
- Comment: The isolated catalytic subunit can have some activity on its own, so it's not clear if the regulatory subunit (ilvH) is always required, but ilvH does always seem to be present. P0ADG1 is annotated with this EC number but not explicitly as the small regulatory subunit, so it was added manually. Q93YZ7 is annotated as this but without the EC number, so is added manually. Most regulatory subunits have an N-terminal ACT domain and a C-terminal ACT-like domain, but E. coli IlvM, which is required for the activity of E. coli acetohydroxyacid synthase isoenzyme II, has the N-terminal ACT domain only. We identified several other short (one-domain) regulatory subunits. In Rhodanobacter and related genera, the putative regulatory subunit has just one ACT domain (i.e., LRK54_RS10305, which is nearly identical to A0A154R0Y7). Based on sequence analysis, short ilvH probably maintains the ability to bind valine and to bind the catalytic subunit, but not the ability to bind ATP or other regulatory subunits. Mutant fitness data confirms that LRK54_RS10305 is involved in amino acid biosynthesis. In Xanthomonas campestris, the one ACT-domain protein Xcc-8004.1058.1 (A0A0H2X4P1), which is conserved next to ilvI, has a similar fitness pattern as ilvI (Alice Castaing, unpublished data). Furthermore, its AlphaFold structure is very similar to that of E. coli IlvM (TM-score 0.89, RMSD 1.49 A, foldseek). So Xcc-8004.1058.1 is another short regulatory subunit. Similarly, in Brevundimonas sp. GW460-12-10-14-LB2, the putative ilvH has the ACT domain only (Brev2_1981 = A0A161J739). Many Thermoproteota seem to have a diverged short regulatory subunit, such as the ACT domain protein KCR_RS03285 (A0A7J3AYJ4), which is conserved next to ilvI. Foldseek shows that this protein is similar to the ACT domain of (p)ppGpp synthase but also to IlvH of Staphylococcus aureus, so we predict that it is the regulatory subunit.
Or cluster all characterized ilvH 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