Finding step ilvI for L-valine biosynthesis in Paraburkholderia sp. CCGE1002
5 candidates for ilvI: acetolactate/acetohydroxybutanoate synthase catalytic 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 ilvI
- HMM TIGR00118
- Curated proteins matching acetohydroxy-acid synthase%large
- Curated proteins matching acetohydroxy acid synthase%large
- Curated proteins matching acetohydroxybutanoate synthase, catalytic subunit
- Curated proteins matching acetohydroxybutanoate synthase, catalytic subunit
- Curated proteins matching acetohydroxyacid synthase subunit B
- Ignore hits to items matching EC 2.2.1.6 when looking for 'other' hits
- Ignore hits to CH_124219 when looking for 'other' hits (threonine deaminase [Arxula adeninivorans])
- Ignore hits to O53554 when looking for 'other' hits (acetolactate synthase (EC 2.2.1.6). Putative acetolactate synthase large subunit IlvX; ALS; Acetohydroxy-acid synthase large subunit; AHAS; EC 2.2.1.6)
- Comment: ilvIH (or ilvGM) is a two-subunit enzyme that forms acetolactate or acetohydroxybutanoate. (S)-2-aceto-2-hydroxybutanoate synthesis is part of isoleucine biosynthesis. Acetolactate synthesis is part of valine or leucine biosynthesis. CH_124129 is probably correct but has limited data and vaguer annotations. IlvX from Mycobacterium tuberculosis (O53554) is ignored because, although annotated with this activity by both SwissProt and BRENDA, we could not find experimental evidence, and it is reported to lack activity (PMID:20884690).
Or cluster all characterized ilvI proteins
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Links
Downloads
Related tools
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