Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate BWI76_RS00965 BWI76_RS00965 acetolactate synthase 2 small subunit
Query= BRENDA::P0ADG1 (87 letters) >FitnessBrowser__Koxy:BWI76_RS00965 Length = 85 Score = 124 bits (312), Expect = 2e-34 Identities = 67/87 (77%), Positives = 74/87 (85%), Gaps = 2/87 (2%) Query: 1 MMQHQVNVSARFNPETLERVLRVVRHRGFHVCSMNMAAASDAQNINIELTVASPRSVDLL 60 MMQHQV + ARFNPETLERVLRVVRHRGF +C+MNM A+DA+NINIELTVAS R V+LL Sbjct: 1 MMQHQVALQARFNPETLERVLRVVRHRGFQICAMNMETAADARNINIELTVASQRPVELL 60 Query: 61 FSQLNKLVDVAHVAICQSTTTSQQIRA 87 FSQL+KLVDVA V I Q TSQQIRA Sbjct: 61 FSQLSKLVDVACVEIQQ--PTSQQIRA 85 Lambda K H 0.323 0.128 0.354 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 61 Number of extensions: 2 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 87 Length of database: 85 Length adjustment: 9 Effective length of query: 78 Effective length of database: 76 Effective search space: 5928 Effective search space used: 5928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 38 (20.7 bits) S2: 38 (19.2 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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