Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 203424 SO4346 acetolactate synthase II, small subunit (NCBI ptt file)
Query= BRENDA::P0ADG1 (87 letters) >FitnessBrowser__MR1:203424 Length = 86 Score = 65.1 bits (157), Expect = 2e-16 Identities = 33/83 (39%), Positives = 51/83 (61%), Gaps = 1/83 (1%) Query: 2 MQHQVNVSARFNPETLERVLRVVRHRGFHVCSMNMAAASDAQNINIELTVASPRSVDLLF 61 M H + ++ + PE +ERVLRV RHRGF V M M +D ++++++ V S R+++LL Sbjct: 1 MIHSLKLTVQQRPEVIERVLRVTRHRGFTVTQMQM-RMNDDTSLSLDMEVDSERAIELLS 59 Query: 62 SQLNKLVDVAHVAICQSTTTSQQ 84 +QLNKL+DV + QQ Sbjct: 60 NQLNKLIDVTQCMVLLPLNLQQQ 82 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: 24 Number of extensions: 2 Number of successful extensions: 2 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: 86 Length adjustment: 9 Effective length of query: 78 Effective length of database: 77 Effective search space: 6006 Effective search space used: 6006 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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