Align Acetolactate synthase isozyme 1 small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase I small subunit; AHAS-I; ALS-I (uncharacterized)
to candidate 17730 b3670 acetolactate synthase small subunit (NCBI)
Query= curated2:P0ADG0 (96 letters) >FitnessBrowser__Keio:17730 Length = 96 Score = 197 bits (502), Expect = 2e-56 Identities = 96/96 (100%), Positives = 96/96 (100%) Query: 1 MQNTTHDNVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSDKSHIWLLVNDDQ 60 MQNTTHDNVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSDKSHIWLLVNDDQ Sbjct: 1 MQNTTHDNVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSDKSHIWLLVNDDQ 60 Query: 61 RLEQMISQIDKLEDVVKVQRNQSDPTMFNKIAVFFQ 96 RLEQMISQIDKLEDVVKVQRNQSDPTMFNKIAVFFQ Sbjct: 61 RLEQMISQIDKLEDVVKVQRNQSDPTMFNKIAVFFQ 96 Lambda K H 0.324 0.137 0.410 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: 108 Number of extensions: 3 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: 96 Length of database: 96 Length adjustment: 10 Effective length of query: 86 Effective length of database: 86 Effective search space: 7396 Effective search space used: 7396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.1 bits) S2: 39 (19.6 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