Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 352404 BT2877 putative acetyltransferase (NCBI ptt file)
Query= BRENDA::P29847 (273 letters) >FitnessBrowser__Btheta:352404 Length = 201 Score = 64.7 bits (156), Expect = 1e-15 Identities = 37/85 (43%), Positives = 48/85 (56%) Query: 162 IVVGETAVIEDDVSILQSVTLGGTGKTSGDRHPKIREGVMIGAGAKILGNIEVGRGAKIG 221 I +GE +I ++V I S TG S I++ IG A IL + VG GA + Sbjct: 111 IEIGENVIISENVIIRDSDNHQITGGNSMFAPVIIKDNAWIGMSAIILKGVTVGEGAIVA 170 Query: 222 AGSVVLQPVPPHTTAAGVPARIVGK 246 AGSVV + VPPHT AGVPAR++ K Sbjct: 171 AGSVVTKDVPPHTIVAGVPARVIKK 195 Lambda K H 0.319 0.136 0.405 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: 148 Number of extensions: 8 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: 273 Length of database: 201 Length adjustment: 23 Effective length of query: 250 Effective length of database: 178 Effective search space: 44500 Effective search space used: 44500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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