Align Serine acetyltransferase; SAT; EC 2.3.1.30 (uncharacterized)
to candidate WP_041100910.1 SUTH_RS16850 serine O-acetyltransferase
Query= curated2:P71405 (171 letters) >NCBI__GCF_000828635.1:WP_041100910.1 Length = 185 Score = 114 bits (284), Expect = 1e-30 Identities = 65/144 (45%), Positives = 86/144 (59%), Gaps = 4/144 (2%) Query: 29 PGIHALLCYRLAHALHKRRFYFIARALSQLARFITGIEIHPGAKIGRGLFIDHGMGVVIG 88 P + ++ RLA H RR +A+ S + + GIE+ P +IG GLF+ H +G VIG Sbjct: 33 PRMVPVVLLRLAEYFHGRRIGLLAKFFSAINVLVFGIEVSPLVEIGGGLFLPHTVGTVIG 92 Query: 89 ETTEIGDDVTIYHGVTLGGTGK---FKGKRHPTLGNRVVVGAGAKVLGAICVGDDVKIGA 145 IGD+ TI GVTLG + F P +GN V++GAGAKV+G I VGD KIGA Sbjct: 93 -AARIGDNCTIMQGVTLGTSEPEIGFTAAARPVVGNGVLIGAGAKVIGGITVGDHAKIGA 151 Query: 146 NAVVLSDLPTGSTAVGSKAKTITK 169 NAVVL D+P+ S AVG A + + Sbjct: 152 NAVVLRDVPSHSVAVGVPATVLAR 175 Lambda K H 0.323 0.142 0.422 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: 111 Number of extensions: 14 Number of successful extensions: 4 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: 171 Length of database: 185 Length adjustment: 19 Effective length of query: 152 Effective length of database: 166 Effective search space: 25232 Effective search space used: 25232 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 (21.9 bits) S2: 44 (21.6 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