Align Serine acetyltransferase; SAT; EC 2.3.1.30 (uncharacterized)
to candidate Ac3H11_4305 Serine acetyltransferase (EC 2.3.1.30)
Query= curated2:Q65PC9 (216 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4305 Length = 227 Score = 148 bits (373), Expect = 9e-41 Identities = 80/167 (47%), Positives = 103/167 (61%), Gaps = 9/167 (5%) Query: 4 KMLKEDVDVVFDQDPAARSYIEVILTYSGLHAIWAHRIAHALYKRKRFFIARAISQIARF 63 ++L DV + DPAARS EV+L Y G+ A+ HR+AH LY+ +AR ++++A Sbjct: 41 RLLDSDVLAAYQGDPAARSVDEVLLCYPGILAMIHHRLAHRLYQLGLPLLARIVAELAHS 100 Query: 64 FTGIEIHPGAKIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKG-------- 115 TGI+IHPGA+IG FFIDHG GVVIGET IG V V+Q VTLG G Sbjct: 101 ETGIDIHPGAQIGAGFFIDHGTGVVIGETAVIGERVRVYQAVTLGAKRFPAGADGHLQKG 160 Query: 116 -KRHPTIEDDALISTGAKVLGSITVGRGAKIGAGSVVLHDVPECSTV 161 RHP ++DD +I GA +LG +T+GRGA IG + HDVP S V Sbjct: 161 LPRHPVVQDDVVIYAGATILGRVTLGRGAVIGGNVWLTHDVPAGSHV 207 Lambda K H 0.323 0.142 0.416 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: 180 Number of extensions: 13 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: 216 Length of database: 227 Length adjustment: 22 Effective length of query: 194 Effective length of database: 205 Effective search space: 39770 Effective search space used: 39770 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: 41 (21.9 bits) S2: 45 (21.9 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