Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate SMc02093 SMc02093 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__Smeli:SMc02093 Length = 354 Score = 47.0 bits (110), Expect = 5e-10 Identities = 43/117 (36%), Positives = 53/117 (45%), Gaps = 10/117 (8%) Query: 57 ISQVSRFFTGIEIHPGATIGRRFFIDHGM--GVVIGETCEIGNNVTVFQGVTLG---GTG 111 I QV R + I IG ID G VIGE +I N V + V +G G Sbjct: 214 IVQVGR----VIIQDHVEIGANTTIDRGTMDDTVIGEGTKIDNLVQIGHNVRIGRYCGIV 269 Query: 112 KEKGKRHPT-IKDDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGR 167 + G T I D +I G V G IT+G+G++I A S V DVP GIP R Sbjct: 270 SQVGIAGSTQIGDGVMIGGGVGVNGHITIGDGAQIAAMSGVASDVPAGERYGGIPAR 326 Score = 24.3 bits (51), Expect = 0.003 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 2/55 (3%) Query: 125 ALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNGKKVRRD 179 A I +G ++ +G+G +IG + ++G V++ G ++ +D Sbjct: 147 AEIGSGTRIAAGAMIGQGVRIGRDCTISAGASILCALIG--NNVIIHPGARIGQD 199 Lambda K H 0.323 0.141 0.413 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: 228 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 217 Length of database: 354 Length adjustment: 25 Effective length of query: 192 Effective length of database: 329 Effective search space: 63168 Effective search space used: 63168 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: 47 (22.7 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