Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_011365808.1 GMET_RS19155 WxcM-like domain-containing protein
Query= BRENDA::P95231 (229 letters) >NCBI__GCF_000012925.1:WP_011365808.1 Length = 309 Score = 63.5 bits (153), Expect = 4e-15 Identities = 49/145 (33%), Positives = 67/145 (46%), Gaps = 22/145 (15%) Query: 53 ARAAAEFTRILTGVDIHPGAVIGA------RVFIDHAT----------GVVIGETAEVGD 96 A+ + T I V + PGAVIG+ FI++A GV I + V D Sbjct: 11 AKQIGQGTSIWQYVVVLPGAVIGSDCNICSHCFIENAVVIGDRVTIKCGVQIWDGLRVED 70 Query: 97 DVTIYHGVTLGGSGMVGGKRHPTVGDRVII------GAGAKVLGPIKIGEDSRIGANAVV 150 DV I VT K+HP + +I GA A +L IG ++ +GA AVV Sbjct: 71 DVFIGPNVTFTNDLFPRSKQHPKEFAKTVIQKGASIGANATILAGSTIGRNAMVGAGAVV 130 Query: 151 VKPVPPSAVVVGVPGQVIGQSQPSP 175 K VPP+A+VVG P ++ G P Sbjct: 131 TKSVPPNAIVVGNPARITGYVSTIP 155 Lambda K H 0.321 0.141 0.443 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: 179 Number of extensions: 15 Number of successful extensions: 3 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: 229 Length of database: 309 Length adjustment: 25 Effective length of query: 204 Effective length of database: 284 Effective search space: 57936 Effective search space used: 57936 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: 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