Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate GFF4893 PS417_25075 hypothetical protein
Query= BRENDA::P95231 (229 letters) >FitnessBrowser__WCS417:GFF4893 Length = 188 Score = 47.0 bits (110), Expect = 3e-10 Identities = 36/100 (36%), Positives = 53/100 (53%), Gaps = 19/100 (19%) Query: 86 VVIGETAEVGDDVTIY---HGV-------------TLGGSGMVGGKRHPTVGDR-VIIGA 128 VV+G+ +G VTI HGV T ++ GK P + ++ V IG+ Sbjct: 78 VVVGDDCLIGSRVTIVDHEHGVYRKPSDHPASLPWTPPDERLLQGK--PIIIEKNVWIGS 135 Query: 129 GAKVLGPIKIGEDSRIGANAVVVKPVPPSAVVVGVPGQVI 168 GA ++G + IGE S IGANAVV + + ++ VG P +VI Sbjct: 136 GAIIVGGVTIGEGSVIGANAVVTRDISRYSLAVGAPAKVI 175 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: 147 Number of extensions: 17 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: 229 Length of database: 188 Length adjustment: 21 Effective length of query: 208 Effective length of database: 167 Effective search space: 34736 Effective search space used: 34736 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: 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