Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate HSERO_RS10040 HSERO_RS10040 O-acetyltransferase
Query= BRENDA::Q6IWF8 (311 letters) >FitnessBrowser__HerbieS:HSERO_RS10040 Length = 188 Score = 79.7 bits (195), Expect = 5e-20 Identities = 46/109 (42%), Positives = 63/109 (57%), Gaps = 2/109 (1%) Query: 171 ISDVFAVDIHPAARIGKGILLDHATGVVIGETAVIGNNVSILHHVTLGGTGKACGDRHPK 230 + VF + + ARIG G+ + H + + VIG ++ VT+G + G P Sbjct: 61 VETVFGISLPRTARIGPGLRIWHFGNIFLHGDVVIGAGCTLRQGVTIGNRRE--GGPVPV 118 Query: 231 IGDGCLIGAGATILGNVKIGAGAKVGAGSVVLIDVPPRATAVGNPARLV 279 +GD +GA A +LG V +G G KVGA SVVL DVPP ATAVG PAR++ Sbjct: 119 LGDNVELGAYAQVLGAVHLGDGCKVGAMSVVLDDVPPGATAVGAPARVI 167 Lambda K H 0.317 0.132 0.392 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: 139 Number of extensions: 9 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: 311 Length of database: 188 Length adjustment: 23 Effective length of query: 288 Effective length of database: 165 Effective search space: 47520 Effective search space used: 47520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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