Align Serine O-acetyltransferase; SAT; Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate 5210107 Shew_2551 homoserine O-succinyltransferase (RefSeq)
Query= SwissProt::A0A1D3PCK2 (262 letters) >FitnessBrowser__PV4:5210107 Length = 321 Score = 144 bits (364), Expect = 2e-39 Identities = 84/257 (32%), Positives = 140/257 (54%), Gaps = 13/257 (5%) Query: 5 VKIGILNLMHDKLDTQSHFIKVLPNADLTFFYPRMHYQNRPIP----PEVNMTSEPLDIN 60 +K+ ILNLM +K++T++ +++L N L + ++ +N + Sbjct: 36 MKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKVSKHTSIDHMNNFYRDFEAV 95 Query: 61 RVSEFDGFIITGAPIDQIDFSKITYIEEIRYLLQALDNHKIQQLYFCWGAMAALNYFYGI 120 R +DG IITGAP+ QI+F ++TY + IR ++ +H L+ CW A AAL + YG+ Sbjct: 96 RHKNYDGLIITGAPLGQIEFEEVTYWDHIREIIDWSQHHVTSVLFLCWAAHAALYHLYGL 155 Query: 121 KKKILAEKIFGVFPHLITEPH-PLLSGLSQGFMAPHARYAEMDKKQIMQDERLAINAVDD 179 ++K+L+ K GVF H T H PLL G F APH+R+AEM+ + + L + A D Sbjct: 156 QRKLLSAKRSGVFNHQRTHKHFPLLRGFDDEFFAPHSRFAEMEVADLKAHKELQVLAESD 215 Query: 180 NSHLFMVSAKDNPERN-FIFSHIEYGKDSLRDEYNRE----INAHPERHYKKPINYSMSN 234 + ++V +++N RN F+ H EY K +L+DEY R+ +N ++Y + + S + Sbjct: 216 EAGAYLVLSRNN--RNLFVMGHPEYQKSTLKDEYQRDLAEGLNPRVPKNYFRGDDPSQA- 272 Query: 235 PSFQWQDTQKIFFNNWL 251 P +W + +NWL Sbjct: 273 PVARWHGHGSLLVSNWL 289 Lambda K H 0.322 0.138 0.420 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: 210 Number of extensions: 10 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: 262 Length of database: 321 Length adjustment: 26 Effective length of query: 236 Effective length of database: 295 Effective search space: 69620 Effective search space used: 69620 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: 48 (23.1 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