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 7025621 Shewana3_2772 homoserine O-succinyltransferase (RefSeq)
Query= SwissProt::A0A1D3PCK2 (262 letters) >FitnessBrowser__ANA3:7025621 Length = 313 Score = 145 bits (366), Expect = 1e-39 Identities = 85/258 (32%), Positives = 137/258 (53%), Gaps = 15/258 (5%) Query: 5 VKIGILNLMHDKLDTQSHFIKVLPNADLTFFYPRMHYQNRPIP----PEVNMTSEPLDIN 60 +K+ ILNLM +K++T++ +++L N L + ++ +N + Sbjct: 36 MKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEDV 95 Query: 61 RVSEFDGFIITGAPIDQIDFSKITYIEEIRYLLQALDNHKIQQLYFCWGAMAALNYFYGI 120 R +DG IITGAP+ QIDF ++TY + IR ++ H L+ CW A A L + YG+ Sbjct: 96 RHKNYDGLIITGAPLGQIDFEEVTYWDHIREIIDWSQQHVTSVLFLCWAAHAGLYHLYGL 155 Query: 121 KKKILAEKIFGVFPHLITEPH-PLLSGLSQGFMAPHARYAEMDKKQIMQDERLAINAVDD 179 +KIL +K GVF H T H PLL G F APH+R+AEMD +++ Q L + A D Sbjct: 156 NRKILQQKRSGVFVHRRTCQHFPLLRGFDDEFFAPHSRFAEMDIEELKQHSELQVLAQSD 215 Query: 180 NSHLFMVSAKDNPERN-FIFSHIEYGKDSLRDEYNREINAH-----PERHYKKPINYSMS 233 + ++V +++N RN F+ H EY K +L DEY+R++ P+ +Y+ + Sbjct: 216 EAGAYLVLSRNN--RNLFVMGHPEYQKSTLNDEYHRDLAQGLNPNVPQNYYRN--DDPKD 271 Query: 234 NPSFQWQDTQKIFFNNWL 251 + +W + +NWL Sbjct: 272 DAIARWHSHGSLLVSNWL 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: 197 Number of extensions: 11 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: 313 Length adjustment: 26 Effective length of query: 236 Effective length of database: 287 Effective search space: 67732 Effective search space used: 67732 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