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 WP_069665168.1 BCR25_RS18890 homoserine O-succinyltransferase
Query= SwissProt::A0A1D3PCK2 (262 letters) >NCBI__GCF_001730305.1:WP_069665168.1 Length = 309 Score = 124 bits (311), Expect = 2e-33 Identities = 75/256 (29%), Positives = 125/256 (48%), Gaps = 11/256 (4%) Query: 5 VKIGILNLMHDKLDTQSHFIKVLPNADLT----FFYPRMHYQNRPIPPEVNMTSEPLDIN 60 ++I ILNLM K +T+ +++L N L F + H + Sbjct: 36 LQILILNLMPKKDETEVQLLRLLSNTPLQINVDFLHMSSHEAKNTSKDHLKRFYHQFSDV 95 Query: 61 RVSEFDGFIITGAPIDQIDFSKITYIEEIRYLLQALDNHKIQQLYFCWGAMAALNYFYGI 120 + +DG I+TGAP++Q+ F ++ Y E+ + Q H + CWGA A L Y + I Sbjct: 96 KEKYYDGLIVTGAPVEQLPFEEVDYWNELTDIFQWSKTHVFSTFHICWGAQAGLYYHHHI 155 Query: 121 KKKILAEKIFGVFPH-LITEPHPLLSGLSQGFMAPHARYAEMDKKQIMQDERLAINAVDD 179 +K L +K+ G++ H ++T +L G F+APH+RY +++ I E LAI A Sbjct: 156 QKHPLDKKLSGIYLHDVLTPTWSILKGFDDVFLAPHSRYTTVNRAAIEGVEELAILAESA 215 Query: 180 NSHLFMVSAKDNPERNFIFSHIEYGKDSLRDEYNRE----INAHPERHYKKPINYSMSNP 235 + +F+V K+N + H+EY +++L+ E+ R+ I HY P + S P Sbjct: 216 EAGIFLVGNKNN-RAFYAMGHLEYDRETLQQEFYRDQAKGIRPKLPEHY-FPNDDSQKYP 273 Query: 236 SFQWQDTQKIFFNNWL 251 +W + F+NWL Sbjct: 274 QLRWHMAASLLFSNWL 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: 211 Number of extensions: 11 Number of successful extensions: 2 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: 309 Length adjustment: 26 Effective length of query: 236 Effective length of database: 283 Effective search space: 66788 Effective search space used: 66788 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 Jul 26 2024. The underlying query database was built on Jul 25 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