Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_034995436.1 DL88_RS09745 hypothetical protein
Query= SwissProt::Q3M5Q6 (359 letters) >NCBI__GCF_000745425.1:WP_034995436.1 Length = 347 Score = 148 bits (373), Expect = 2e-40 Identities = 112/315 (35%), Positives = 165/315 (52%), Gaps = 17/315 (5%) Query: 19 PFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSADADEWWEGLLGANKALDSD 78 PF LE GG + +Q+AY T+G+L++AGDN +L +G+ E + +G +ALD D Sbjct: 20 PFLLENGGTIRNLQLAYATFGELSAAGDNAILFPTWYSGTTKILE--QAYIGPGRALDPD 77 Query: 79 RDFIICSNILGSCYGTTGATSINPQTGIPYGAS-FPAITIRDMVRLQAALI-QHLGIKSL 136 R FII N +G+ G + A S NP P+ A+ FP ++I D VR Q L+ +H G+ L Sbjct: 78 RYFIILVNQIGN--GLSSAPSNNPA---PFNAARFPLVSIGDDVRAQHRLVTEHFGLTRL 132 Query: 137 QLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLSEAQRQAIYADPNWKGG 196 QLV+GGS+G Q EWA+ YPE V+ APIA + R SA L E+ +AI +D + G Sbjct: 133 QLVLGGSMGAQQTYEWAVRYPEFVRRAAPIAGTARASAHNQLLVESFIEAITSDRAYDNG 192 Query: 197 NYTKEQPPSQGL-AVARMMAMSAYRSWQSFTARFGRQYDAVADQFAIASYLQHHGQKLVQ 255 Y +GL AR+ A +A+ + + R + + + +++ G L Q Sbjct: 193 WYDNAGDIHRGLRRHARLFATAAFTP-RLYAEEGWRDLGFSSTEDFLTGFVE--GHFLPQ 249 Query: 256 RFDANTYITLTQAMDSHDVAQ--GRDYKSVLQSIKQPALVVAIDSDILYPPTEQQELADF 313 D N I L + DV + G D K L I V+AID D L+P ++ Sbjct: 250 --DPNNLILLARKWQGGDVGRNSGGDIKKALSHIIATTYVIAIDEDGLFPLSDIAAEQTL 307 Query: 314 IPDAQLGWLQSSYGH 328 +P +QL L S +GH Sbjct: 308 VPGSQLKHLSSIWGH 322 Lambda K H 0.319 0.134 0.406 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: 295 Number of extensions: 16 Number of successful extensions: 4 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: 359 Length of database: 347 Length adjustment: 29 Effective length of query: 330 Effective length of database: 318 Effective search space: 104940 Effective search space used: 104940 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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