Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_012591475.1 MSIL_RS12645 hypothetical protein
Query= curated2:Q6ADB9 (402 letters) >NCBI__GCF_000021745.1:WP_012591475.1 Length = 345 Score = 130 bits (328), Expect = 4e-35 Identities = 97/310 (31%), Positives = 147/310 (47%), Gaps = 33/310 (10%) Query: 48 IGAFGFESGESLPFVRIAYETWGELSPARDNAVLVLHALTGDSHAVGAAGPGHRTSGWWQ 107 +G F ESG+ + +++AY T+GEL+P + NA+L +G ++ + +A Sbjct: 18 LGDFDLESGDKIRGLKLAYATFGELAPDKSNAILFPTWYSGTTNILESA----------- 66 Query: 108 GIIGPGKAIDTDRWFVAVPNMLGGCQGTTGPTSIAPDGAEWGARFPFTTIRDQVKAQAAF 167 +G G+A+D ++F+ + N +G T+ + AP A ARFP +I D V+AQ Sbjct: 67 -YLGEGRALDASKYFIILVNQIGNGLSTSPSNTPAPFNA---ARFPKISIADDVRAQRRL 122 Query: 168 -ADALGIGRWAAVVGGSMGGMQALEWAVGFPERVERLAVIAAPPHSTADQIAFNSVQLGA 226 A+ G+ + A V+GGSMG EWAV FPE VER A IA TA S + A Sbjct: 123 IAEKFGLEKLALVLGGSMGAQMTFEWAVRFPEAVERAAPIAGTARGTAHNRLLVSTFIEA 182 Query: 227 IRTDPLFHGGSYYDEKDGEGPHQGLALARRMALITYRSLSELNDRFER-TWQSGISPLGD 285 I +DP F GG Y D H+GL R+ + + D + R W+S Sbjct: 183 IESDPAFDGGWYAD----GAAHRGLRRHARL----FAAAGFTPDLYNRAAWRS------- 227 Query: 286 GGRFAVESYLDFHGNKFTRRFDANSYLTLVQAMNSHDVGHD-GSGLAAALSRVTATTLVV 344 G + E +L D N+ + L +D G + AAL+ + A T V+ Sbjct: 228 LGFTSSEDFLTGFVEAHFLPQDPNNLILLATKWRENDAARRFGGDIVAALASIKAKTFVI 287 Query: 345 GIDSDRLFPV 354 I+ D FP+ Sbjct: 288 AIEEDGFFPL 297 Lambda K H 0.319 0.137 0.427 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: 399 Number of extensions: 21 Number of successful extensions: 5 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: 402 Length of database: 345 Length adjustment: 30 Effective length of query: 372 Effective length of database: 315 Effective search space: 117180 Effective search space used: 117180 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