Align Homoserine O-acetyltransferase; HAT; HTS-like HTA; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012102026.1 CKL_RS08015 homoserine O-succinyltransferase
Query= SwissProt::Q9WZY3 (304 letters) >NCBI__GCF_000016505.1:WP_012102026.1 Length = 304 Score = 409 bits (1050), Expect = e-119 Identities = 187/304 (61%), Positives = 241/304 (79%), Gaps = 1/304 (0%) Query: 1 MPINVPSGLPAVKVLAKEGIFVMTEKRAIHQDIRPLEILILNLMPDKIKTEIQLLRLLGN 60 MPIN+P+ LPA KVL E IFVM E A+ QDIRPL I+ILNLMP K TEIQLLRLL N Sbjct: 1 MPINIPNNLPASKVLKAENIFVMNENHAVRQDIRPLNIIILNLMPLKTVTEIQLLRLLSN 60 Query: 61 TPLQVNVTLLYTETHKPKHTPIEHILKFYTTFSAVKDRKFDGFIITGAPVELLPFEEVDY 120 +P+QV+++L+Y ++H K+TP E+++K+Y TF +KD+KFDG IITGAPVE FE+VDY Sbjct: 61 SPIQVDISLMYLKSHNSKNTPAEYLIKYYETFEEIKDKKFDGMIITGAPVEKFEFEDVDY 120 Query: 121 WEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKDSV-LF 179 W+ELTEIM+WS NVYST++ICWA+QAGLY+ + IPKY L QK+SG++ H + + ++ LF Sbjct: 121 WKELTEIMDWSTRNVYSTIYICWASQAGLYHHFKIPKYTLEQKISGIFSHTLNEANIKLF 180 Query: 180 RGHDDFFWAPHSRYTEVKKEDIDKVPELEILAESDEAGVYVVANKSERQIFVTGHPEYDR 239 RG DD F+APHSRYT VK++DI++VPEL+I++ES EAGVY+VA K RQIF+ GHPEYD Sbjct: 181 RGFDDIFYAPHSRYTFVKRKDIERVPELKIISESKEAGVYIVATKGGRQIFIAGHPEYDT 240 Query: 240 YTLRDEYYRDIGRNLKVPIPANYFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQKTPYR 299 TL+ EY RDI NL + IP NYFP+D+P KTP+ W SH++L F NWLNY +YQ+TPY Sbjct: 241 LTLKSEYERDIALNLPIDIPQNYFPDDNPDKTPLSNWKSHSNLLFLNWLNYYVYQETPYD 300 Query: 300 LEDI 303 L + Sbjct: 301 LNKL 304 Lambda K H 0.322 0.140 0.440 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: 436 Number of extensions: 20 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: 304 Length of database: 304 Length adjustment: 27 Effective length of query: 277 Effective length of database: 277 Effective search space: 76729 Effective search space used: 76729 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 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