Align homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate Ac3H11_3736 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= BRENDA::P45131 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3736 Length = 355 Score = 96.7 bits (239), Expect = 9e-25 Identities = 96/297 (32%), Positives = 125/297 (42%), Gaps = 45/297 (15%) Query: 19 GGKLSHINVAYQTYGTLNAEKNNAVLICHALTGDAEPYFDDGRDGWWQNFMGAGLALDTD 78 G L + +AY T G E VL+ H G AE G G G G LD Sbjct: 46 GQTLPELKLAYSTVGEPTGEP---VLVLHGTNGSAESMLTPGFAG---TLFGPGQPLDAR 99 Query: 79 RYFFISSNVLGGCKGTTGPSSINPQTGKPYGSQFPNIVVQDIVKVQKALL-DHLGISHLK 137 ++F I + +G TG SS P G + FP D+V+ Q LL +HLG+ H++ Sbjct: 100 KHFIILPDAIG-----TGRSS-KPSDG--LRAAFPAYNYDDVVQAQYRLLTEHLGVRHVR 151 Query: 138 AIIGGSFGGMQANQWAIDYPDFMDNIVNLCSSIYFSAEAIGFNHVMR----QAVINDPNF 193 AIIG S GGM WA YPDFMD V + S A G N +MR +A+ NDP + Sbjct: 152 AIIGNSMGGMHTWVWAQRYPDFMDIAVPMAS---LPAAMSGRNWMMRRLLVEAIRNDPEW 208 Query: 194 NGGDYYEGTPPDQGLSIARM-LGMLTYRTDLQLAKAFGRATKSDGSFWGDYFQVESYLSY 252 GG+Y T + L A + G T L K +D L Sbjct: 209 QGGNY---TRQPRSLQFASVFFGTGTNGGHQGLQKLAPNRVAADA------------LVE 253 Query: 253 QGKKFLERFDANSYLHLLRALDMYDPSLGYDNVKEALSRIKARYTLVSVTTDQLFKP 309 Q K R DAN +++ A YDP G L RI AR ++ D+ P Sbjct: 254 QRLKAPFRGDANDHIYQWEASRDYDPEPG-------LERITARVLAINSADDERNPP 303 Lambda K H 0.320 0.139 0.422 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: 315 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: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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 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