Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_012334052.1 M446_RS20660 homoserine O-succinyltransferase
Query= curated2:Q65IA5 (302 letters) >NCBI__GCF_000019365.1:WP_012334052.1 Length = 315 Score = 110 bits (274), Expect = 5e-29 Identities = 88/285 (30%), Positives = 121/285 (42%), Gaps = 39/285 (13%) Query: 36 LNIVILNLMPQKI--KTETQLLRMLGNSPLQVYFTFLIPSTHTPKHT----PRQHLEQFY 89 L + +LN MP T+ Q +LG + F H P+ R L Sbjct: 24 LTVGLLNNMPDAALAATDRQFSALLGREVRLLRF-------HLPEIARGPEARDMLAPLS 76 Query: 90 TTFSSIRDRKFDGMIITGAPIEHLEYEEVSYWEELREILDWSKTHVTSTLHICWGAQAGL 149 ++ D +I+TG + + YW L ++DW++ H STL C A A + Sbjct: 77 APADALEGAGLDALIVTGCEPRAADLRDEPYWPALAGVIDWARDHTVSTLFSCLAAHAAV 136 Query: 150 YHHYGIRKVKLPKKTFGVFEHRIMEKNERLVRGFEEFYYVPHSRHTDINMDDLKAVSHLK 209 H GI + ++ +K G+F R + + L+ G VPHSR D+ DL A S Sbjct: 137 LHLDGIARRRMARKRSGIFACRPVAAHP-LLAGMPAVLPVPHSRWNDLAEADL-AASGYH 194 Query: 210 VLSISDEAGVCLIASKDEK-QVFLTGHPEYDTDTLKEEYERDL------ARNMEIDPPVN 262 VL+ SDEAGV L + VFL GHPEYD D+L EY RDL R D PV+ Sbjct: 195 VLTRSDEAGVDLFVKPERSLLVFLQGHPEYDPDSLAREYRRDLKRFGRGERAEPPDRPVH 254 Query: 263 YFKEGPDGAV-----------------PVNRWKAHATLLFMNWLN 290 YF + A+ W A LF NWL+ Sbjct: 255 YFDPEIEAALDDHARGGWAGEPSCAPPAAPAWPPVAAQLFRNWLS 299 Lambda K H 0.321 0.138 0.426 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: 251 Number of extensions: 16 Number of successful extensions: 3 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: 302 Length of database: 315 Length adjustment: 27 Effective length of query: 275 Effective length of database: 288 Effective search space: 79200 Effective search space used: 79200 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: 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