Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_011654184.1 RL_RS28060 homoserine O-acetyltransferase
Query= curated2:Q67NS3 (383 letters) >NCBI__GCF_000009265.1:WP_011654184.1 Length = 391 Score = 226 bits (577), Expect = 6e-64 Identities = 131/358 (36%), Positives = 199/358 (55%), Gaps = 10/358 (2%) Query: 26 VLESGQRLTDVTLCYEVFGRLNPAGDNAILVCHALTGDSHVAGRYRPDDPKPGWWDDAVG 85 V G+ + ++ L YE +G LN A DNAIL+ H +G+SH AG+Y+ D G+WD +G Sbjct: 34 VTRGGRTVPEMRLGYETYGTLNDAKDNAILIPHYFSGNSHAAGKYKEADVSAGYWDAIIG 93 Query: 86 PGKALDTDRYCVICSNV---LGGCQGS---TGPSSVNPATGRPYGLDFPLVTVRDMVRAQ 139 GK +DTD+Y V+ + LG + TGP++ NP TG+P+G+DFP++T+ D V Q Sbjct: 94 SGKPVDTDKYFVVSVDTPVNLGANDPNVITTGPATTNPKTGKPWGMDFPIMTIGDFVDTQ 153 Query: 140 ARLLDLLGVRRLLAVIGGSLGAMQALEWAATYPDRMRGIIPIGGAGRFHPQGIAFNEVQR 199 L++ LG+ + AV+G S+G +Q+ EWAA YPD++ +IP+ +G IA+ +V Sbjct: 154 KGLMEQLGIGKWHAVMGASMGGLQSYEWAARYPDKLERVIPVISSGWADANLIAWLDVWA 213 Query: 200 QAILNDPGFLGGQYYGTPGPVRGLATARMLGMITYRSDESMWTQ--FGRNPQGEANPLHQ 257 I DP + GG YY P GLA A + +T +++ + WT FGR+ E Q Sbjct: 214 SPIKLDPNWNGGDYYTGQAPNAGLAQA--MKTLTLQANSAEWTDGTFGRDWASEGADPGQ 271 Query: 258 GFAVAYQVESYLHYQGRKLVERFDANSYLYLTRAMDLMDLGRGRGSYEEAHARIQARVLA 317 +A Y+V + L+ G V + DAN +LYL RA L G+ + S + I V+ Sbjct: 272 SWANDYKVVTKLNEAGAARVAQSDANHFLYLARANQLFVAGQPKDSLYKGLLNIDVPVML 331 Query: 318 VGIRSDLLFPTYLQRETVELVRASGGRAEYVEMDSPWGHDAFLLDFPLIEEPIRRFLQ 375 + DL+FP R T ++++ G E+VE++ GH LL E IR FL+ Sbjct: 332 IYTDEDLIFPGDAVRGTGTIIKSDGTPVEFVELEGTRGHMDGLLSIAQAGERIRAFLE 389 Lambda K H 0.321 0.140 0.432 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: 437 Number of extensions: 18 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: 383 Length of database: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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: 50 (23.9 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