Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_024851720.1 N745_RS0108625 alpha/beta fold hydrolase
Query= SwissProt::Q12XS2 (488 letters) >NCBI__GCF_000526715.1:WP_024851720.1 Length = 337 Score = 120 bits (301), Expect = 7e-32 Identities = 104/344 (30%), Positives = 162/344 (47%), Gaps = 49/344 (14%) Query: 18 GEFQLEGGHTLKNIRLAYETYGNLNKEKSNAILVCHALTGDAHAAGRHSDDDKKPGWWDD 77 G+F ++GG TL++ +LAY+T+G LN K N I+ +G+H D++ W Sbjct: 10 GDFVIQGGATLRDAKLAYKTFGTLNDAKDNVIVY------PTWYSGQHYDNE-----W-- 56 Query: 78 IIGPGKALDTDRYFVLCSNVLG-GCKGTTGPASLDPDTGRQYGITFPVITIRDMVNVQKR 136 +IG G ALD D+YF++ N+LG G + + D R FP T+ D V Q + Sbjct: 57 LIGSGMALDPDKYFIIIPNMLGNGLSSSPSNMPVPYDKAR-----FPGTTLFDNVTAQHK 111 Query: 137 LIDHM-GITTLFAVVGGSMGGMQTLQWCVAYPELVKKAVVIASTAVSSPQQIAFNEVGRN 195 L+ + GI + V G SMG QT QW YP++V++ +A +SP F E ++ Sbjct: 112 LVTELFGIGKIALVTGWSMGAQQTYQWGAQYPDMVERIAPFCGSAKTSPHNFVFLEGVKS 171 Query: 196 AIISDPDWNGGDYYEGEPPVNGL-STARMIAHITYLSDASMHEKFGRRLQQGESYK---F 251 A+ +D + G +YE +PP GL + AR+ A F + + E YK + Sbjct: 172 ALTADSAFEHG-WYE-KPPTKGLRAMARVYA----------GWGFSQPFYRQELYKVLGY 219 Query: 252 DMSNDFQVGSYLKYQGDTFTGRFDANSYLYATKAVDYFDLSMN----GSLAEGLKYVQAK 307 DF V + + D DAN+ L Y D+S N G + L + AK Sbjct: 220 SSLEDFLVAFWEGFFLDR-----DANNLLAMLWTWQYGDISANPIYEGDFEKALGSITAK 274 Query: 308 MLVISITSDWLYSPYHSKKIVEGLTVKEHDVSYREIESSYGHDA 351 +V+ +D + P ++ V K + +R I S +GH A Sbjct: 275 AIVMPGATDLYFPPEDNEYEVS----KMPNAEFRPIPSVWGHFA 314 Lambda K H 0.318 0.134 0.397 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: 371 Number of extensions: 23 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: 488 Length of database: 337 Length adjustment: 31 Effective length of query: 457 Effective length of database: 306 Effective search space: 139842 Effective search space used: 139842 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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