Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_066919752.1 ACG33_RS06625 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_001579945.1:WP_066919752.1 Length = 365 Score = 389 bits (998), Expect = e-113 Identities = 199/363 (54%), Positives = 252/363 (69%), Gaps = 4/363 (1%) Query: 8 ASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPT 67 A + ++L F M RGG L G IAYET+G DNA+L+ TGL+P AHAAS DP+ Sbjct: 4 ARKILKLDRPFEMHRGGTLQGVEIAYETWGDPAHRGDNAILIFTGLTPSAHAASSESDPS 63 Query: 68 PGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIA 127 PGWWE M+GPG+P+DT + VICVNSLGS GST P S +P TG YRL+FP L++EDIA Sbjct: 64 PGWWEDMIGPGRPIDTRRFFVICVNSLGSPFGSTSPVSINPATGRAYRLTFPVLTVEDIA 123 Query: 128 DAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRS 187 A V +LGI +L VVG S+GGM+ LA A P AR+ +S+S A +LPF+IA+RS Sbjct: 124 HAGHEVVVSLGIEKLLAVVGPSLGGMTVLAYCALFPGAARSVVSISAAARSLPFAIALRS 183 Query: 188 LQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRAD 247 LQRE IR D W +G Y P GM ARKLGM+TYRSA+EW RFGR R +RR Sbjct: 184 LQREIIRRDSAWREGDYAADAIPVEGMRLARKLGMITYRSAKEWGLRFGRERADLQRRPG 243 Query: 248 QGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMR 307 FG +FEVESYL+ HA++F ++DPN YLY+S AMD FDL D GG AL R Sbjct: 244 D-PFGIDFEVESYLENHAEKFTGQYDPNCYLYISRAMDLFDLAD---HGGSVNEALRRFT 299 Query: 308 VERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVA 367 VERALV+G TD+LFP+ QQQE+A+GL+AGG +V+F+ + + GHD+FLVD++RF P +A Sbjct: 300 VERALVIGVETDLLFPIEQQQELAEGLAAGGREVTFVRLPSLQGHDSFLVDMDRFRPVIA 359 Query: 368 KFL 370 +FL Sbjct: 360 EFL 362 Lambda K H 0.321 0.138 0.427 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: 469 Number of extensions: 19 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: 374 Length of database: 365 Length adjustment: 30 Effective length of query: 344 Effective length of database: 335 Effective search space: 115240 Effective search space used: 115240 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 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