Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_012399486.1 BPHY_RS00305 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000020045.1:WP_012399486.1 Length = 381 Score = 233 bits (593), Expect = 9e-66 Identities = 139/348 (39%), Positives = 192/348 (55%), Gaps = 8/348 (2%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDP-TPGWWEAMVGP 77 ++ G +L + ET+G LNAAR NAVLV L+ H A DDP GWW+ MVGP Sbjct: 20 LQNGSSLANYDLVVETYGKLNAARSNAVLVCHALNASHHVAGVYADDPKNVGWWDNMVGP 79 Query: 78 GKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRAL 137 GKP+DT+ + VI VN+LGSC GSTGP S DP TG PY SFP +++ED +A A Sbjct: 80 GKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPSTGRPYGASFPVVTVEDWVNAQARVADEF 139 Query: 138 GISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDP 197 GI + A V+G S+GGM ALA +P+ I ++ +IA + R +I SDP Sbjct: 140 GIEKFAAVMGGSLGGMQALAWSMMYPDRLEHCIVVASTPKLSAQNIAFNEVARSSILSDP 199 Query: 198 GWLQG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRT--RIGERRRADQGRFGPE 254 + G +Y G P+RG+ AR +G +TY S + +FGR R +A F E Sbjct: 200 DFHGGDYYAHGVKPKRGLRVARMIGHITYLSDDDMAAKFGRALRRAEGAEKAYNFNFDVE 259 Query: 255 FEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVM 314 FEVESYL + +FAD FD N+YL ++ A+D FD G AL+ + + L+ Sbjct: 260 FEVESYLRYQGDKFADYFDANTYLLITRALDYFD--PAKAYDGDLTAALAHTKA-KYLIA 316 Query: 315 GARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 TD F ++ +E+ L V++ +D P GHDAFL+D R+ Sbjct: 317 SFTTDWRFAPARSRELVKALLDHKRQVTYGEIDAPHGHDAFLLDDARY 364 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: 396 Number of extensions: 17 Number of successful extensions: 5 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: 381 Length adjustment: 30 Effective length of query: 344 Effective length of database: 351 Effective search space: 120744 Effective search space used: 120744 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 Jul 25 2024. The underlying query database was built on Jul 25 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