Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate BPHYT_RS01595 BPHYT_RS01595 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__BFirm:BPHYT_RS01595 Length = 381 Score = 231 bits (589), Expect = 2e-65 Identities = 142/352 (40%), Positives = 195/352 (55%), Gaps = 16/352 (4%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPTP-GWWEAMVGP 77 ++ G +L G + ET+G+LNAAR NAVLV L+ H A D+P GWW+ MVGP Sbjct: 20 LQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYADNPKDIGWWDNMVGP 79 Query: 78 GKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRAL 137 GKP+DTD + VI VN+LGSC GSTGP S DP TG PY +FP +++ED +A A Sbjct: 80 GKPLDTDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPVVTVEDWVNAQARVADQF 139 Query: 138 GISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDP 197 GI+R A V+G S+GGM ALA +PE I ++ +IA + R AI SDP Sbjct: 140 GITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKLSAQNIAFNEVARSAILSDP 199 Query: 198 GWLQG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQG------R 250 + G +Y P+RG+ AR +G +TY S + +FGR+ RRA+ Sbjct: 200 DFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGRS----LRRAEGAVDAYNFN 255 Query: 251 FGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVER 310 F EFEVESYL + +FAD FD N+YL ++ A+D FD G A A + + Sbjct: 256 FDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFDGDLTAAVAHT---TAK 312 Query: 311 ALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 L+ TD F ++ +E+ L V++ +D P GHDAFL+D R+ Sbjct: 313 YLIASFSTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLDDARY 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: 397 Number of extensions: 19 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 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