Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_276609542.1 BQ4888_RS07655 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_900111775.1:WP_276609542.1 Length = 366 Score = 259 bits (661), Expect = 1e-73 Identities = 145/364 (39%), Positives = 210/364 (57%), Gaps = 9/364 (2%) Query: 9 SRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR--PDDP 66 ++F E + G L +AYET+G LNA R N +LV + DAHAA + PDD Sbjct: 6 TQFAEFDVELRLESGRLLGPLTLAYETYGELNADRSNVILVAHAWTGDAHAAGKNTPDDR 65 Query: 67 TPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDI 126 PGWW+ M+GPGK +DTD + V+C N +GSCKGSTGP ST+PRTG+PY L+FP L + D+ Sbjct: 66 KPGWWDDMIGPGKVLDTDRYFVLCSNVIGSCKGSTGPTSTNPRTGKPYNLTFPVLMVRDM 125 Query: 127 ADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVR 186 A + LGI L V+G SMG M AL +PE+ R+ I ++G P +IA+ Sbjct: 126 VRAQKLLLDRLGIDSLLTVIGGSMGAMQALEWSILYPEMVRSIIPIAGTGRTSPMAIALN 185 Query: 187 SLQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRA 246 +L R+AI +DP W +G+Y P G+ R +G +++ S +FGR R R Sbjct: 186 ALARQAIFNDPLWKKGNYKPEHPPADGLALGRAVGHISFLSDVSMQLKFGR-RFSARH-- 242 Query: 247 DQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRM 306 Q F +FE+E YLD++ F DRFD N++LYL+ A+D +D+ AL ++ Sbjct: 243 GQFDFFGQFEIERYLDYNGASFVDRFDTNAFLYLAKALDLYDV---AWNFESLEEALDQL 299 Query: 307 RVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPV 366 R +L +D L+ SQ +E+ L G V++ +++ GHD+FLV+ E+F P V Sbjct: 300 RCP-SLWFAFTSDWLYTPSQTEEVVTVLRKLGKPVAYHLIESDYGHDSFLVEPEKFTPKV 358 Query: 367 AKFL 370 +FL Sbjct: 359 VEFL 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: 388 Number of extensions: 17 Number of successful extensions: 4 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: 366 Length adjustment: 30 Effective length of query: 344 Effective length of database: 336 Effective search space: 115584 Effective search space used: 115584 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 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