Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate Ga0059261_2301 Ga0059261_2301 homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Korea:Ga0059261_2301 Length = 371 Score = 249 bits (635), Expect = 1e-70 Identities = 144/363 (39%), Positives = 194/363 (53%), Gaps = 6/363 (1%) Query: 9 SRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPT 67 SR + LP + G L IAYET+G+L NA+L+ L+ D H AS P Sbjct: 10 SRHVTLPGPLRLDGGVLLSPVEIAYETYGTLAPDGGNAILICHALTGDQHVASPHPVTGK 69 Query: 68 PGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIA 127 PGWW MVGPGKPVD D ++C N LGSC GS+GPA+ +P TG P+ + FP ++I D+ Sbjct: 70 PGWWTRMVGPGKPVDPDRHFIVCANVLGSCMGSSGPATVNPATGRPWGMDFPVITIRDMV 129 Query: 128 DAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRS 187 A A + LG+ RL VVG SMGGM AL+ A P+ + ++ +IA Sbjct: 130 RAQAMLLDHLGVGRLKAVVGGSMGGMQALSWPATFPDRVDAVVVIASTARHSAQNIAFHE 189 Query: 188 LQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRAD 247 + R+A+ +DP W G Y +G+ P G+ AR +TY S +FGR + R A Sbjct: 190 VGRQAVMADPRWNGGAYYDGDPPAAGLAVARMAAHITYLSEAGLTEKFGRRL--QAREAK 247 Query: 248 QGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMR 307 F +F++ESYL F DRFD N+YLY++ AMD FDL + GG A R Sbjct: 248 SFGFDADFQIESYLRHQGLSFVDRFDANAYLYITRAMDYFDLAE--EHGGLLANAFRETR 305 Query: 308 VERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVA 367 LV TD L+P + I L+A GA VSF+ + +P GHDAFL++ V Sbjct: 306 ARFCLV-SFDTDWLYPTRDSRAIVHALNAAGAPVSFVELSSPFGHDAFLLEAPELNRVVD 364 Query: 368 KFL 370 FL Sbjct: 365 GFL 367 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: 475 Number of extensions: 26 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: 371 Length adjustment: 30 Effective length of query: 344 Effective length of database: 341 Effective search space: 117304 Effective search space used: 117304 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