Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_043768587.1 U743_RS11950 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000733765.1:WP_043768587.1 Length = 383 Score = 226 bits (576), Expect = 8e-64 Identities = 136/366 (37%), Positives = 195/366 (53%), Gaps = 9/366 (2%) Query: 12 IELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--RPDDPTPG 69 + D + G +L G + +ET+G LNA R NAVLV LS D HAA ++ PG Sbjct: 19 LHFDDHLELECGRSLNGFDLVFETYGRLNAERSNAVLVCHALSGDHHAAGYHSAEERKPG 78 Query: 70 WWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADA 129 WW+A +GPGKP+DT+ V+ +N+LG C GS+GP S +P TG P+ FP +++ D A Sbjct: 79 WWDACIGPGKPIDTNRLFVVSLNNLGGCAGSSGPTSINPETGHPWGADFPMVTVRDWVRA 138 Query: 130 AAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQ 189 A LGI + A VG S+GGM + PE R + ++ A +IA + Sbjct: 139 QALLADRLGIDQWAAAVGGSLGGMQVMQWAIDEPERLRHAVVIAAAPKLSAQNIAFNEIA 198 Query: 190 REAIRSDPGWLQGHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQ 248 R+AI +DP + G Y + G P RG+ AR LG +TY S + +FGR R R Sbjct: 199 RQAIFADPDFHAGRYLEHGVTPERGLRLARMLGHITYLSDEAMREKFGRMR---RSDILG 255 Query: 249 GRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRV 308 F EFEVESYL + Q+F RFD N+YL ++ A+D FD GG + R++ Sbjct: 256 YHFDVEFEVESYLRYQGQQFVSRFDANTYLLMTKALDYFD--PASEYGGDLAATMERVQA 313 Query: 309 ERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAK 368 R+LV+ D F + +EI L A V+++ V + GHD FL+ I + + Sbjct: 314 -RSLVIAFEADWRFSPERSREIVQALVAARKPVAYVCVPSSLGHDDFLMPIPYYHRILGD 372 Query: 369 FLAIVA 374 ++A VA Sbjct: 373 YIARVA 378 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: 441 Number of extensions: 26 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: 383 Length adjustment: 30 Effective length of query: 344 Effective length of database: 353 Effective search space: 121432 Effective search space used: 121432 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