Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_245543356.1 BTUS_RS03205 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000092905.1:WP_245543356.1 Length = 383 Score = 260 bits (664), Expect = 5e-74 Identities = 142/351 (40%), Positives = 200/351 (56%), Gaps = 7/351 (1%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPTPGWWEAMVGPGK 79 + G L IAYE +G ARD +LV L+ DAHA + D PGWW+ ++GPG+ Sbjct: 28 LESGRVLDEVDIAYEAYGDPENARDRTILVCHALTGDAHAGNL--DGQPGWWDGLIGPGR 85 Query: 80 PVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGI 139 +DTD ++++C N LG C GSTGPAS P G P+ L FP ++I D+ +A + LGI Sbjct: 86 VLDTDRFYIVCSNVLGGCAGSTGPASPGP-DGRPWGLRFPPITIRDMVEAQRLWLEKLGI 144 Query: 140 SRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGW 199 + L V+G SMGGM AL +P+ I ++ + +IA + R AI +DP W Sbjct: 145 THLYAVIGGSMGGMQALEWAVTYPDRVERCIPIATSARLSAMAIAYNDVMRLAIMNDPMW 204 Query: 200 LQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVES 259 G Y GE P G+ AR +GM+TYR Q ++ RFGR+ +G F F+VES Sbjct: 205 NGGDYYNGEKPAAGLALARMVGMITYRGPQLYNARFGRSVVGREEADGPVDFEARFQVES 264 Query: 260 YLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTD 319 YL + ++ RFD NSYLYL AMD D+ G G GG A +R E L +G +D Sbjct: 265 YLRYQGEKLVRRFDANSYLYLIKAMDLHDI---GRGRGGVHAAYARTEAE-FLCIGIDSD 320 Query: 320 ILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFL 370 IL+P ++Q EIA+GL+A G V + + + GHDAFLV+ ++ + +FL Sbjct: 321 ILYPAAEQIEIAEGLAATGKRVQYREIRSVYGHDAFLVEFQQMSGALGEFL 371 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: 460 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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 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