Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_086511565.1 BZY95_RS19555 homoserine acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_002151265.1:WP_086511565.1 Length = 410 Score = 167 bits (424), Expect = 4e-46 Identities = 118/368 (32%), Positives = 181/368 (49%), Gaps = 22/368 (5%) Query: 16 DGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR--PDDPTPGWWEA 73 D + G + RI +E +G+LN RDN +L+ S +HAA R DD PG+W+A Sbjct: 52 DEYTTVGGDTIAPVRIGWEAYGTLNEERDNVILITHFFSGTSHAAGRYTEDDAAPGYWDA 111 Query: 74 MVGPGKPVDTDLWHVICVNSLGSCK------GSTGPASTDPRTGEPYRLSFPELSIEDIA 127 ++GPGKP+DTD +++I ++L + +TGPA+ +P TGEP+ FP ++I D Sbjct: 112 IIGPGKPLDTDEYYIISSDTLVNLNVHDPNVTTTGPATPNPETGEPWGTDFPLVTIRDFV 171 Query: 128 DAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRS 187 + + + GI RL V+G SMG + A + +PE I + G A P+ +A S Sbjct: 172 EVQKALLESQGIERLHAVMGPSMGALQAYEWASTYPERVERLIPVIGGGVADPWLLATLS 231 Query: 188 LQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEW---DCRFGRTRIGERR 244 IR D W +G Y + E P G+ A KL + +A W + F R+ E Sbjct: 232 AWAAPIRLDANWNEGDYYDSEPPLDGLREALKLVTL---NANHWLWANETFDRSWADE-- 286 Query: 245 RADQGR-FGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGAL 303 AD R + +E LD A A+ D N LYL A F G GG G L Sbjct: 287 DADPTRELDARYAIEQTLDDIAAARAELADANHLLYLVKANQSFIAGHGGSLEEG----L 342 Query: 304 SRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFG 363 R+ L++ + D++F ++ A+ + GGADV + ++ GH ++ I++ G Sbjct: 343 GRIEAP-TLILYSENDLVFAPEGVRQTAELIEDGGADVELVTLEGKRGHLDGILAIDQAG 401 Query: 364 PPVAKFLA 371 + FLA Sbjct: 402 ERIRAFLA 409 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: 394 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: 410 Length adjustment: 31 Effective length of query: 343 Effective length of database: 379 Effective search space: 129997 Effective search space used: 129997 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 10 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