Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_041101080.1 SUTH_RS17455 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000828635.1:WP_041101080.1 Length = 372 Score = 229 bits (585), Expect = 7e-65 Identities = 138/357 (38%), Positives = 198/357 (55%), Gaps = 13/357 (3%) Query: 19 AMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPTP--GWWEAMVG 76 A++ GG L + YET+G+LNAA+ NA+LV LS H A + GWW+ +VG Sbjct: 19 ALKGGGLLPAFDLVYETYGTLNAAKSNAILVCHALSGHHHVAGHTEGNPANIGWWDNIVG 78 Query: 77 PGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRA 136 PG+P+DT+ + ++ VN+LG C GSTGPAST+P TG+P+ FP +++ED DA A Sbjct: 79 PGRPLDTERFFIVGVNNLGGCHGSTGPASTNPATGKPWGADFPVVTVEDWVDAQARLADH 138 Query: 137 LGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSD 196 LGI A V+G S+GGM AL P+ R + ++ A +IA + R+AI +D Sbjct: 139 LGIGAWAAVMGGSLGGMQALQWTLSFPDRVRHALVIAAAPKLSAENIAFNDVARQAILTD 198 Query: 197 PGWLQGH-YDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFG--P 253 P + GH Y+ G P RG+ AR LG +TY S + +FGR R R G +G Sbjct: 199 PDFHGGHFYEHGVRPVRGLRLARMLGHITYLSDDQMAEKFGR-----RLRTGAGSYGFDV 253 Query: 254 EFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALV 313 EFE+ESYL + +FA FD N+YL ++ A+D FD AL+R R + LV Sbjct: 254 EFEIESYLRYQGDKFAGVFDANTYLRMTKALDYFD--PAQDFDDDLARALARARA-KFLV 310 Query: 314 MGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFL 370 + TD F + +EI L G V++ +D+ GHD+FL+D + V +L Sbjct: 311 VAFSTDWRFSPERSREIVHALVHNGQAVAYAEIDSAHGHDSFLMDEPHYHAVVDTYL 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: 435 Number of extensions: 18 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: 372 Length adjustment: 30 Effective length of query: 344 Effective length of database: 342 Effective search space: 117648 Effective search space used: 117648 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