Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_020173605.1 A3OQ_RS0101625 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000385335.1:WP_020173605.1 Length = 397 Score = 262 bits (669), Expect = 1e-74 Identities = 147/357 (41%), Positives = 201/357 (56%), Gaps = 7/357 (1%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPTPGWWEAMVGPG 78 M G L +AY+T+G+LNA + NA+LV L+ D H A+ P PGWWE MVGPG Sbjct: 33 MDAGVLLSPLTVAYQTYGTLNAQKSNAILVCHALTGDQHVANTHPVTGKPGWWEIMVGPG 92 Query: 79 KPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALG 138 +P+DTD + VI N +G C G+TGP+ST+P TG Y L P ++I+D+ A A V LG Sbjct: 93 RPIDTDRYFVISSNVVGGCMGTTGPSSTNPATGRAYGLDLPVVTIKDMVRAQAMLVDHLG 152 Query: 139 ISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPG 198 I L CVVG SMGGM L A +PE + ++ A +IA + R+AI +DP Sbjct: 153 IDTLCCVVGGSMGGMQVLQWAASYPERVFAAMPIATAARHSSQNIAFHEVGRQAIMADPD 212 Query: 199 WLQGHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEV 257 W +G Y DEG P +G+ AR +TY S + +FGR + R A F +F++ Sbjct: 213 WCKGRYLDEGRQPTKGLAVARMAAHITYMSDEALQRKFGRKL--QDRIAPTFSFDADFQI 270 Query: 258 ESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGAR 317 E+YL + F DRFD NSYLY++ A D FDL + GG S+ R V+ Sbjct: 271 ENYLRYQGSSFVDRFDANSYLYVTRACDYFDLAEDYGGSLALAFKGSKTRF---CVVSFN 327 Query: 318 TDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFLAIVA 374 +D L+P + + I L+AGGA VSF+ ++T GHDAFL+D+ F FL A Sbjct: 328 SDWLYPTAASRAIVHALNAGGASVSFVDIETERGHDAFLLDVPDFIATTRGFLEAAA 384 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: 428 Number of extensions: 27 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: 397 Length adjustment: 30 Effective length of query: 344 Effective length of database: 367 Effective search space: 126248 Effective search space used: 126248 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