Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate YP_004140744.1 Mesci_1536 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000185905.1:YP_004140744.1 Length = 389 Score = 248 bits (634), Expect = 2e-70 Identities = 137/338 (40%), Positives = 193/338 (57%), Gaps = 7/338 (2%) Query: 23 GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPTPGWWEAMVGPGKPV 81 G L +IAY+T+G+LN AR NA+LV L+ D H AS P PGWWE ++GPGK + Sbjct: 34 GTLLSPFQIAYQTYGTLNDARSNAILVCHALTGDQHVASTNPVTGKPGWWEVLIGPGKII 93 Query: 82 DTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGISR 141 DT+ + VIC N +G C GSTGPAST+P TG+PY L P ++I D+ A + GI + Sbjct: 94 DTNRFFVICSNVIGGCLGSTGPASTNPATGKPYGLDLPIITIRDMVRAQQMLIDHFGIEK 153 Query: 142 LACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWLQ 201 L CV+G SMGGM L + +PE + + ++ +IA + R+A+ +DP W Sbjct: 154 LFCVLGGSMGGMQVLEWASSYPERVFSALPIATGARHSSQNIAFHEVGRQAVMADPDWHG 213 Query: 202 GHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVESY 260 G Y + G+ P +G+ AR +TY S +FGR + R A F +F++ESY Sbjct: 214 GKYFEHGKRPEKGLAVARMAAHITYLSEAALHRKFGRNL--QDREALTFGFDADFQIESY 271 Query: 261 LDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTDI 320 L F DRFD NSYLY++ +MD FDL GG A ++ R ++ +D Sbjct: 272 LRHQGMTFVDRFDANSYLYMTRSMDYFDLAADHGGRLADAFAGTKTRF---CLVSFTSDW 328 Query: 321 LFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVD 358 LFP + + I L+A GA VSF+ ++T GHDAFL+D Sbjct: 329 LFPTEESRSIVHALNAAGASVSFVEIETDRGHDAFLLD 366 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: 431 Number of extensions: 23 Number of successful extensions: 4 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: 389 Length adjustment: 30 Effective length of query: 344 Effective length of database: 359 Effective search space: 123496 Effective search space used: 123496 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