Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate CA265_RS08175 CA265_RS08175 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Pedo557:CA265_RS08175 Length = 352 Score = 161 bits (408), Expect = 2e-44 Identities = 106/354 (29%), Positives = 173/354 (48%), Gaps = 30/354 (8%) Query: 18 FAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPTPGWWEAMVGP 77 F + G + +IAY+T+G LNA +DN + V L+ +A WWE + G Sbjct: 13 FKLESGKKIRNLQIAYQTYGKLNANKDNVIWVCHALTANADVFE--------WWEGLFGQ 64 Query: 78 GKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRAL 137 + + +++C N LGS GS+ P ST+P TG PY LSFP+ +I D+ A L Sbjct: 65 NSLFNPEEHYIVCANVLGSHYGSSNPLSTNPVTGLPYYLSFPQFTIRDLVSAHQLLASHL 124 Query: 138 GISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDP 197 GI + ++G S+GG A+ P I ++ P+ IA QR AI +D Sbjct: 125 GIDYIKLLIGGSLGGQQAVEWSISEPNKIENLILIATNAAHSPWGIAFNESQRLAITTDR 184 Query: 198 GWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRI-GERRRADQGRFGPEFE 256 + + ++ G +G+ TAR + +++YR+ +G T++ + D F Sbjct: 185 TF---YANQPNGGSKGLKTARSIALLSYRTYS----AYGSTQVESVNDKTD------NFR 231 Query: 257 VESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGA 316 SY ++ ++ +RF+ SY YL+ AMD ++G A ++ LV+G Sbjct: 232 SSSYQNYQGEKLINRFNAYSYYYLTKAMDSHNVGRNRKSIADA----LKLITANTLVIGI 287 Query: 317 RTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFL 370 D+LFPLS+Q+ +AD + GA+ S L D GHD FL++ + + F+ Sbjct: 288 ENDVLFPLSEQKYLADHIP--GAEFSALHSD--YGHDGFLIETDALTNVIGNFI 337 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: 269 Number of extensions: 14 Number of successful extensions: 6 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: 352 Length adjustment: 29 Effective length of query: 345 Effective length of database: 323 Effective search space: 111435 Effective search space used: 111435 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: 49 (23.5 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