Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate Echvi_3285 Echvi_3285 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Cola:Echvi_3285 Length = 351 Score = 179 bits (454), Expect = 1e-49 Identities = 115/350 (32%), Positives = 170/350 (48%), Gaps = 29/350 (8%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPTPGWWEAMVGPGK 79 + G +L G I+Y T G L +DN + +L L+ DA+ WW +VG K Sbjct: 25 LESGESLPGFEISYTTQGHLTPKKDNVIWILHALTGDANVHE--------WWSGLVGEDK 76 Query: 80 PVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGI 139 D + ++C N LGSC GST P S +P+TG+PY FP LS D+A A + LGI Sbjct: 77 FFDPTKYFIVCANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLSTRDMAKAFDRLRQHLGI 136 Query: 140 SRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGW 199 ++ ++G S+GG AL E + I ++ P++I QR AI SD W Sbjct: 137 QQIDTIIGGSLGGQVALEWSYNLQEQVKKTIIVASNAKTSPWTIGFNEAQRMAIESDSTW 196 Query: 200 LQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVES 259 Q D G ++G+ AR +GM++YR I +A+ F V S Sbjct: 197 GQNSPDAG---KKGLEAARAIGMLSYRHQD----------IFHASQAETEEKTDHFRVSS 243 Query: 260 YLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTD 319 YL + Q+ ++RF+ SY L+ AMD DLG G GG A A+ + L +G TD Sbjct: 244 YLRYQGQKLSNRFNALSYWVLTKAMDSHDLGRGRGGTAKALSAIK----AKVLSIGINTD 299 Query: 320 ILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKF 369 +LF + Q I+ + G ++ + + GHDAFLV+ E+ + F Sbjct: 300 LLFTKEESQFISKNVPNG----TYREISSIYGHDAFLVENEQLNYILTSF 345 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: 278 Number of extensions: 10 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: 351 Length adjustment: 29 Effective length of query: 345 Effective length of database: 322 Effective search space: 111090 Effective search space used: 111090 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