Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate N515DRAFT_2885 N515DRAFT_2885 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Dyella79:N515DRAFT_2885 Length = 368 Score = 452 bits (1163), Expect = e-132 Identities = 225/363 (61%), Positives = 270/363 (74%), Gaps = 2/363 (0%) Query: 8 ASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPT 67 A R+ LP F M+RGG L+GAR+A+ET+G+L+ ARDNA+L+LTGLSP AHAAS DP+ Sbjct: 5 ARRYFSLPSPFPMKRGGELHGARVAFETWGALSDARDNALLILTGLSPSAHAASNEQDPS 64 Query: 68 PGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIA 127 PGWWEAM+GPGK +DTD W VICVNSLGS KGST PAS DP TGEPYRLSFPEL++ED+A Sbjct: 65 PGWWEAMIGPGKAIDTDRWFVICVNSLGSDKGSTCPASIDPATGEPYRLSFPELALEDVA 124 Query: 128 DAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRS 187 +AA V +LGI +LAC+VG SMGGMSALA + HP RTHIS+ A A PF+IA+RS Sbjct: 125 NAAHAAVSSLGIEQLACLVGCSMGGMSALAYMLLHPGSVRTHISVDTAPQAQPFAIAIRS 184 Query: 188 LQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRAD 247 LQREAIR DP W G YD+ P GM ARKLG++TYRSA EW+ RF R R+ +R D Sbjct: 185 LQREAIRLDPQWNNGRYDDAHYPETGMSIARKLGVITYRSAMEWNGRFARIRLDAEQRDD 244 Query: 248 QGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMR 307 FG EF+VESYL+ HAQRF FDPNSYLYLS A D FD+ + G G L R+R Sbjct: 245 DVPFGFEFQVESYLEGHAQRFVRTFDPNSYLYLSRASDWFDISE--YGEGSIQAGLKRIR 302 Query: 308 VERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVA 367 VE+ALV+G TDILFPL QQ++IA+GL A GA V F+ +D+P GHDAFLVDIE + + Sbjct: 303 VEQALVIGVSTDILFPLEQQEQIAEGLEAAGAAVEFVALDSPQGHDAFLVDIENYSRAIG 362 Query: 368 KFL 370 FL Sbjct: 363 GFL 365 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: 469 Number of extensions: 15 Number of successful extensions: 2 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: 368 Length adjustment: 30 Effective length of query: 344 Effective length of database: 338 Effective search space: 116272 Effective search space used: 116272 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