Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate N515DRAFT_4362 N515DRAFT_4362 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__Dyella79:N515DRAFT_4362 Length = 339 Score = 146 bits (369), Expect = 7e-40 Identities = 112/325 (34%), Positives = 160/325 (49%), Gaps = 47/325 (14%) Query: 47 VLVLTGLSPDAHAASRPDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPAST 106 V+V G+S + + D+ TPGWW+ VG G+P+D D + V+C++ L PA Sbjct: 62 VIVQGGISANREVVALDDEATPGWWQEAVGAGRPIDLDRYRVLCIDWLT-------PAEL 114 Query: 107 DPRTGEPYRLSFPELSIEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELA 166 D T +S ED ADA A V ALGI+R+ +G+S G M+ LA ARHP Sbjct: 115 DGATA---------VSSEDQADALAALVEALGIARVHAFIGSSYGAMAGLAFAARHPYAL 165 Query: 167 RTHISLSGAVHALPFSIAVRSLQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYR 226 + L+GA P + A R++QR +R E P + + AR+L M TYR Sbjct: 166 DRLVLLAGAHRPHPLATAQRAVQRGIVRLGV--------ETGQPEQALSLARQLAMTTYR 217 Query: 227 SAQEWDCRFGRTRIGERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQ 286 ++E+ RF T E R +GRF F VE YL +RF +RFD +L LS ++D Sbjct: 218 GSEEFSRRF--TAAPEFR---EGRF--HFPVEDYLVHQGRRFVERFDVERFLALSESIDL 270 Query: 287 FDLGDGGGGGGGAPGALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPV 346 D+ P ++ A ++G +D L PLS E+ L G A + L Sbjct: 271 HDV---------TPERIA----APATLIGFPSDRLVPLSDLCELQRRLH-GPATLEVL-- 314 Query: 347 DTPAGHDAFLVDIERFGPPVAKFLA 371 ++P GHDAFL + R P + LA Sbjct: 315 ESPYGHDAFLKETHRLAPLLRDALA 339 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: 330 Number of extensions: 13 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: 339 Length adjustment: 29 Effective length of query: 345 Effective length of database: 310 Effective search space: 106950 Effective search space used: 106950 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