Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_084276344.1 B8779_RS08945 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_900176045.1:WP_084276344.1 Length = 369 Score = 207 bits (528), Expect = 3e-58 Identities = 130/349 (37%), Positives = 189/349 (54%), Gaps = 13/349 (3%) Query: 20 MRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPD-DPTPGWWEAMVGPG 78 + G L I YET+G LN R N V+V LS HAA + D PGWW+A++G G Sbjct: 16 LESGRILEPYEIVYETYGQLNEDRSNVVVVCHALSGSHHAAGWYEGDRKPGWWDALIGDG 75 Query: 79 KPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALG 138 K +DT + VIC N+LGSC G+TGP S + EPYR FP ++I+D+ A LG Sbjct: 76 KAIDTKKFFVICTNTLGSCFGTTGPMSKMYPSDEPYRFKFPVITIKDMVKAQRILFAKLG 135 Query: 139 ISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPG 198 I R+ VVG SMGGM AL P A+ I+L+ P+ IA + +EAI DP Sbjct: 136 IDRVHAVVGGSMGGMQALRFAVDFPGFAKNIIALAATHATRPWVIAFNEIAKEAIIKDPD 195 Query: 199 WLQGHYDEGEGPRR---GMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEF 255 + G YD E ++ G+ R G +++ S D +FGR + + FG F Sbjct: 196 FKNGQYDPKELEQKGLTGLAIGRMAGHISFLSHYSMDRKFGRDYVPNEGIYE--LFG-RF 252 Query: 256 EVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMG 315 +VE YL+++ F+ FDP SYLY++ A++ FDL G AL R+R + ++G Sbjct: 253 QVERYLEYNGYNFSKWFDPLSYLYITKAINLFDLST---GYDSLEEALERIR-SKLYLIG 308 Query: 316 ARTDILFPLSQQQEIADGL-SAGGADVS-FLPVDTPAGHDAFLVDIERF 362 D+LF + ++I + + G ++S + V + GHDAFLV+I++F Sbjct: 309 FEKDLLFLPEEMRQIDEAMQKCGKGELSEYYEVKSDYGHDAFLVEIDKF 357 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: 377 Number of extensions: 21 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: 369 Length adjustment: 30 Effective length of query: 344 Effective length of database: 339 Effective search space: 116616 Effective search space used: 116616 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 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