Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_005455200.1 SACCYDRAFT_RS07935 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000244975.1:WP_005455200.1 Length = 376 Score = 238 bits (607), Expect = 2e-67 Identities = 147/371 (39%), Positives = 199/371 (53%), Gaps = 23/371 (6%) Query: 6 PPASRFIELPDG-FAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--R 62 PP R P+ + G L G IAYET+G+LNA NAVL+ L+ D+HAA Sbjct: 21 PPGRRQWFRPEAVLRLESGQELPGVEIAYETWGTLNADASNAVLIEHALTGDSHAAGDIE 80 Query: 63 PDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELS 122 P P+PGWW+ ++GPGK +DTD V+ N LG C+GSTGPAS G + FP ++ Sbjct: 81 PGHPSPGWWDGLIGPGKALDTDELFVVVPNVLGGCQGSTGPAS-PAEDGRYWGSRFPRIT 139 Query: 123 IEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFS 182 + D ALG+ R A V+G SMGGM AL P R + L+ + Sbjct: 140 VRDQVAVEVALADALGVERWAAVLGGSMGGMRALEWAVMEPSRVRALMVLASPAASSADQ 199 Query: 183 IAVRSLQREAIRSDPGWLQGHY---DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTR 239 IA + Q AI +DP W G Y GEGP G+ AR++ TYRSA+E + RFG Sbjct: 200 IAWSAPQLHAILADPNWKGGDYHAGGPGEGPHLGLGVARRIAHATYRSAEELNERFG--- 256 Query: 240 IGERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGA 299 R+ QG P F VESYLD HA + RFD SY+ L+ +M+ D+G G GG G Sbjct: 257 -----RSPQGEGDPRFAVESYLDHHADKLVRRFDAASYVLLTRSMNGHDVGRGRGGVG-- 309 Query: 300 PGALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDI 359 ALSR+ R + +G +D L+P Q +E+ADG+ + + +P GHD+FLV+ Sbjct: 310 -EALSRV-TARTIAVGVDSDRLYPPGQVRELADGIPT----ARYAEISSPYGHDSFLVET 363 Query: 360 ERFGPPVAKFL 370 E+ V + L Sbjct: 364 EQVATLVKELL 374 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: 495 Number of extensions: 35 Number of successful extensions: 7 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: 376 Length adjustment: 30 Effective length of query: 344 Effective length of database: 346 Effective search space: 119024 Effective search space used: 119024 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: 50 (23.9 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