Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_012281269.1 HM1_RS00420 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000019165.1:WP_012281269.1 Length = 391 Score = 273 bits (697), Expect = 8e-78 Identities = 144/367 (39%), Positives = 203/367 (55%), Gaps = 7/367 (1%) Query: 6 PPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR--P 63 P F E D F + G L + YET+G LN R NA+L+ L+ D HAA + P Sbjct: 21 PQTFTFAEGSDAFVLESGSRLGPITVVYETYGVLNRERSNAILIAHALTGDHHAAGKNHP 80 Query: 64 DDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSI 123 + TPGWW+ ++GPGKP DT+ + +IC N LG C+G+TGPAS +P TG PY ++FP +I Sbjct: 81 SEKTPGWWDDLIGPGKPFDTNRFFIICSNVLGGCRGTTGPASINPATGRPYGMNFPVYTI 140 Query: 124 EDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSI 183 D+ + LGI RL V G SMGGM L +P++ + ++ A I Sbjct: 141 RDMVRVQKALIDHLGIERLLLVAGGSMGGMQVLEWGVTYPDMMDGLLPIATAGRMTAMGI 200 Query: 184 AVRSLQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGER 243 A + R+ I DP W G Y G+GP +G+ AR LGM+TYRS + + RFGR + Sbjct: 201 AFNEIMRQTIMLDPAWNGGDYAPGKGPAQGLAIARMLGMVTYRSDELFTARFGRRMTNNQ 260 Query: 244 RRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGAL 303 +A F FE+ESYL + + RFD N+Y+YL AMD D+G G GG A ++ Sbjct: 261 PKA-YFDFNNRFEIESYLHYQGDKLVRRFDANTYIYLCKAMDLLDVGRGRGGYEKALASI 319 Query: 304 SRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFG 363 + R L +G +D L+P E+A+ + G D + + +P GHDAFL++ ER Sbjct: 320 T----ARTLFIGVDSDWLYPPVYMIEMAEIMKKAGCDARYWELKSPHGHDAFLIEFERMR 375 Query: 364 PPVAKFL 370 P VA F+ Sbjct: 376 PLVASFV 382 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: 399 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: 391 Length adjustment: 30 Effective length of query: 344 Effective length of database: 361 Effective search space: 124184 Effective search space used: 124184 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