Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_011386326.1 AMB_RS20100 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000009985.1:WP_011386326.1 Length = 393 Score = 240 bits (612), Expect = 6e-68 Identities = 136/343 (39%), Positives = 188/343 (54%), Gaps = 7/343 (2%) Query: 30 RIAYETFGSLNAARDNAVLVLTGLSPDAHAAS-RPDDPTPGWWEAMVGPGKPVDTDLWHV 88 ++AY+T+G LNA + NA+L+ L+ D + A P PGWW +VGPG+ DTD + + Sbjct: 39 QVAYQTYGRLNADKSNAILICHALTGDHYVADPHPITAKPGWWHELVGPGRVFDTDRYFL 98 Query: 89 ICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGISRLACVVGA 148 IC N LG C G+TGP +P TG+ + L FP ++I D+ A V LGI +L CVVG Sbjct: 99 ICSNVLGGCMGTTGPVDENPATGQAWGLDFPVITIGDMVKVQARLVDHLGIDQLFCVVGG 158 Query: 149 SMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWLQGHY-DEG 207 SMGGM L +PE + I ++ A +IA + R+AI +DP W +G+Y EG Sbjct: 159 SMGGMQVLKWAQVYPERVFSAIPIASAARHSAQNIAFHEVGRQAIMADPDWCEGNYLQEG 218 Query: 208 EGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVESYLDFHAQR 267 + P RG+ AR +TY S +FGR + R G F +F+VESYL Sbjct: 219 KRPHRGLAVARMAAHITYLSEPALHQKFGR-NLQNRDTVTYG-FDADFQVESYLRHQGNT 276 Query: 268 FADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTDILFPLSQQ 327 F DRFD NSYLY++ AMD FDL GG R R V+ +D LFP + Sbjct: 277 FVDRFDANSYLYITRAMDYFDL---AAESGGVLANAFRGTRTRFCVVSFTSDWLFPTPES 333 Query: 328 QEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFL 370 + + L+A A+VSF+ + + GHDAFL+D F + FL Sbjct: 334 RAVVHALNAVAANVSFVEIKSDKGHDAFLLDEPEFHATLTGFL 376 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: 438 Number of extensions: 26 Number of successful extensions: 5 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: 393 Length adjustment: 30 Effective length of query: 344 Effective length of database: 363 Effective search space: 124872 Effective search space used: 124872 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 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