Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate Ac3H11_4277 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4277 Length = 401 Score = 236 bits (603), Expect = 6e-67 Identities = 146/389 (37%), Positives = 207/389 (53%), Gaps = 32/389 (8%) Query: 1 MREFIPPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAA 60 M F P S + P+ ++ G +L +AYET+G+LNA R NAVLV L+ H A Sbjct: 1 MSFFATPQS--LHFPEVLPLQSGASLRDYHLAYETYGTLNADRSNAVLVCHALNASHHVA 58 Query: 61 S--RPDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSF 118 D + GWW+ M+GPGKPVDTD + VI VN+LGSC GSTGP P TGE Y F Sbjct: 59 GVYAGQDKSEGWWDNMIGPGKPVDTDRFFVIGVNNLGSCFGSTGPMHNHPDTGEVYGADF 118 Query: 119 PELSIEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHA 178 P +++ED +A A + LGI++LA V+G S+GGM AL+ ++PE R + ++ A + Sbjct: 119 PVVTVEDWVNAQARLLDRLGITQLAAVLGGSLGGMQALSWTLQYPERMRHAVVVASAPNL 178 Query: 179 LPFSIAVRSLQREAIRSDPGWLQGH-YDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGR 237 +IA + R AI +DP + GH Y G P+RG+ AR +G +TY S + +FGR Sbjct: 179 TAENIAFNEVARRAIVTDPDFHGGHFYRHGVIPKRGLRIARMIGHITYLSDDVMNEKFGR 238 Query: 238 TRIGERRRADQGRFGP------------------------EFEVESYLDFHAQRFADRFD 273 + A +G P EF++ESYL + +F+D FD Sbjct: 239 SLRAPTLPAARGSLPPEGAGPARGGPAPDLRDYLYSTQDIEFQIESYLRYQGDKFSDYFD 298 Query: 274 PNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTDILFPLSQQQEIADG 333 N+YL ++ A+D FD GG AL+R + L++ TD F + +EI Sbjct: 299 ANTYLLITRALDYFD--PARAHGGNLTRALAR-ATAKFLLVSFTTDWRFSPQRSREIVKA 355 Query: 334 LSAGGADVSFLPVDTPAGHDAFLVDIERF 362 L VS+ +D P GHDAFL+D R+ Sbjct: 356 LLDNRRRVSYAEIDAPHGHDAFLLDDARY 384 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: 446 Number of extensions: 17 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: 401 Length adjustment: 30 Effective length of query: 344 Effective length of database: 371 Effective search space: 127624 Effective search space used: 127624 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