Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate AZOBR_RS14580 AZOBR_RS14580 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__azobra:AZOBR_RS14580 Length = 398 Score = 182 bits (463), Expect = 1e-50 Identities = 117/359 (32%), Positives = 187/359 (52%), Gaps = 16/359 (4%) Query: 23 GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR--PDDPTPGWWEAMVGPGKP 80 GG + RI +E++G LN ARDN +LV S ++HAA + +DP PG+W++++GPGKP Sbjct: 45 GGTIKNVRIGWESYGKLNDARDNVILVTHFFSGNSHAAGKYKMEDPAPGYWDSIIGPGKP 104 Query: 81 VDTDLWHVICVNSLGSCKG------STGPASTDPRTGEPYRLSFPELSIEDIADAAAHTV 134 +DTD + +I ++L + +TGPAS +P TG+PY +SFP ++I D + + Sbjct: 105 LDTDKFFIISSDTLVNLSPKDPTVTTTGPASVNPDTGKPYGMSFPVVTIRDFVNVQKALL 164 Query: 135 RALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIR 194 +L + L V+G SMG + AL A HPE+ + +++ G A PF I +L IR Sbjct: 165 DSLNVKSLHAVMGGSMGSLQALEWGATHPEMVKRVVAVIGGAEADPFLIGWLNLWAAPIR 224 Query: 195 SDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPE 254 DP W G Y P+ G+ A KL + R + D FGR E + + Sbjct: 225 VDPNWQGGDYYGKAEPKAGLTEALKLVTLHARHWKWADATFGR-GWAEEGKDPAASMNNQ 283 Query: 255 FEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVM 314 + +E++LD A A D N +LYL A F + GGGG L++++ L+ Sbjct: 284 YAIEAWLDKAAAARAAVSDANHFLYLVKANQTFLV----GGGGSLDEGLAKIKAPVLLIP 339 Query: 315 GARTDILFPLSQ-QQEIADGLSAGGADVSFL-PVDTPAGHDAFLVDIERFGPPVAKFLA 371 A D++FP + + + + L G V++ + T GH + +I + G ++ F+A Sbjct: 340 SA-DDLVFPPERAMRPLKERLEKQGIAVTYTDAITTSLGHLDGIANIAKAGDAISAFMA 397 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: 412 Number of extensions: 19 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: 398 Length adjustment: 30 Effective length of query: 344 Effective length of database: 368 Effective search space: 126592 Effective search space used: 126592 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