Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate Dsui_0741 Dsui_0741 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__PS:Dsui_0741 Length = 375 Score = 224 bits (571), Expect = 3e-63 Identities = 133/355 (37%), Positives = 196/355 (55%), Gaps = 9/355 (2%) Query: 23 GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR-PDDP-TPGWWEAMVGPGKP 80 G L + YET+G LNA R NAVLV LS H A D+P GWW+ +VGPGKP Sbjct: 26 GATLAAYDLVYETYGRLNADRSNAVLVCHALSGSHHVAGHYADNPKNVGWWDNLVGPGKP 85 Query: 81 VDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGIS 140 +DTD + V+ VN+LG C GSTGP S +P TG+PY FP +++ED ++ A LGI+ Sbjct: 86 LDTDKFFVVGVNNLGGCYGSTGPGSINPATGKPYGADFPVVTVEDWVESQARLADRLGIN 145 Query: 141 RLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWL 200 + A ++G S+GGM AL +PE R + ++ A +IA + R+AI +DP + Sbjct: 146 QWAAIIGGSLGGMQALQWSLEYPERVRHALVIASAPKLTAQNIAFNEVARQAILTDPDFH 205 Query: 201 QG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVES 259 G +Y+ G P RG+ AR +G +TY S + +FGR R + + +FE+ES Sbjct: 206 GGNYYEHGVVPARGLRLARMVGHITYLSDDQMGEKFGRQL---REGVLKYNYDVDFEIES 262 Query: 260 YLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTD 319 YL + +FA FD N+YL + A+D FD GG AL+R + L++ TD Sbjct: 263 YLRYQGDKFAGFFDANTYLITTKALDYFD--PARDFGGDLKAALARASA-KFLLVSFTTD 319 Query: 320 ILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFLAIVA 374 F + +E+ L +VS+ +D AGHD+FL+D ++ + +L +A Sbjct: 320 WRFAPERSREMVYALLHNNREVSYAEIDCNAGHDSFLLDDAQYHAVMGAYLHNIA 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: 407 Number of extensions: 18 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: 375 Length adjustment: 30 Effective length of query: 344 Effective length of database: 345 Effective search space: 118680 Effective search space used: 118680 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