Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate AZOBR_RS20475 AZOBR_RS20475 homoserine acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >FitnessBrowser__azobra:AZOBR_RS20475 Length = 394 Score = 254 bits (648), Expect = 4e-72 Identities = 147/352 (41%), Positives = 195/352 (55%), Gaps = 6/352 (1%) Query: 23 GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASR-PDDPTPGWWEAMVGPGKPV 81 G L +AY+T+G+LNA R NA+L+ L+ D + + P PGWWE +VGPGKPV Sbjct: 30 GAELGPFEVAYQTYGALNADRSNAILICHALTGDHYVLDQHPVTGKPGWWEMLVGPGKPV 89 Query: 82 DTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGISR 141 DTD + VIC N +G C GSTGP TDP TGEPY L FP ++I D+ A V LGI + Sbjct: 90 DTDRYFVICSNVIGGCMGSTGPKETDPATGEPYGLGFPVITIGDMVRAQKLLVEHLGIDQ 149 Query: 142 LACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWLQ 201 L CV+G SMGGM L +PE + ++ A +IA + R+AI +DP W Sbjct: 150 LFCVIGGSMGGMQVLQWAVAYPESVFAAVPIATAARHSAQNIAFHEVGRQAIMADPDWAG 209 Query: 202 GHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVESY 260 G+Y EG P RG+ AR +TY S +FGR + R+ G F +F+VESY Sbjct: 210 GNYLLEGTRPHRGLAVARMAAHITYLSEPALHRKFGR-NLQNRQTVTYG-FDADFQVESY 267 Query: 261 LDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGG--GGAPGALSRMRVERALVMGART 318 L F +RFD NSYLY++ AMD FDL GGG A + R + + Sbjct: 268 LRHQGITFVERFDANSYLYITRAMDYFDLAADYGGGTLSNAFRKDGKGTPVRFCLASFSS 327 Query: 319 DILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVAKFL 370 D LFP S+ + I L+A A+VSF+ + T GHD+FL+D F + FL Sbjct: 328 DWLFPTSESRAIVHALNAVAANVSFVEIRTDKGHDSFLLDEPEFHQVIRGFL 379 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: 467 Number of extensions: 24 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: 394 Length adjustment: 30 Effective length of query: 344 Effective length of database: 364 Effective search space: 125216 Effective search space used: 125216 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