Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_011778808.1 MVAN_RS07820 homoserine O-acetyltransferase
Query= SwissProt::D2Z028 (374 letters) >NCBI__GCF_000015305.1:WP_011778808.1 Length = 375 Score = 219 bits (559), Expect = 7e-62 Identities = 136/378 (35%), Positives = 192/378 (50%), Gaps = 18/378 (4%) Query: 2 REFIPPASRFIELPDG-FAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAA 60 R +PP + G + G + IA + +G L+A RDN V+VL L+ D+H Sbjct: 10 RVALPPEGEIAIVDIGPLTLENGEVIDDVSIAVQRWGELSARRDNVVVVLHALTGDSHIT 69 Query: 61 --SRPDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSF 118 + PD PTPGWW+ + GPG P+DTD W I N LG C+GSTGP+S P G+ + F Sbjct: 70 GPAGPDHPTPGWWDGVAGPGAPIDTDRWCAISTNVLGGCRGSTGPSSLAP-DGKAWGSRF 128 Query: 119 PELSIEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHA 178 P +SI D A + GI+ +A V+G SMGG AL + HP+ R + L+ A Sbjct: 129 PTISIRDQVAADVAALERFGITEVAAVIGGSMGGARALEWMMLHPDSVRAALVLAVGARA 188 Query: 179 LPFSIAVRSLQREAIRSDPGWLQGHY-DEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGR 237 I + Q AI+SDP W G Y G P G+ AR+ +TYR E D RFG Sbjct: 189 TADQIGTQCTQVAAIKSDPNWRGGDYHGTGRSPDHGLEIARRFAHLTYRGETELDERFG- 247 Query: 238 TRIGERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGG 297 + + + G + V+SYL+ ++ RFD +Y+ L+ A+ D+ G G G Sbjct: 248 ---NDAQPGEDPATGGRYSVQSYLEHQGRKLLARFDAGTYVTLTDALSSHDI---GRGRG 301 Query: 298 GAPGALSRMRVERALVMGARTDILFPLSQQQEIADGL-SAGGADVSFLPVDTPAGHDAFL 356 G AL V +V G +D L+PL Q E+A+ L G DV VD+ GHD FL Sbjct: 302 GVAAALQSCPVP-TVVGGITSDRLYPLRLQAELAELLPGCDGLDV----VDSACGHDGFL 356 Query: 357 VDIERFGPPVAKFLAIVA 374 V+ + G + + L + A Sbjct: 357 VETDAVGKLIRRTLELAA 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: 445 Number of extensions: 20 Number of successful extensions: 7 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 10 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