Align serine O-acetyltransferase (EC 2.3.1.30); homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate RR42_RS01160 RR42_RS01160 homoserine O-acetyltransferase
Query= BRENDA::D2Z028 (374 letters) >FitnessBrowser__Cup4G11:RR42_RS01160 Length = 390 Score = 232 bits (591), Expect = 1e-65 Identities = 141/360 (39%), Positives = 200/360 (55%), Gaps = 13/360 (3%) Query: 8 ASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--RPDD 65 A + + + +R G +L + ET+G+LNAAR NAVLV L+ H A D Sbjct: 22 APQCMHFTEPLKLRNGTSLADYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYEHDP 81 Query: 66 PTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIED 125 GWW+ MVGPGKP+DTD + VI VN+LGSC GSTGP S +P TG+PY +FP +++ED Sbjct: 82 RDVGWWDNMVGPGKPLDTDRFFVIGVNNLGSCFGSTGPMSANPATGQPYGATFPVVTVED 141 Query: 126 IADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAV 185 +A A GI++ A V+G S+GGM ALA +P+ R I ++ +IA Sbjct: 142 WVNAQARVADRFGITQFAAVMGGSLGGMQALAWSLMYPDRLRHCIVVASTPKLSAQNIAF 201 Query: 186 RSLQREAIRSDPGWLQG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERR 244 + R AI SDP + G +Y G P+RG+ AR +G +TY S ++ +FGR Sbjct: 202 NEVARSAILSDPDFHGGNYYAHGVKPKRGLRVARMIGHITYLSDEDMAEKFGR-----EL 256 Query: 245 RADQGRFG--PEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGA 302 + D RF EF+VESYL + +FA+ FD N+YL ++ A+D FD GG A Sbjct: 257 KTDDIRFSFDVEFQVESYLRYQGDKFAEYFDANTYLLITRALDYFD--PALAFGGDLTRA 314 Query: 303 LSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 +S+ + LV TD F ++ +E+ L VS+ +D P GHDAFL+D R+ Sbjct: 315 VSQTQAS-FLVASFTTDWRFAPNRSRELVKALLDNKRPVSYAEIDAPHGHDAFLLDDPRY 373 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: 436 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: 390 Length adjustment: 30 Effective length of query: 344 Effective length of database: 360 Effective search space: 123840 Effective search space used: 123840 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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