Align serine O-acetyltransferase (EC 2.3.1.30); homoserine O-acetyltransferase (EC 2.3.1.31) (characterized)
to candidate GFF285 HP15_284 homoserine O-acetyltransferase
Query= BRENDA::D2Z028 (374 letters) >FitnessBrowser__Marino:GFF285 Length = 382 Score = 219 bits (557), Expect = 1e-61 Identities = 130/343 (37%), Positives = 190/343 (55%), Gaps = 9/343 (2%) Query: 23 GGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAAS--RPDDPTPGWWEAMVGPGKP 80 G +L + ET+G+LNA NAVL+ LS HAA +D PGWW++ +GPGKP Sbjct: 29 GQSLENYDLVVETYGTLNADASNAVLICHALSGHHHAAGYHSAEDRKPGWWDSCIGPGKP 88 Query: 81 VDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIADAAAHTVRALGIS 140 +DTD + V+ +N+LG C GSTGP S +P TG+P+ FP +++ D + A LGI Sbjct: 89 IDTDRFFVVSLNNLGGCHGSTGPNSINPETGKPFGPEFPVITVGDWVKSQALLADRLGIQ 148 Query: 141 RLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRSLQREAIRSDPGWL 200 A VVG S+GGM AL +P+ R + ++ +IA + R+AI SD + Sbjct: 149 CWAAVVGGSLGGMQALQWSLDYPDRLRHAVVIASTPRLTAQNIAFNEVARQAITSDREFH 208 Query: 201 QG-HYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRADQGRFGPEFEVES 259 G +YD PRRG++ AR +G +TY S +FGR R +A + + EF+VES Sbjct: 209 DGRYYDFDTVPRRGLMLARMVGHITYLSDASMGEKFGREL---RDQAYKFGYDAEFQVES 265 Query: 260 YLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMRVERALVMGARTD 319 YL + +RF++ FD N+YL ++ A+D FD GG AL+ E LV+ TD Sbjct: 266 YLRYQGERFSESFDANTYLLMTRALDYFD--PAYEFGGDLSKALAAASCE-YLVLSFSTD 322 Query: 320 ILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERF 362 F ++ +E+ + + VS+ VD P GHDAFL+ R+ Sbjct: 323 WRFTPARSEEMVNAMIGARRKVSYAEVDAPWGHDAFLIPTPRY 365 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: 455 Number of extensions: 29 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: 382 Length adjustment: 30 Effective length of query: 344 Effective length of database: 352 Effective search space: 121088 Effective search space used: 121088 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