Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate 18041 b4013 homoserine O-succinyltransferase (NCBI)
Query= SwissProt::E8LIC0 (301 letters) >FitnessBrowser__Keio:18041 Length = 309 Score = 375 bits (963), Expect = e-109 Identities = 175/299 (58%), Positives = 224/299 (74%) Query: 1 MPINIPNGLPAASVLAGEQIFVMTEERATHQDIRPLTLLFLNLMPKKIATEIQYMRKLSN 60 MPI +P+ LPA + L E +FVMT RA+ Q+IRPL +L LNLMPKKI TE Q++R LSN Sbjct: 1 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN 60 Query: 61 TPLQVNIDLLRVDKHISKNTPQPHLDTFYKDFEEIEGRNYDGMIITGAPLDQIDFSDVTY 120 +PLQV+I LLR+D S+NTP HL+ FY +FE+I+ +N+DG+I+TGAPL ++F+DV Y Sbjct: 61 SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY 120 Query: 121 WDKLEKIITWSKEHVTSTLFSCWGVAAGLKIFYDLPLINRKEKLSGVFLHHTAQSLNPLI 180 W ++++++ WSK+HVTSTLF CW V A L I Y +P R EKLSGV+ HH L Sbjct: 121 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT 180 Query: 181 RGFDDTFLAPHSRFIDFPSDVIRKHTDLEILADSEITGMFLAATPDRRQVFVTGHPEYDA 240 RGFDD+FLAPHSR+ DFP+ +IR +TDLEILA++E +L A+ D+R FVTGHPEYDA Sbjct: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240 Query: 241 TTLSDEYRRDLAAGKDPKLPENYFPHDDPTQIPSCVWRSHASLLFGNWLNYYVYQITPY 299 TL+ E+ RD+ AG DP +P NYFPH+DP P WRSH +LLF NWLNYYVYQITPY Sbjct: 241 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPY 299 Lambda K H 0.321 0.139 0.432 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: 371 Number of extensions: 15 Number of successful extensions: 1 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: 301 Length of database: 309 Length adjustment: 27 Effective length of query: 274 Effective length of database: 282 Effective search space: 77268 Effective search space used: 77268 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 (21.9 bits) S2: 48 (23.1 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