Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_012784196.1 AFER_RS00545 acetyl-CoA C-acetyltransferase
Query= SwissProt::P45855 (393 letters) >NCBI__GCF_000023265.1:WP_012784196.1 Length = 398 Score = 372 bits (956), Expect = e-108 Identities = 201/393 (51%), Positives = 258/393 (65%), Gaps = 1/393 (0%) Query: 1 MRKTVIVSAARTPFGKFGGVLKEVKAAELGGIVMKEALQQAGVSGDDVEGNVMGMVVQAG 60 M ++VIVS ARTP GK G L + A ELGG + AL++AGV+ D V+ MG V+QAG Sbjct: 1 MSRSVIVSYARTPIGKLQGALASLSAMELGGRAIAGALERAGVAPDSVDYVFMGHVLQAG 60 Query: 61 SGQIPSRQAARLAGMPWSVPSETLNKVCASGLRAVTLCDQMIRAQDADILVAGGMESMSN 120 GQI +RQAA A +P +VP+ T+NKVC SGL AV L D ++ ++VAGGMESMS Sbjct: 61 QGQITARQAAVAANIPMTVPATTVNKVCLSGLNAVFLADLLLAQGRTSVVVAGGMESMSR 120 Query: 121 IPYAVPAGRWGARMGDGELRDLMVYDGLTCAFDEVHMAVHGNTAAK-EYAISRREQDEWA 179 PY +P R G RMGD L D M+YDGL CAFD + M + ++ +SR QD +A Sbjct: 121 APYVLPGARGGLRMGDAALIDSMLYDGLFCAFDRMAMGASTEHYCRVDHPVSRDRQDAFA 180 Query: 180 LRSHARAAKAADEGKFQDEIVPVNWIGRKGKPNVVDKDEAIRRDTSLDQLAKLAPIYASD 239 RSH AA+AA EG+ DEIVPV GR+G+ +VV+ DE IR +T+++ LA+L P +A D Sbjct: 181 ARSHELAARAAKEGRLADEIVPVTVAGRRGEVHVVEDDEGIRPETTVETLARLRPAFAED 240 Query: 240 GSITAGNAPGVNDGAGAFVLMSEEKAAELGKRPLATILGFSTTGMPAHELAAAPGFAINK 299 G+ITAGNA ++DGA A V+M E+A G PL ILG+ P L P AI Sbjct: 241 GTITAGNASQISDGAAALVVMRAEEAERRGLTPLGEILGYGQVAGPDASLLHQPSNAIRA 300 Query: 300 LLKKNGLTVQDIDLFEVNEAFASVVLTCEKIVGFDLEKVNVNGGAIALGHPIGASGARIL 359 GL +DL E+NEAFA+V L +G D +VNVNGGAIALGHPIGASGARIL Sbjct: 301 AASDAGLDPASLDLVEINEAFAAVALASMDDLGIDPARVNVNGGAIALGHPIGASGARIL 360 Query: 360 MTLVYELKRRGGGLGVAAICSGAAQGDAVLVQV 392 +L+ EL+RRGGG+G AA+C G QGDA++V+V Sbjct: 361 GSLLLELRRRGGGVGAAALCGGGGQGDAMIVRV 393 Lambda K H 0.317 0.134 0.387 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: 453 Number of extensions: 17 Number of successful extensions: 2 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: 393 Length of database: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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