Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase
Query= SwissProt::P45855 (393 letters) >NCBI__GCF_003194585.1:WP_110204929.1 Length = 395 Score = 354 bits (909), Expect = e-102 Identities = 197/395 (49%), Positives = 260/395 (65%), Gaps = 6/395 (1%) Query: 1 MRKTVIVSAARTPFGKFGGVLKEVKAAELGGIVMKEALQQAGVSGDDVEGNVMGMVVQAG 60 M +VIV+ ARTP G+ G LK++ AA+LGG+ +K AL++AG+SGD V+ VMG V+QAG Sbjct: 1 MSGSVIVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAG 60 Query: 61 SGQIPSRQAARLAGMPWSVPSETLNKVCASGLRAVTLCDQMIRAQDADILVAGGMESMSN 120 +GQI +RQAA G+P VPS T+NKVC SG+ A+ L DQ+IRA + +I+VAGGMESM+ Sbjct: 61 AGQITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQ 120 Query: 121 IPYAVPAGRWGARMGDGELRDLMVYDGLTCAFDEVHMA---VHGNTAAKEYAISRREQDE 177 P+ +P R G + GD +L D M YD L F + M N A ++R EQD Sbjct: 121 APHLLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGGN--LTREEQDA 178 Query: 178 WALRSHARAAKAADEGKFQDEIVPVNWIGRKGKPNVVDKDEAIRRDTSLDQLAKLAPIYA 237 ++ RSH AA A G F DEIVPV R+G VV DE +R DT+ + L L P +A Sbjct: 179 FSARSHQLAAAAQKNGVFDDEIVPVTISSRRGDV-VVSVDEGVRGDTTAESLGGLRPAFA 237 Query: 238 SDGSITAGNAPGVNDGAGAFVLMSEEKAAELGKRPLATILGFSTTGMPAHELAAAPGFAI 297 DG+ITAG++ ++DGA A V+MS+ KA ELG LA I P L P AI Sbjct: 238 KDGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAI 297 Query: 298 NKLLKKNGLTVQDIDLFEVNEAFASVVLTCEKIVGFDLEKVNVNGGAIALGHPIGASGAR 357 K ++K G+ V DIDLFE+NEAFA+V + + +G +KVNVNGGAIA+GHP+G SGAR Sbjct: 298 AKAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGAR 357 Query: 358 ILMTLVYELKRRGGGLGVAAICSGAAQGDAVLVQV 392 I++ L ELKRRGGG+G AA+C G QGDA++V+V Sbjct: 358 IVLHLALELKRRGGGIGAAALCGGGGQGDALIVRV 392 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: 516 Number of extensions: 28 Number of successful extensions: 3 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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