Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_086508403.1 BZY95_RS02365 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_002151265.1:WP_086508403.1 Length = 395 Score = 458 bits (1179), Expect = e-133 Identities = 230/394 (58%), Positives = 300/394 (76%), Gaps = 2/394 (0%) Query: 1 MTMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCV 60 M+ HD IV +SA RTPMGG G L SL+AP+L A AIRAA+ERAG+ A +++E + GCV Sbjct: 1 MSSPHD-IVFLSATRTPMGGMLGSLASLTAPELAATAIRAAIERAGIEAGSIDEGIMGCV 59 Query: 61 LSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGME 120 L G+ Q PARQA AG+ TT+NK+CGSGM+AA+LAHD++ AGS +V++AGGME Sbjct: 60 LPGGVKQGPARQAMRQAGIPDGIGATTINKLCGSGMKAAMLAHDLIRAGSGEVILAGGME 119 Query: 121 SMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQ 180 SMSNAP++L +AR+GYR+GHG++ DHMFLDGLEDA + G+LMG FA+D A G++RE Sbjct: 120 SMSNAPHVLTKARTGYRLGHGELKDHMFLDGLEDA-ETGKLMGVFAQDIASQRGYSRERL 178 Query: 181 DEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFR 240 D+FAIAS RA A G AE+ P+ V + + ++ DEQP +AKLDKI L+PAF Sbjct: 179 DDFAIASLERAMAATNAGHLAAEMAPVTVTSRQGESVVEHDEQPFQAKLDKIRQLRPAFA 238 Query: 241 DGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAI 300 GT+TAANSSSISDGA+AL+L +S A++ G KPLA + GH+ + P F +APVGAI Sbjct: 239 KDGTITAANSSSISDGASALILASQSAADRLGSKPLARMLGHSTHSQHPSEFTIAPVGAI 298 Query: 301 KKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGAR 360 KL+KK GW + +V+LFE+NEAFAVV+L+ M L+IPH KVNV GGACA GHPIG++G+R Sbjct: 299 DKLMKKLGWGVADVDLFEINEAFAVVTLLAMDGLDIPHDKVNVFGGACAQGHPIGSTGSR 358 Query: 361 ILVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 I+ TL+ ALR KG KRG+A++CIGGGEATA+A+E Sbjct: 359 IIATLIHALRTKGGKRGIASLCIGGGEATAVAIE 392 Lambda K H 0.318 0.133 0.378 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: 499 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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