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_057508008.1 ABB28_RS07330 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_001431535.1:WP_057508008.1 Length = 391 Score = 424 bits (1091), Expect = e-123 Identities = 223/389 (57%), Positives = 285/389 (73%), Gaps = 1/389 (0%) Query: 8 IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67 IVI +A RT +G F G+ + P LGA AI AA+E +GV A V EV+ GCVL A LGQ Sbjct: 4 IVIAAAKRTAIGSFLGQFNGVPTPTLGATAIAAALEASGVPASDVTEVIMGCVLPANLGQ 63 Query: 68 APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127 APARQAA+ GL ST TTLNK+CGSGM+A +L HD++ AGSA +VVAGGMESMSNAP+ Sbjct: 64 APARQAAIAGGLPLSTGATTLNKVCGSGMKAIMLGHDLIKAGSASIVVAGGMESMSNAPH 123 Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187 LL +R+G R G+ + +DHM DGL +AYD G+ MG FAE + F+RE QD +AI S Sbjct: 124 LLPNSRTGNRFGNFQAVDHMAHDGLVNAYD-GKAMGEFAECAVDKYQFSREEQDAYAIES 182 Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247 RAQ A G+F EIV ++V K + I+ DEQP +A + KI +L+PAF+ G+VTA Sbjct: 183 VKRAQAAQASGAFADEIVAVKVASRKGEVEISIDEQPTRADIAKIPTLRPAFKKDGSVTA 242 Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307 A+SSSISDGAAA++L+ +A+ RGL+PLA I HA + P F AP+GAI KLL K Sbjct: 243 ASSSSISDGAAAVVLLSEEDAQARGLQPLARIVAHATHSQEPEWFTTAPIGAIHKLLDKA 302 Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367 GW+L +V+LFEVNEAFAVV++ M +L I H K+NV+GGACALGHPIGASGAR++VTL+ Sbjct: 303 GWTLADVDLFEVNEAFAVVAMAPMRELGIAHDKLNVNGGACALGHPIGASGARLVVTLVH 362 Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVECL 396 ALR +G KRG+A +CIGGGEATA+A+E + Sbjct: 363 ALRSRGGKRGIATLCIGGGEATAIAIELI 391 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: 478 Number of extensions: 11 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: 391 Length adjustment: 31 Effective length of query: 366 Effective length of database: 360 Effective search space: 131760 Effective search space used: 131760 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