Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_022950067.1 H035_RS0116515 acetyl-CoA C-acyltransferase
Query= BRENDA::B1YB71 (392 letters) >NCBI__GCF_000421465.1:WP_022950067.1 Length = 435 Score = 238 bits (608), Expect = 2e-67 Identities = 166/425 (39%), Positives = 230/425 (54%), Gaps = 41/425 (9%) Query: 3 VVVVGYVRTPIGKFGGAFKDVKPPHLAAFTIKKLLERTGVDGKLVEEVIFGSTLQGGVGQ 62 V VV RTP K G LA + LL R + ++++VI G + G Sbjct: 14 VYVVDGSRTPCLKARGKPGPFTAADLALRAAQPLLARQPFEPPVLDQVILGCAIPGPDEA 73 Query: 63 NVARYAALLAGLPVDVSAFTVNRVCSSGMQAIIEAYREIALGDASVVIAGGVESMSTQPI 122 N+AR AL AG A++V R C SGMQAI A R+IA G +++V+AGG E+MS P+ Sbjct: 74 NIARVVALRAGCGRSTPAWSVQRNCGSGMQAIDSAARDIAAGRSNLVLAGGAEAMSHAPV 133 Query: 123 CVSHE-----ARWGLRHSIGRRFE-LTDLM---------VFDGLTDPATGMLMGEEADMV 167 ++ +W ++ R T L + GLTDP G+ MG A+++ Sbjct: 134 LFNNAMVAWLGQWQKARTLPARLRHFTRLRPAHLKPIIGLLRGLTDPTVGLSMGRTAEIL 193 Query: 168 AKEHKIAREELDKVAYESHMRAWRA-TENKWFDDMEPV---EGEFGGVKLDRDEGIRPDT 223 A I+R E+D A+ SH R A E + D++E + EG F D D+G+RPD Sbjct: 194 AWRFDISRREMDLYAHASHHRLAAAQAEGRLADEIESIYDGEGHF----YDHDDGVRPDL 249 Query: 224 SLEKLAKLKPAF-KPDGLHTAGNSSQLSDGAAALLLMSEEKARELGVKPIARILGYSWHM 282 +LE+LA LKP F + GL TAGNSSQ++DGAA LLL SEE + +K + R+L +W Sbjct: 250 TLEQLAALKPVFDRKFGLVTAGNSSQVTDGAAWLLLASEEAVQRYDLKVMGRVLDCTWAG 309 Query: 283 LEPWRFTEAPVYAIQKLLRKLGVSVDYFDYYEANEAFA--VVNVL--------VNRVLGV 332 L+P + PVY+ LL + + +D DY+E NEAFA V+ L L + Sbjct: 310 LDPAQMGLGPVYSSAALLGRNRLDLDQIDYWELNEAFAGQVLACLKAFADERFCRETLDL 369 Query: 333 P-------YDRMNVFGGAIALGHPLGASGTRIVTTLISVLRRMGGRRGVAALCHGTGGGT 385 P DR+N+ GGA+A+GHP+G SGTRIV L+ V+ GG+RGVA LC G G G Sbjct: 370 PGALGEIDRDRLNMDGGAVAVGHPVGMSGTRIVLHLLRVMAARGGKRGVATLCIGGGQGG 429 Query: 386 AVALE 390 A+ LE Sbjct: 430 AMLLE 434 Lambda K H 0.320 0.138 0.406 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: 471 Number of extensions: 18 Number of successful extensions: 5 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: 392 Length of database: 435 Length adjustment: 31 Effective length of query: 361 Effective length of database: 404 Effective search space: 145844 Effective search space used: 145844 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 (21.8 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