Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_046010134.1 OLEAN_RS16515 acetyl-CoA acetyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000967895.1:WP_046010134.1 Length = 402 Score = 281 bits (719), Expect = 2e-80 Identities = 160/402 (39%), Positives = 240/402 (59%), Gaps = 15/402 (3%) Query: 3 QAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQAG 62 +A I DAIR+P GR K A E+ LL+ ++ L ERN+ D VDD++ GCVT G Sbjct: 4 EAYIFDAIRTPRGRGKASGALHEVKPITLLSDLLISLQERNQFDTAAVDDIVMGCVTAVG 63 Query: 63 EQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMS 122 +Q A + A LAAG+ + V ++R C S +AV+ AA + +G +V+A G+ESMS Sbjct: 64 DQGAVIAKTAALAAGWNEDVAGVVLNRFCASGLEAVNIAAMKVRSGWEHLVVAGGVESMS 123 Query: 123 RVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAAT 182 RVPMGS + E A G + QG+ A+L+ SR D+D+++ RSH AA Sbjct: 124 RVPMGS---DGGAWAMDPETNVATGFMPQGIGADLIGTLGGYSREDVDAFAMRSHHKAAA 180 Query: 183 ARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFR-------NDELSAR 233 A + AF++ I+ ++ NGL+ E DE IR +SVE LG L+ SF+ ++ R Sbjct: 181 AWKKNAFQKSIIPVTDRNGLILLEHDELIRAESSVETLGKLKPSFKMMGDMGFDNVAKER 240 Query: 234 FPQIGWNV---TAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLT 290 +PQ+ + + GN+S I DGA+ +L+ S + ++ + PRAR VA V G +P +MLT Sbjct: 241 YPQVEFINHIHSPGNSSGIVDGAAVVLIGSAAAGKQFNMTPRARIVATAVVGAEPTIMLT 300 Query: 291 APIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPL 350 P PA+++A+K +G+ + ID +E+NEAFA V + + +G +N GG+IA+GHPL Sbjct: 301 GPAPAARKALKVAGMDVSDIDLFEVNEAFASVVMRFIDEMGISEDIVNVNGGSIAMGHPL 360 Query: 351 GASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 GA+G ++ T+L LE + GL ++C GGM ATIIER+ Sbjct: 361 GATGAMILGTLLDELEARDLKTGLVTLCVGGGMGIATIIERV 402 Lambda K H 0.318 0.132 0.384 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: 408 Number of extensions: 16 Number of successful extensions: 4 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: 402 Length adjustment: 31 Effective length of query: 361 Effective length of database: 371 Effective search space: 133931 Effective search space used: 133931 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