Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_086510729.1 BZY95_RS15085 acetyl-CoA C-acyltransferase FadA
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_002151265.1:WP_086510729.1 Length = 392 Score = 253 bits (645), Expect = 9e-72 Identities = 160/397 (40%), Positives = 220/397 (55%), Gaps = 23/397 (5%) Query: 5 VIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERN-KLDPGLVDDVITGCVTQAGE 63 V+VD +R+ M ++K G AF + A L A V++ L +RN LDP VDDVI GCV Q E Sbjct: 9 VVVDGVRTAMAKAKNG-AFRNVRAENLSAAVMQALFDRNANLDPAEVDDVIWGCVNQTLE 67 Query: 64 QSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMSR 123 QS R A + G P VPA T++R CGSS A+H AA I AG D + G+E M Sbjct: 68 QSMNIARNAAIMTGIPRTVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYVIGGVEHMEH 127 Query: 124 VPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAATA 183 VPM + NP A+ A + G+ AEL+ + ++R D D + RSH+ AA A Sbjct: 128 VPMAHG-VDVNPAASKYAAKAA---MMMGLTAELLGKMHGVTREDQDKFGVRSHQRAAAA 183 Query: 184 RESGAFRREILGISTPN-----GLVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIG 238 + G F EI+G+ + LV++DE IR S+E++ +L F G Sbjct: 184 SDKGYFDNEIVGVEGHDERGFRQLVKRDEVIRIDASLEEMA---------KLKPVFDPRG 234 Query: 239 WNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQR 298 V+AG +S +S GASAM +MS A+ LGL+P AR ++ V G D +M P+PAS++ Sbjct: 235 GTVSAGTSSALSVGASAMAIMSYERARALGLEPIARVLSTGVAGCDASIMGYGPVPASKK 294 Query: 299 AIKKSGLKLDQIDHYEINEAFACVPLAWQRALG---ADPARLNPRGGAIALGHPLGASGV 355 A+K +GL I E+NEAFA + + LG A ++N GGAIALGHPLG SG Sbjct: 295 ALKAAGLSAQDIQTVELNEAFAAQAIPVLKDLGFLEAMDEKVNLNGGAIALGHPLGCSGS 354 Query: 356 RLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 R+ TT+L+ + GL +MC G AT+ ERL Sbjct: 355 RICTTLLNVMRQQDTTLGLATMCIGMGQGVATVFERL 391 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: 367 Number of extensions: 19 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: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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 Apr 09 2024. 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