Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_054341133.1 Nant_RS08065 acetyl-CoA C-acyltransferase FadA
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_001305295.1:WP_054341133.1 Length = 392 Score = 280 bits (716), Expect = 5e-80 Identities = 175/397 (44%), Positives = 230/397 (57%), Gaps = 23/397 (5%) Query: 5 VIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERN-KLDPGLVDDVITGCVTQAGE 63 VIVD IR+PMG+SK GS F + A L A ++KGL+ RN ++P ++DV+ GCV Q E Sbjct: 9 VIVDGIRTPMGKSKGGS-FRNVRAESLSASIMKGLLARNPNVNPADIEDVVWGCVNQTKE 67 Query: 64 QSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMSR 123 Q R A + AG P V TI+R CGSS A+H AAQ IM G D I G+E M Sbjct: 68 QGFNIARNALVLAGLPHTVGGQTINRLCGSSMSALHNAAQSIMTGNGDTFIVGGVEHMGH 127 Query: 124 VPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAATA 183 + + + M A + G+ AE++ +SR D + ARSH LA A Sbjct: 128 LNI----LHGIDLNSEMSKYVAKAAMMMGITAEMLGKMNGISREMQDEFGARSHRLAHEA 183 Query: 184 RESGAFRREILGIS--TPNG---LVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIG 238 RE+G F EI+ I NG L+EQDE IRP T+ E L +L+ +F P++G Sbjct: 184 RETGRFDNEIIAIEGHDANGFKSLLEQDEVIRPETTFEVLQSLKPAF--------VPKVG 235 Query: 239 WNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQR 298 VTAG +S SDGAS ML+MS + AQ LGLKPRA + V G DP +M P+PA+Q+ Sbjct: 236 -TVTAGTSSAFSDGASGMLVMSAAKAQSLGLKPRAVIRSMAVAGCDPSIMGYGPVPATQK 294 Query: 299 AIKKSGLKLDQIDHYEINEAFACVPLA---WQRALGADPARLNPRGGAIALGHPLGASGV 355 A+K++GLK+D ID+ E+NEAFA LA + L +N GGAIALGHPLG SG Sbjct: 295 ALKRAGLKMDDIDYIELNEAFAAQGLAVLKGLKLLDRMEENVNLNGGAIALGHPLGCSGT 354 Query: 356 RLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 R+ TT+L+ LE +GL +MC G AT+ ERL Sbjct: 355 RISTTLLNVLEQKNGTFGLATMCIGMGQGVATVFERL 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: 389 Number of extensions: 19 Number of successful extensions: 6 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 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