Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__Smeli:SMc00966 Length = 397 Score = 258 bits (658), Expect = 3e-73 Identities = 161/389 (41%), Positives = 230/389 (59%), Gaps = 21/389 (5%) Query: 5 VIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAGSGQN 64 V++AA RT VG GSLA++ L A +I R++ TG+D A++D+V++G A S N Sbjct: 12 VVIAALRTPVGRVNGSLAAVEPARLAALLIERIIADTGIDRAEIDDVLVGNA--ANSAGN 69 Query: 65 PARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYV 124 AR A++ AGLP A+P +T+++ CGSGL+A+ L A+ I+ G +AGG E+ S A Sbjct: 70 LARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRAHIR 129 Query: 125 L-PAARTGLR---MGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 L P G + A+M D+ D MG+ AEN+ GISRE QD FA Sbjct: 130 LRPPLTRGEEPQPVKRARMAP--------DSIGDPDMGVAAENVATACGISRERQDRFAL 181 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 S ++A AA GRF EI P+ P+ P+A DE PRA +AE+L++L+P F G Sbjct: 182 ESHRRAVAAEAEGRFSREIVPVPTPE---GPIAR--DECPRANASAETLSRLRPVFVAGG 236 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 +VTAGNA +NDGAA VL+ + +A+ LG A AGV+P ++G+GPV A + Sbjct: 237 TVTAGNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGLGPVPAMAKL 296 Query: 301 LDK-AGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVL 359 + + +D IE NEAFA+Q L +L+ E+VN +GGAIA+GHP GASG ++ Sbjct: 297 RARNPALDVARVDFIEFNEAFASQVLGSLDQLDIAPERVNRDGGAIALGHPYGASGAILV 356 Query: 360 VTLLHEMIKRDA-KKGLATLCIGGGQGVA 387 V L +M+ + +GLA + IGGG G+A Sbjct: 357 VRLFSQMLAASSPAEGLAMMGIGGGMGIA 385 Lambda K H 0.317 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: 398 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: 393 Length of database: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 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 17 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