Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012755213.1 RLEG_RS23510 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >NCBI__GCF_000023185.1:WP_012755213.1 Length = 401 Score = 262 bits (670), Expect = 1e-74 Identities = 166/398 (41%), Positives = 235/398 (59%), Gaps = 26/398 (6%) Query: 5 VIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAGSGQN 64 V+VAA R+ +G GSLA++ A +L A ++ R+L +TG+ P +D+V++G AG G N Sbjct: 14 VVVAAYRSPIGRAFGSLATVAAEDLLAPIMHRILLETGIAPDTIDDVLVGNA--AGGGGN 71 Query: 65 PARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYV 124 AR A++ AGLP +VP + +++ CGSGL+A+ + A+ I+ +AGG+E++S AP+ Sbjct: 72 IARLAALTAGLPMSVPGVAIDRQCGSGLEAIIMAARLIQAKAGACFLAGGVESVSTAPWR 131 Query: 125 LPAARTGLR----MGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 + + G A+ I D MGI AEN+ ++GISR+ QD FA Sbjct: 132 VERPKANGMPPRFYGRARFSPETI--------GDPEMGIAAENVARQFGISRQRQDEFAL 183 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 S + A AA EAG F EI I P+ DE PRA T+ E+LA L+P F DG Sbjct: 184 RSHRLAVAAAEAGIFRPEIVEISTGH---GPIER--DECPRASTSLEALANLRPVFLADG 238 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNA LNDGA VL+MS A+++G+ A AGVDP ++GIGPV++TR+ Sbjct: 239 SVTAGNACPLNDGACLVLVMSRGMARSMGVEKGLAFIDSAAAGVDPNLLGIGPVASTRKL 298 Query: 301 LDK-AGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVL 359 L + SL D+D IE NEAFAAQ LA +L A+ +N +GGAIA+GHP GASG ++ Sbjct: 299 LKRQPELSLLDIDAIEFNEAFAAQVLASLDQLAIPADAINKDGGAIALGHPFGASGAILV 358 Query: 360 VTLLHEMIKRDAKKG------LATLCIGGGQGVALALE 391 L ++I+ + G LA + IGGG G+ E Sbjct: 359 TRLYSQLIRNTGEVGAPGATALAMIGIGGGIGLTAMFE 396 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: 367 Number of extensions: 13 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: 393 Length of database: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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