Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_029133089.1 A3GO_RS0108835 acetyl-CoA C-acetyltransferase
Query= SwissProt::P45369 (394 letters) >NCBI__GCF_000428045.1:WP_029133089.1 Length = 394 Score = 633 bits (1633), Expect = 0.0 Identities = 310/393 (78%), Positives = 353/393 (89%) Query: 1 MNENIVIVDAGRSAIGTFSGSLSSLSATEIGTAVLKGLLARTGLAPEQIDEVILGQVLTA 60 M++NIVIV AGR+AIG+FSG+LS + A+E+G V+ GLL RT L+PEQIDEVILGQVLTA Sbjct: 1 MSDNIVIVAAGRTAIGSFSGTLSGIPASELGAKVIAGLLERTKLSPEQIDEVILGQVLTA 60 Query: 61 GVGQNPARQTTLKAGLPHSVPAMTINKVCGSGLKAVHLAMQAIACGDADIVIAGGQESMS 120 G GQNPARQ TL AGLP VPAMTINKVCGSGLKAVHLAMQA+ACGD++IVIAGGQE+MS Sbjct: 61 GCGQNPARQATLGAGLPQEVPAMTINKVCGSGLKAVHLAMQAVACGDSEIVIAGGQENMS 120 Query: 121 QSSHVLPRSRDGQRMGDWSMKDTMIVDGLWDAFNNYHMGTTAENIAQKYGFTREQQDAFA 180 + HV+P SR GQ MGDW +KD+MIVDGLWDAFN YHMG TAEN+A K+ F+RE QD FA Sbjct: 121 LAPHVVPGSRKGQMMGDWKLKDSMIVDGLWDAFNQYHMGVTAENVANKFKFSREAQDQFA 180 Query: 181 AASQQKTEAAQKAGRFQDEIIPIEIPQRKGDPKVFDADEFPRHGTTAESLGKLRPAFSRD 240 AASQQK EAAQKA RFQDEIIP+EIPQRKGDP +F +DEFPRHGTTAE+LGKLRPAF RD Sbjct: 181 AASQQKAEAAQKANRFQDEIIPLEIPQRKGDPVIFSSDEFPRHGTTAETLGKLRPAFDRD 240 Query: 241 GSVTAGNASGINDGAAMVVVMKESKAKELGLKPMARLVAFASAGVDPAIMGTGPIPASTK 300 G+VTAGNASG+NDGAA V+VMKESKA ELGL PMAR+ AFA++GVDPAIMGTGPI A+TK Sbjct: 241 GTVTAGNASGLNDGAAAVIVMKESKALELGLTPMARIKAFAASGVDPAIMGTGPITATTK 300 Query: 301 CLEKAGWTPADLDLIEANEAFAAQAMSVNQDMGWDLSKVNVNGGAIAIGHPIGASGARVL 360 CLEKAGW+ +DLDL+EANEAFAAQAMSVN+++GWD K+NVNGGAIA+GHPIGASGAR+L Sbjct: 301 CLEKAGWSVSDLDLVEANEAFAAQAMSVNKELGWDAEKINVNGGAIALGHPIGASGARIL 360 Query: 361 VTLLYEMQKRDAKKGLATLCIGGGQGVALAVER 393 V+LL+EM KRDAKKGLATLCIGGG GVALAVER Sbjct: 361 VSLLHEMAKRDAKKGLATLCIGGGMGVALAVER 393 Lambda K H 0.315 0.131 0.375 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: 578 Number of extensions: 14 Number of successful extensions: 1 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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 (21.6 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