Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase
Query= SwissProt::P50174 (393 letters) >NCBI__GCF_000185905.1:YP_004140539.1 Length = 392 Score = 636 bits (1641), Expect = 0.0 Identities = 315/389 (80%), Positives = 350/389 (89%) Query: 5 SIVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEG 64 SIVIASAART VGSFNGAF T AHELGA I+ +L RAGVE GEVDEVILGQVL A +G Sbjct: 4 SIVIASAARTPVGSFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLTAAQG 63 Query: 65 QNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAP 124 QNPARQA++ AGLP+E TAWG+NQ+CGSGLRA+ALGMQQIA GDA+VI+AGG ESMS++ Sbjct: 64 QNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLST 123 Query: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQ 184 H HLR GVKMGD+K+IDTMIKDGL DAF GYHMG TAENVAR++Q+TRE+QD+FALASQ Sbjct: 124 HAQHLRAGVKMGDFKLIDTMIKDGLWDAFNGYHMGNTAENVARQFQITREDQDQFALASQ 183 Query: 185 NKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTA 244 NKAEAAQKAG+F DEIV +K +KGD VDQDEYIRHGAT+D++ KL+PAFDK+GTVTA Sbjct: 184 NKAEAAQKAGKFKDEIVAVTIKGKKGDTIVDQDEYIRHGATIDAMTKLKPAFDKDGTVTA 243 Query: 245 GNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304 NASG+NDGAA ALLM+EAEA RRGI PLARIVSWATAGVDPQIMGTGPIPASRKALEKA Sbjct: 244 ANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 303 Query: 305 GWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364 GWSV D++LVEANEAFAAQACAVNKD+GWDPSIVNVNGGAIAIGHPIGASGARV NTL+F Sbjct: 304 GWSVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVFNTLVF 363 Query: 365 EMKRRGVSKGLATLCIGGGMGVAMCVERL 393 EM+RRG KGLATLCIGGGMGVAMCVE L Sbjct: 364 EMRRRGAKKGLATLCIGGGMGVAMCVEAL 392 Lambda K H 0.317 0.132 0.381 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: 526 Number of extensions: 12 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: 393 Length of database: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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