Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012383438.1 BIND_RS02165 acetyl-CoA C-acetyltransferase
Query= SwissProt::P07097 (392 letters) >NCBI__GCF_000019845.1:WP_012383438.1 Length = 391 Score = 583 bits (1502), Expect = e-171 Identities = 285/390 (73%), Positives = 332/390 (85%) Query: 1 MSTPSIVIASARTAVGSFNGAFANTPAHELGATVISAVLERAGVAAGEVNEVILGQVLPA 60 MS+ +++ +ARTAVGSF+GAF NTPAHELGATVI A LERA V A +V+EVILGQVL A Sbjct: 1 MSSDVVIVGAARTAVGSFSGAFGNTPAHELGATVIKATLERAKVEAADVDEVILGQVLTA 60 Query: 61 GEGQNPARQAAMKAGVPQEATAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMS 120 GQNPARQ A+KAG+P TAW +NQ+CGSGLRAVALG+QQI GDA IIVAGG E+MS Sbjct: 61 ASGQNPARQTAIKAGIPDSKTAWTVNQVCGSGLRAVALGLQQINNGDAKIIVAGGQENMS 120 Query: 121 MAPHCAHLAGGVKMGDFKMIDTMIKDGLTDAFYGYHMGTTAENVAKQWQLSRDEQDAFAV 180 ++PH A L GG KMGD K DTM++DGLTDAF Y MG TAE++A +WQ+SR+EQD FAV Sbjct: 121 LSPHAAFLRGGTKMGDVKFTDTMMRDGLTDAFANYPMGNTAEHIATKWQISREEQDQFAV 180 Query: 181 ASQNKAEAAQKDGRFKDEIVPFIVKGRKGDITVDADEYIRHGATLDSMAKLRPAFDKEGT 240 ASQNKAEAAQK+GRF +EI+PF V G+KGDI VD DEYIR GAT+++MAKL+PAF K+GT Sbjct: 181 ASQNKAEAAQKEGRFNEEIIPFTVPGKKGDIIVDKDEYIRIGATIEAMAKLKPAFVKDGT 240 Query: 241 VTAGNASGLNDGAAAALLMSEAEASRRGIQPLGRIVSWATVGVDPKVMGTGPIPASRKAL 300 VTAGN+SG+NDGAAA +LMS EA RG+ PL RI SWAT GVDP +MG+GPIPASRKAL Sbjct: 241 VTAGNSSGINDGAAAVVLMSADEAKARGLTPLARIASWATAGVDPSIMGSGPIPASRKAL 300 Query: 301 ERAGWKIGDLDLVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARILNT 360 E+AGWK+ DLDL+EANEAFAAQA AVNKD+GWD S+VNVNGGAIAIGHPIGASGAR+L T Sbjct: 301 EKAGWKVKDLDLIEANEAFAAQAIAVNKDMGWDTSLVNVNGGAIAIGHPIGASGARVLVT 360 Query: 361 LLFEMKRRGARKGLATLCIGGGMGVAMCIE 390 LL EMKRR A+KG+ATLCIGGGMG+AM IE Sbjct: 361 LLHEMKRRDAKKGIATLCIGGGMGIAMTIE 390 Lambda K H 0.317 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: 504 Number of extensions: 16 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: 392 Length of database: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 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