Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101588593.1 BJEO58_RS06055 thiolase family protein
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_900169175.1:WP_101588593.1 Length = 379 Score = 407 bits (1047), Expect = e-118 Identities = 222/392 (56%), Positives = 283/392 (72%), Gaps = 14/392 (3%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 M +A IVAA RT G++ G LSG HPADL+A VL+ LV+ G DPALVEDVI GCV+Q G Sbjct: 1 MTDAVIVAARRTPTGKREGVLSGVHPADLSAHVLEDLVQTAGVDPALVEDVIWGCVTQAG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQ G++AR A L++ PE+V G +VDRQCGSSQQA+HFAA ++SG DIVIA GVESM+ Sbjct: 61 EQTGDIARTAALSAGFPETVTGVTVDRQCGSSQQAVHFAAAGIVSGQYDIVIAGGVESMS 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 R PMG SS KN +G RY GV+ +Q GAEMIA K+ LSR Q+D AL+S Sbjct: 121 RNPMGSSSM--GKNPYG----DRFMERY-GVKPNQGVGAEMIAEKWGLSRSQVDDLALES 173 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLI-AEGGR 239 H RA AAT SG F ++I PV+ T DG + + DEG+R T E +G +K + E G Sbjct: 174 HARAAAATDSGAFESQITPVQ--TEDG----LVSADEGIRRGGTPEGLGKLKTVFKEDGI 227 Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299 VTA ++SQI DG++ L++++ K+LG+KP+ARVH + G DPV+ML AP+PAT+ AL Sbjct: 228 VTAGNSSQISDGSSALLMMSSDRAKELGLKPIARVHTAVLAGTDPVIMLTAPIPATQKAL 287 Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359 KK+GL + DI +FEVNEAFA VPLAW + GAD A++N +GGAIA+GHPLGGSG++LMTT Sbjct: 288 KKSGLSVDDIGVFEVNEAFATVPLAWQRELGADFAKVNPNGGAIAMGHPLGGSGSRLMTT 347 Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 +VH + +G YGLQTMCEGGG AN TI+E L Sbjct: 348 MVHHMQNNGITYGLQTMCEGGGQANATILELL 379 Lambda K H 0.317 0.132 0.379 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: 458 Number of extensions: 14 Number of successful extensions: 4 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: 391 Length of database: 379 Length adjustment: 30 Effective length of query: 361 Effective length of database: 349 Effective search space: 125989 Effective search space used: 125989 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