Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101588547.1 BJEO58_RS05920 thiolase family protein
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_900169175.1:WP_101588547.1 Length = 388 Score = 401 bits (1030), Expect = e-116 Identities = 214/390 (54%), Positives = 269/390 (68%), Gaps = 6/390 (1%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 M EA IV A RTA GR+GG L HP DL A VL LVER G DPAL+EDV+ GCV+QVG Sbjct: 1 MPEAVIVDAARTAVGRRGGALRDVHPVDLGAHVLRGLVERNGLDPALIEDVVFGCVTQVG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQ NV R A LA+ PE+V GT+VDR CGSSQQAL FA +V++G DIVIA GVESMT Sbjct: 61 EQGSNVGRWAALAAGFPETVAGTTVDRACGSSQQALTFAVASVIAGHSDIVIAGGVESMT 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 RVPMG NG G P +E RY FSQ GAEM+A +++L+R QLD AL+S Sbjct: 121 RVPMGSQRN----NGPGKAFGPAVEERYGRDSFSQGEGAEMVAERWNLTRTQLDELALES 176 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLI-AEGGR 239 H RA+AAT++G + +ILP+ +T +G + DEG+R TLE +G++ + E G Sbjct: 177 HARALAATEAGVLSEQILPIAGQTKEGETQDFRR-DEGIRPGGTLEKLGTLPTVFKEDGV 235 Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299 VTA ++SQI DGA+ L+V+ ++LG+ P+ARVH + DPV+ML AP+PATE AL Sbjct: 236 VTAGNSSQISDGASALLVMTPERARELGLTPIARVHTAALAATDPVIMLTAPIPATEKAL 295 Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359 KK+GL DI +FEVNEAFA VPLAW++ G R+N +GGAIA GHPLG SGA++MT Sbjct: 296 KKSGLSPADIGVFEVNEAFASVPLAWMQEFGVGADRVNPNGGAIAFGHPLGASGARIMTD 355 Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVE 389 L+H + G +YGLQTMCE GG AN TI+E Sbjct: 356 LIHTMRATGTQYGLQTMCEAGGQANATILE 385 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: 456 Number of extensions: 15 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: 388 Length adjustment: 30 Effective length of query: 361 Effective length of database: 358 Effective search space: 129238 Effective search space used: 129238 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