Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101587838.1 BJEO58_RS03590 thiolase family protein
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_900169175.1:WP_101587838.1 Length = 393 Score = 338 bits (868), Expect = 1e-97 Identities = 184/392 (46%), Positives = 254/392 (64%), Gaps = 8/392 (2%) Query: 3 EAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVGEQ 62 +A IV AVRT G++GG L HP DL A + LVER+G D L++D I+G Q GEQ Sbjct: 7 QAVIVDAVRTPVGKRGGALREHHPVDLMATTIGHLVERSGVDQELLDDAIVGVGLQRGEQ 66 Query: 63 AGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMTRV 122 GNVARNA+L + LP ++PGT++DRQCGS QQA+ FAAQAV +G +A GVESM+R Sbjct: 67 TGNVARNAVLGAGLPVALPGTTIDRQCGSGQQAVQFAAQAVRAGDYRFALAGGVESMSRT 126 Query: 123 PMG--LSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 +G P +G AR+ G SQ +++ ++Y +RE++DA+A++S Sbjct: 127 DLGPLFDPAGPQGEWYGTQAL----ARFDGDLPSQGRSIDLVVKEYGFTREEMDAFAIRS 182 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK-LIAEGGR 239 H RA AAT++GRFT +++P+ T DGA + T DEG+R + S+ + + G+ Sbjct: 183 HHRAAAATEAGRFTHDLVPLNGLTKDGAEVAL-TADEGIRPSVDPAKVASLAPVFSPDGK 241 Query: 240 VTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVAL 299 VTA ++SQI DGAA L++ + + G++P AR+ A DPV+ A LPA+ +AL Sbjct: 242 VTAGNSSQISDGAAALLIADRDAAESAGLRPRARIVASVARAADPVLQFTAILPASHLAL 301 Query: 300 KKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTT 359 KAGL IGD+DL EVNEAFAPVPL + + G LNV+GG+IA+GHP+G +GA+L+T Sbjct: 302 AKAGLTIGDMDLIEVNEAFAPVPLLFQREFGVSDDILNVNGGSIAIGHPIGSTGARLLTG 361 Query: 360 LVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 LV L RYGL T+CEGGG+AN TI+ERL Sbjct: 362 LVSELERRDARYGLLTICEGGGMANATIIERL 393 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: 476 Number of extensions: 21 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 360 Effective length of database: 362 Effective search space: 130320 Effective search space used: 130320 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