Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate CCNA_00820 CCNA_00820 3-ketoacyl-CoA thiolase
Query= BRENDA::Q0K368 (391 letters) >FitnessBrowser__Caulo:CCNA_00820 Length = 390 Score = 612 bits (1578), Expect = e-180 Identities = 302/391 (77%), Positives = 348/391 (89%), Gaps = 1/391 (0%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 M EAYIVAA RTAGGRKGG++SGWHPADLA +VL+ALV+R+GADPAL+EDVIMGCV QVG Sbjct: 1 MGEAYIVAAARTAGGRKGGRVSGWHPADLAGEVLNALVDRSGADPALIEDVIMGCVGQVG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQA N+ARNA+LAS+LPESVP TSVDRQCGSSQQ++HFAA VMSGAMDIVIAAGVESM+ Sbjct: 61 EQAINIARNAVLASKLPESVPATSVDRQCGSSQQSIHFAAATVMSGAMDIVIAAGVESMS 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 RVPMGLSS LP KNGFG KSP +E RYPG+QFSQF GAEM+A+KYDLSREQLDA+AL S Sbjct: 121 RVPMGLSSALPYKNGFGTYKSPRMEERYPGIQFSQFAGAEMLAKKYDLSREQLDAFALAS 180 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGRV 240 HQRA+AATK G+F AEI+P++V DG + E H DEG+R+DAT+ESIG VKL++E GR+ Sbjct: 181 HQRAMAATKGGKFAAEIVPIKVTLPDG-SVETHDADEGIRWDATMESIGGVKLLSEDGRL 239 Query: 241 TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALK 300 TAA++SQICDGAAG+M+VNE GLK LGV PLAR+H MTVIGHDPV+MLEAP+PAT+ AL+ Sbjct: 240 TAATSSQICDGAAGVMIVNERGLKALGVAPLARIHHMTVIGHDPVIMLEAPIPATQKALE 299 Query: 301 KAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTTL 360 +AG++I DIDL+EVNEAFA VP AWL+ TG DP +LNV+GGAIALGHPLGGSGAKLMTTL Sbjct: 300 RAGMKIDDIDLYEVNEAFASVPTAWLQVTGGDPDKLNVNGGAIALGHPLGGSGAKLMTTL 359 Query: 361 VHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 VHAL G RYGLQTMCEGGGLANVTIVERL Sbjct: 360 VHALKDRGARYGLQTMCEGGGLANVTIVERL 390 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: 605 Number of extensions: 22 Number of successful extensions: 2 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: 390 Length adjustment: 31 Effective length of query: 360 Effective length of database: 359 Effective search space: 129240 Effective search space used: 129240 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 17 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