Align 3-ketoacyl-CoA thiolase 1, peroxisomal; Acetyl-CoA acyltransferase 1; Beta-ketothiolase 1; Peroxisomal 3-oxoacyl-CoA thiolase 1; EC 2.3.1.16 (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases
Query= SwissProt::Q8LF48 (443 letters) >FitnessBrowser__Korea:Ga0059261_2160 Length = 398 Score = 293 bits (749), Expect = 9e-84 Identities = 178/403 (44%), Positives = 241/403 (59%), Gaps = 25/403 (6%) Query: 43 DVVIVAAQRTALCKAKRGSFKDTFPDELLASVLRALIEKTNVNPSEVGDIVVGTVLGPGS 102 + IV+ RT + KA RG+F T L V+ A +E+ V+P+ + DI G G+ Sbjct: 3 EAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQWGT 62 Query: 103 QRASECRMAAFYAGFPETVPIRTVNRQCSSGLQAVADVAAAIKAGFYDIGIGAGLESMTT 162 Q + RMA F AG P++VP T++R+C SGL A+A A +I AG DI + G+ES++ Sbjct: 63 QGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESISL 122 Query: 163 N-----PRGWKGSVNPNVKKFEQAHNCLLPMGITSENVAHRFNVSREEQDQAAVDSHRKA 217 PR SV N + +PM T+E VA R+ +SR QD+ S ++A Sbjct: 123 TVTKDAPRYANQSVLANEP------HAYMPMIETAEIVAERYGISRARQDEYGAMSQQRA 176 Query: 218 ASATASGKFKDEITPVKTK--IVDP---KTGDEKPITVSVDDGIRPNTTLSGLAKLKPVF 272 + ASG F +EI P+ + I D +TG E+ +TV+ D+GIR TT LA LK V+ Sbjct: 177 EAGLASGAFAEEIAPITVEKAIFDKEGNRTGSER-VTVTQDEGIRAGTTAEALAGLKTVW 235 Query: 273 KEDGTT------TAGNSSQLSDGAGAVLLMRRNVAMQKGLPILGVFRTFSAVGVDPAIMG 326 K+ TAGN+SQLSDGA A ++M R +A +G ILG++R F A G P MG Sbjct: 236 KDGQVVKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMG 295 Query: 327 VGPAVAIPAAVKAAGLELNDVDLFEINEAFASQFVYCRNKLGLDAEKINVNGGAIAIGHP 386 +GP AIP + AGLE+ D+ L+E+NEAFASQ +YCR+ LG+D EK NVNGGAIAIGHP Sbjct: 296 IGPVFAIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHP 355 Query: 387 LGATGARCVATLLHEMKRRGKDCRFGVVSMCIGSGMGAAAVFE 429 G TGAR + L E ++RG R+ VVSMC GMGAA +FE Sbjct: 356 FGMTGARLIGHALIEGRKRG--VRWVVVSMCTAGGMGAAGLFE 396 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: 402 Number of extensions: 16 Number of successful extensions: 5 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: 443 Length of database: 398 Length adjustment: 32 Effective length of query: 411 Effective length of database: 366 Effective search space: 150426 Effective search space used: 150426 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