Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__Korea:Ga0059261_2160 Length = 398 Score = 278 bits (710), Expect = 3e-79 Identities = 173/399 (43%), Positives = 234/399 (58%), Gaps = 16/399 (4%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96 + +V RT I +A RG F T L VM A ++ + P ++ DI G Q G Sbjct: 3 EAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQWGT 62 Query: 97 -GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155 G R+A F + +P++VP T++R+C SGL A+A A I G DI ++ G+ES+SL Sbjct: 63 QGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESISL 122 Query: 156 A-DRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214 + P ++ E +PM T+E VAER+GISR +QD + SQQ+A Sbjct: 123 TVTKDAPRYANQSVLANEP--HAYMPMIETAEIVAERYGISRARQDEYGAMSQQRAEAGL 180 Query: 215 SKGCFQAEIVPVTT--TVHDDKGTKRS---ITVTQDEGIRPSTTMEGLAKLKPAFK---- 265 + G F EI P+T + D +G + +TVTQDEGIR TT E LA LK +K Sbjct: 181 ASGAFAEEIAPITVEKAIFDKEGNRTGSERVTVTQDEGIRAGTTAEALAGLKTVWKDGQV 240 Query: 266 -KDGS-TTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAY 323 K+G TAGN+SQ+SDGAAA ++ R+ AE G ILG+ R + G PD MGIGP + Sbjct: 241 VKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMGIGPVF 300 Query: 324 AIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTG 383 AIP L +AGL V+D+ ++E+NEAFASQ YC + L + PEK N GGA+A+GHP G TG Sbjct: 301 AIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHPFGMTG 360 Query: 384 ARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 422 AR + L E ++RG R + VVSMC GMGAA +FE P Sbjct: 361 ARLIGHALIEGRKRGVR-WVVVSMCTAGGMGAAGLFEIP 398 Lambda K H 0.317 0.134 0.385 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: 440 Number of extensions: 17 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: 424 Length of database: 398 Length adjustment: 31 Effective length of query: 393 Effective length of database: 367 Effective search space: 144231 Effective search space used: 144231 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