Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate BPHYT_RS03230 BPHYT_RS03230 acetyl-CoA acetyltransferase
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__BFirm:BPHYT_RS03230 Length = 399 Score = 292 bits (747), Expect = 1e-83 Identities = 175/392 (44%), Positives = 241/392 (61%), Gaps = 9/392 (2%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELL-SAVMTAVLKDVNLRPEQLGDICVGNVL-QP 94 D +V RT I +A RG FK+T PDELL A+ +AV + L + + D +G + + Sbjct: 7 DAYIVAASRTPIGKAPRGMFKNTRPDELLVHAIKSAVAQVPGLDTKVIEDAIIGCAIPEA 66 Query: 95 GAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G +AR+ L+ +P +V TVNR C+SGL A+A A IR G D +A G ESMS Sbjct: 67 EQGLNVARMGALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCESMS 126 Query: 155 LADR-GNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARA 213 + GN +++ + ++ + MG+T+E VAER+ ISRE QD F++ S ++A A Sbjct: 127 MVPMMGNKPSMSPHIFDRNEDVGIAYGMGLTAEKVAERWKISREAQDAFSVESHRRAIAA 186 Query: 214 QSKGCFQAEIVPVTTTVH-DDKGTK----RSITVTQDEGIRPSTTMEGLAKLKPAFKKDG 268 Q G F EI T T D T ++ V+ DEG R T++EGLAKL+ F G Sbjct: 187 QQAGEFNDEIAAYTITERFPDLATGEVRVKTREVSLDEGPRAETSLEGLAKLRAVFANKG 246 Query: 269 STTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVA 328 S TAGNSSQ SDGA A+++ +E L L S+AV GVPP+IMGIGP AIP A Sbjct: 247 SVTAGNSSQTSDGAGALIVVSEKMLKEFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPAA 306 Query: 329 LQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVI 388 L+ AGL + D+D E+NEAFA+Q+ ++ L L P K+NPLGGA+ALGHPLG TGA + Sbjct: 307 LKAAGLKIDDLDWIELNEAFAAQSLAVIQDLGLDPAKINPLGGAIALGHPLGATGAIRAS 366 Query: 389 TLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 T+++ L+RR + YG+V+MC+GTGMGAA + E Sbjct: 367 TVVHGLRRRNYK-YGMVTMCVGTGMGAAGIIE 397 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: 423 Number of extensions: 23 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: 399 Length adjustment: 31 Effective length of query: 393 Effective length of database: 368 Effective search space: 144624 Effective search space used: 144624 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