Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_092350127.1 BLU87_RS14570 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_900107645.1:WP_092350127.1 Length = 390 Score = 302 bits (774), Expect = 1e-86 Identities = 175/386 (45%), Positives = 242/386 (62%), Gaps = 18/386 (4%) Query: 45 RTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA-GAIMARI 103 RT CRA +G FKD PD+L +A + +++ + P ++ D+ +G G G +AR+ Sbjct: 11 RTPGCRANKGKFKDMRPDDLAAAALAGLIERTKIDPMRIDDVILGCAFPEGEQGMNVARV 70 Query: 104 AQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLADRG---- 159 A + IP VP T+NR CSSGLQ++A A I G D +A G ESM+ G Sbjct: 71 AALKAGIPYQVPAQTINRFCSSGLQSIALAAERIMAGFADCIIAGGTESMTTVPMGGNKY 130 Query: 160 --NPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKG 217 NPG ++ + + MG+T+E VAE++ ISR+ QD F++AS QKAA A + G Sbjct: 131 SANPGLVS-------QWPETFASMGVTAELVAEKYQISRQDQDAFSVASHQKAAAAIAAG 183 Query: 218 CFQAEIVPVT---TTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGN 274 F EI+PV T + K K + V D+G+R T++EGLAKLK FK+ GS TAG+ Sbjct: 184 RFSDEIIPVEIEKTAIVKGKIQKTTELVDIDDGVRADTSLEGLAKLKTPFKQGGSVTAGS 243 Query: 275 SSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGL 334 SSQ++DGAAA L+ +++G L ++AV GVPP+IMGIGP AIP AL+ AGL Sbjct: 244 SSQMTDGAAAALVVSEDFIKQIGGEPLARFVAFAVKGVPPEIMGIGPIEAIPAALKLAGL 303 Query: 335 TVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNEL 394 + D+ + E+NEAFA+Q+ + +L L E +N GGA+ALGHPLGCTGA+ TLL+E+ Sbjct: 304 QLGDIGLIELNEAFAAQSLAVIRELGLNTETLNVNGGAIALGHPLGCTGAKLTATLLHEM 363 Query: 395 KRRGKRAYGVVSMCIGTGMGAAAVFE 420 +RR R YG+VSMCIG GMGAA +FE Sbjct: 364 QRRELR-YGMVSMCIGGGMGAAGIFE 388 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: 414 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: 390 Length adjustment: 31 Effective length of query: 393 Effective length of database: 359 Effective search space: 141087 Effective search space used: 141087 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