Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate Pf6N2E2_2539 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 Length = 394 Score = 287 bits (735), Expect = 3e-82 Identities = 171/391 (43%), Positives = 237/391 (60%), Gaps = 9/391 (2%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96 +VV+V RT + ++ RG F T PD++ + + A+L ++ P + D VG GA Sbjct: 3 EVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLARNDINPASVEDCIVGAGSNEGA 62 Query: 97 -GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155 G + R LS + T+NR CSSGLQA+A A I +G DI +A GVES+SL Sbjct: 63 QGYNIGRNVAVLSRLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESISL 122 Query: 156 ADRG-NPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214 + N ++ + L+ KE+ PMG T+E VA R+ +SRE+QD +AL SQQ+ A+AQ Sbjct: 123 TMKSVNTDHLINPLL-KEQVPGIYFPMGQTAEIVARRYQVSREEQDRYALQSQQRTAKAQ 181 Query: 215 SKGCFQAEIVPVTTTVH-DDKGTKR----SITVTQDEGIRPSTTMEGLAKLKPAFKKDGS 269 + G F EI+P+ +DK T V +D+ RP TT E LA LKP F +DGS Sbjct: 182 AAGLFDDEIIPMAIKYRVEDKNTGAVQILDGVVDRDDCNRPDTTYESLAGLKPVFAEDGS 241 Query: 270 TTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVAL 329 TAGNSSQ+SDGA+ L+ KA LGL R + V G PD MGIGP +++P L Sbjct: 242 VTAGNSSQLSDGASMTLVISLEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFSVPKLL 301 Query: 330 QKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVIT 389 + GL ++D+D++E+NEAFASQ Y +L + P K N GG++++GHP G TG+RQV Sbjct: 302 KAKGLQIADIDLWELNEAFASQCLYSRNRLEIDPGKYNVNGGSISIGHPFGMTGSRQVGH 361 Query: 390 LLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 L+ EL+RR R YGVV+MC+G GMGA +FE Sbjct: 362 LVRELQRRNLR-YGVVTMCVGGGMGATGLFE 391 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: 437 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: 394 Length adjustment: 31 Effective length of query: 393 Effective length of database: 363 Effective search space: 142659 Effective search space used: 142659 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