Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate CCNA_03575 CCNA_03575 3-ketoacyl-CoA thiolase
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__Caulo:CCNA_03575 Length = 395 Score = 278 bits (711), Expect = 2e-79 Identities = 172/394 (43%), Positives = 239/394 (60%), Gaps = 13/394 (3%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96 + V+V RT + ++ RGGF +T + + + L ++ D+ +G GA Sbjct: 3 EAVIVSYARTGLAKSVRGGFNNTHGAAMAGHAIQHAVSRAGLEGAEVEDVVLGCGGPEGA 62 Query: 97 -GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155 G +AR A + +P T T+NR CSSGLQA+A+ A +RN ++ + GVES+SL Sbjct: 63 TGMNVARNAAMWAGLPVTTSGQTINRFCSSGLQAIATAANYVRNDGANVAIGGGVESISL 122 Query: 156 ADRG---NPGNITS-RLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAA 211 + G N +IT +LM+ A + M T++ VA+R+ +SRE QD +AL SQQ+ A Sbjct: 123 VNAGGHMNRFHITEEKLMQTHPA--LWMAMIDTADIVAKRYNVSREYQDEYALRSQQRIA 180 Query: 212 RAQSKGCFQAEIVPVTTTVHD-DKGTKRS----ITVTQDEGIRPSTTMEGLAKLKPAFKK 266 AQ+ G F+ EIVP+ T + +K TK V +DE R TT+EGLA LKP + Sbjct: 181 AAQAAGLFKDEIVPMATKMKVVNKETKEESFVDYVVDKDECNRADTTLEGLASLKPVMGE 240 Query: 267 DGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIP 326 TAGN+SQ+SDGAAA+++ +AE+ GL LG R +AV G PD MGIGP +A+P Sbjct: 241 GKFITAGNASQLSDGAAAVVVMEAKEAEKRGLTPLGAFRGFAVAGCEPDEMGIGPVFAVP 300 Query: 327 VALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQ 386 L++ GL V D+DI+E+NEAFASQ Y ++L + PEK N GG++A+GHP G TGAR Sbjct: 301 RLLERHGLKVDDIDIWELNEAFASQCLYSRDRLGIDPEKYNVNGGSIAIGHPFGMTGARC 360 Query: 387 VITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 LL E KRR K GVV+MCIG GMGAA +FE Sbjct: 361 AGHLLLEGKRR-KAKLGVVTMCIGGGMGAAGLFE 393 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: 445 Number of extensions: 18 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: 395 Length adjustment: 31 Effective length of query: 393 Effective length of database: 364 Effective search space: 143052 Effective search space used: 143052 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