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_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_003194585.1:WP_110204929.1 Length = 395 Score = 244 bits (624), Expect = 3e-69 Identities = 152/396 (38%), Positives = 219/396 (55%), Gaps = 19/396 (4%) Query: 39 VVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGA 98 V+V G RT + R GG KD + +L + L+ + +Q+ + +G+V+Q GAG Sbjct: 5 VIVAGARTPVGRL-LGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAGAGQ 63 Query: 99 IMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLADR 158 I AR A IP VP T+N+ C SG+ A+A IR G ++I +A G+ESM+ A Sbjct: 64 ITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQAPH 123 Query: 159 GNPGNITSRLMEKEKARDCLIPMGITSENVAERFG------------ISREKQDTFALAS 206 P + K D + + + + G ++RE+QD F+ S Sbjct: 124 LLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGGNLTREEQDAFSARS 183 Query: 207 QQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKK 266 Q AA AQ G F EIVPVT + + + V+ DEG+R TT E L L+PAF K Sbjct: 184 HQLAAAAQKNGVFDDEIVPVTIS-----SRRGDVVVSVDEGVRGDTTAESLGGLRPAFAK 238 Query: 267 DGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIP 326 DG+ TAG+SSQ+SDGA A+++ ++KAEELGL L + + V P + + PA AI Sbjct: 239 DGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAIA 298 Query: 327 VALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQ 386 A++K G+ VSD+D+FE+NEAFA+ +L + +KVN GGA+A+GHP+G +GAR Sbjct: 299 KAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGARI 358 Query: 387 VITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 422 V+ L ELKRRG G ++C G G G A + P Sbjct: 359 VLHLALELKRRG-GGIGAAALCGGGGQGDALIVRVP 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: 495 Number of extensions: 25 Number of successful extensions: 3 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 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