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_013075085.1 BTUS_RS05310 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_000092905.1:WP_013075085.1 Length = 392 Score = 338 bits (867), Expect = 2e-97 Identities = 192/398 (48%), Positives = 259/398 (65%), Gaps = 20/398 (5%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVL-QP 94 + V+V G RTA+ +A +G ++T P++L V+ L+ V + P ++ D+ +G + + Sbjct: 3 EAVIVSGVRTAVGKAPKGALRETRPEDLAGLVVAEALRRVPQVEPAEVEDVIIGCAIPEA 62 Query: 95 GAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G + RI + +P +VP TVNR CSSGLQ +A A I G D+ +A GVESMS Sbjct: 63 EQGMNLGRIVALRAGLPTSVPGVTVNRFCSSGLQTIAMAAERIMAGFADVIVAGGVESMS 122 Query: 155 LAD------RGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQ 208 L R NP + E + MG+T+E VA RF +SRE QD FAL S Q Sbjct: 123 LVPMTGHTVRPNPYLV-------EHYPQVYLSMGLTAEQVARRFDVSREDQDAFALRSHQ 175 Query: 209 KAARAQSKGCFQAEIVPVTTT---VHDD-KGTKRSITVTQDEGIRPSTTMEGLAKLKPAF 264 +AARA +G + EIVPV T V DD K K S +DEG+R T++E LA+L+PAF Sbjct: 176 RAARAIDEGLCRDEIVPVPVTRTVVGDDGKVVKTSFEFVEDEGVRRDTSLEALAQLRPAF 235 Query: 265 KKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYA 324 KDG+ TAGNSSQ SDGAAA+++ +A +LGL + RS+AV GV PDIMGIGP A Sbjct: 236 AKDGTVTAGNSSQTSDGAAAVVVMSAERAAQLGLEPKLIFRSFAVGGVDPDIMGIGPVEA 295 Query: 325 IPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGA 384 +P AL+KAGL++ D+D+FE+NEAFA+Q+ + KL + PEK N GGA+ALGHPLGCTG+ Sbjct: 296 VPKALKKAGLSIDDIDLFELNEAFAAQSLAVMRKLGMDPEKTNVNGGAIALGHPLGCTGS 355 Query: 385 RQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 422 + ++L+NE++RRG R YGVV+MCIG GMGAA VFE P Sbjct: 356 KLTVSLMNEMRRRGSR-YGVVTMCIGGGMGAAGVFERP 392 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: 452 Number of extensions: 20 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: 392 Length adjustment: 31 Effective length of query: 393 Effective length of database: 361 Effective search space: 141873 Effective search space used: 141873 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