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_050461610.1 AKL27_RS04625 acetyl-CoA acetyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_001189915.1:WP_050461610.1 Length = 398 Score = 293 bits (750), Expect = 6e-84 Identities = 178/394 (45%), Positives = 234/394 (59%), Gaps = 14/394 (3%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVLQPG 95 D +V RT I +A RG FK+ PD+LL M + L V L P+ + D +G G Sbjct: 7 DAYIVAATRTPIGKAPRGMFKNVRPDDLLVRAMQSALAQVPGLDPKLIEDAIIGCSFPEG 66 Query: 96 A-GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 A G MAR A L+ +P TV T+NR C+SG+ AVA A IR G D+ +A G ESMS Sbjct: 67 AQGLNMARNAVLLAGLPNTVGGVTINRYCASGITAVAMAADRIRVGQADVMIAGGAESMS 126 Query: 155 LADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQ 214 + + K++ MG+T+ENVA+++ +SRE QD F+LAS QKA AQ Sbjct: 127 MVPMMGFHPSINMGAFKDENIGMAYGMGLTAENVAKQWKVSREAQDQFSLASHQKAIAAQ 186 Query: 215 SKGCFQAEIV--------PVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKK 266 G F E P T D T+ TV +DEG R +++E L KLKP F Sbjct: 187 LAGEFNEETTSVDIIERFPNLATGEIDLKTR---TVNKDEGARADSSIEALTKLKPVFAA 243 Query: 267 DGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIP 326 GS TAGNSSQ SDGA ++L ++ L L S+AV GVPP+IMGIGP AIP Sbjct: 244 KGSVTAGNSSQTSDGAGVLILVSEKILKQFNLVPLARFASFAVRGVPPEIMGIGPKEAIP 303 Query: 327 VALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQ 386 VAL+ AG+T +D E+NEAFA+QA ++ L L P KVNP+GGA+ALGHPLG TGA + Sbjct: 304 VALRAAGITQDQLDWIELNEAFAAQALAVIQDLGLDPSKVNPMGGAIALGHPLGATGAIR 363 Query: 387 VITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 T ++ L+R+ + YG+V+MC+GTGMGAA +FE Sbjct: 364 AATTIHALRRKNLK-YGMVTMCVGTGMGAAGIFE 396 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: 409 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: 398 Length adjustment: 31 Effective length of query: 393 Effective length of database: 367 Effective search space: 144231 Effective search space used: 144231 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