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_029001172.1 H537_RS0132200 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_000430725.1:WP_029001172.1 Length = 400 Score = 310 bits (793), Expect = 7e-89 Identities = 181/392 (46%), Positives = 244/392 (62%), Gaps = 9/392 (2%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVLQPG 95 D +V RT I ++GRG F++T PD+LL A + LK V L P + D VG G Sbjct: 8 DAYIVAATRTPIGKSGRGVFRNTRPDDLLVAALRGALKQVPTLDPAAIEDAIVGCSFPEG 67 Query: 96 A-GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G +AR+A L+ +P +V +TVNR C+SGL A+A A IR G D+ +A GVESMS Sbjct: 68 EQGMNVARMAVLLAGLPPSVGGATVNRFCASGLTALAMAADRIRVGEADVLIAGGVESMS 127 Query: 155 LADRG-NPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARA 213 L G N + + +++ MG+T+E VA ++ +SR+ QD FALAS QKA A Sbjct: 128 LVPMGGNKPSFNPEMFTRDENVGIAYGMGLTAEKVAAQWKVSRQAQDEFALASHQKAVAA 187 Query: 214 QSKGCFQAEIVPVTTT-----VHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDG 268 G F+ EI PV + + K V DEG RP TT+E LAKLKP F G Sbjct: 188 IQSGEFRDEITPVEVIERRPDLETGEVVKTPRVVDTDEGPRPETTLEALAKLKPVFAAKG 247 Query: 269 STTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVA 328 S TAGNSSQ SDGA A+++A + + L L S++V GVPP+IMGIGP AIP A Sbjct: 248 SVTAGNSSQTSDGAGALIVASEAAVKRFNLQPLARFVSFSVKGVPPEIMGIGPIDAIPAA 307 Query: 329 LQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVI 388 L++AG+ +SD+D E+NEAFA+QA V+ + + K+NPLGGA+ALGHPLG TGA + Sbjct: 308 LKRAGIQLSDLDWIELNEAFAAQALAVVDSVGIDRAKLNPLGGAIALGHPLGATGALRAA 367 Query: 389 TLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 T+++ L+RRG R YG+++MC+GTG GAA +FE Sbjct: 368 TVVHGLRRRGGR-YGMLTMCVGTGQGAAGIFE 398 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: 440 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: 400 Length adjustment: 31 Effective length of query: 393 Effective length of database: 369 Effective search space: 145017 Effective search space used: 145017 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