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_058857241.1 AS188_RS00800 acetyl-CoA C-acetyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_001482365.1:WP_058857241.1 Length = 396 Score = 228 bits (580), Expect = 3e-64 Identities = 159/395 (40%), Positives = 214/395 (54%), Gaps = 17/395 (4%) Query: 33 ASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVL 92 +S DVVV+ G RT + G T EL + + L+ + PEQ+ + +G+VL Sbjct: 2 SSPTDVVVLSGARTPQGKI-LGQLASFTAAELGAHAVRHALERAGVAPEQVDYVLMGHVL 60 Query: 93 QPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVES 152 Q GAG AR A + IP VP TVN+ C SGL AV A IR G ++ +A G ES Sbjct: 61 QAGAGQNPARQAAVTAGIPLDVPAETVNKVCLSGLVAVTHAARMIRAGEAEVVVAGGQES 120 Query: 153 MSLADRGNPG-----NITSRLMEKEKARDCLIP------MGITSENVAERFGISREKQDT 201 M+ A G + +E A+D L+ MG +E+ ISR +QD Sbjct: 121 MTSAPHLALGVRQGKSYGDLKLEDAVAKDGLVDVAACVSMGSLTESGNGERAISRAEQDE 180 Query: 202 FALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLK 261 A S ++AARA +G F+ EI PVT V KG + V D+G+RP T E +A+L+ Sbjct: 181 VAAQSHRRAARAAEEGVFREEIAPVT--VPQRKGDP--LVVDTDQGVRPEATAESMARLR 236 Query: 262 PAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGP 321 PAF +DG+ TAGNSS +SDGAAA++L+ R A+ GL L V+ + V P + P Sbjct: 237 PAFAQDGTITAGNSSPLSDGAAALVLSTREYAQRHGLEWLAVVGAPGQVAGPDTSLHSQP 296 Query: 322 AYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGC 381 + AI A+ KAG +V D+D EINEAFAS + L P E+ N GGAVA+GHP+G Sbjct: 297 SRAIEAAVAKAGWSVQDLDFIEINEAFASVLIQSLRDLDYPLERANVHGGAVAVGHPIGA 356 Query: 382 TGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAA 416 +GAR + EL RRG VS+C G G G A Sbjct: 357 SGARLALHAAFELARRG-TGRAAVSLCGGGGQGEA 390 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: 441 Number of extensions: 27 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: 396 Length adjustment: 31 Effective length of query: 393 Effective length of database: 365 Effective search space: 143445 Effective search space used: 143445 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