Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_033100059.1 JG50_RS0105240 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000763315.1:WP_033100059.1 Length = 392 Score = 331 bits (848), Expect = 3e-95 Identities = 189/390 (48%), Positives = 258/390 (66%), Gaps = 8/390 (2%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVLQPG 95 + V+V G RT +G+A +G K T PD+L + V+ +++ V + P+++ D+ +G G Sbjct: 3 EAVIVAGARTAVGKAHKGTLKTTRPDDLAAQVVKDLMRRVPQADPKEVEDVILGCAFPEG 62 Query: 96 A-GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G MAR+ +G+P VP TVNR CSSGLQ +A A I DI +A GVESM+ Sbjct: 63 EQGMNMARLVALRAGLPTDVPGMTVNRFCSSGLQTIAIAAEKIMCNFADIIIAGGVESMS 122 Query: 155 LSQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQ 214 + G + + L + + + MG T+E VA+R+ VSR+ QD FALAS QKA +A Sbjct: 123 MVPMGGYKPAPNPWLMDHLP-EAYMSMGHTAEEVAKRYNVSREDQDRFALASHQKAYAAI 181 Query: 215 SRGCFHAEIVPVT--TTVLNDKGDKKTI--TVSQDEGVRPSTTMQGLAKLKPAFKDGGST 270 G F EIVPVT T V ++KG + DEGVRP T+++ L KL+PAF+ GG+ Sbjct: 182 QEGKFKDEIVPVTVKTHVFDEKGKLRVEERVFDTDEGVRPDTSLEVLGKLRPAFQSGGTV 241 Query: 271 TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQ 330 TAGNSSQ SDGAAAV++ R KAEELG+ L V R + + GV PDVMGIGP A+P L+ Sbjct: 242 TAGNSSQTSDGAAAVMVMSREKAEELGVEPLAVFRGFVLGGVDPDVMGIGPVAAVPKLLK 301 Query: 331 KAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTL 390 K G+++++ID+ E+NEAFASQA+ + +LG+ + VN GGAIALGHPLGCTGA+ V++ Sbjct: 302 KTGVSLDEIDLVELNEAFASQAIAVIRELGLNPDIVNVNGGAIALGHPLGCTGAKLTVSI 361 Query: 391 LNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 LNELKRR +R YG+V+MCIG GMGAA + E Sbjct: 362 LNELKRRNKR-YGLVTMCIGGGMGAAGLIE 390 Lambda K H 0.317 0.133 0.377 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: 456 Number of extensions: 22 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 (21.6 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