Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_041098264.1 SUTH_RS07380 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000828635.1:WP_041098264.1 Length = 398 Score = 299 bits (766), Expect = 9e-86 Identities = 175/392 (44%), Positives = 245/392 (62%), Gaps = 10/392 (2%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLS-AVLTAVLQDVKLKPEQLGDISVGNVLQPG 95 D +V RTPIG+A RG F++T PD+LL A+ +A+ Q L P+ + D +G G Sbjct: 7 DAYIVAATRTPIGKAPRGMFRNTRPDDLLVYAIQSAMAQVPGLDPKLIEDAIIGCSFPEG 66 Query: 96 -AGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 +G MAR A L+G+P TV TVNR C+SG+ AVA A IR G D+ +A G ESM+ Sbjct: 67 ESGLNMARNAVLLAGLPNTVGGVTVNRFCASGITAVAMAADRIRVGQADVMIAGGAESMS 126 Query: 155 L-SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASA 213 + GNH +I+ + ++E MG+T+E VA ++ ++R+ QD FAL S Q+A + Sbjct: 127 MVPMGGNHPSINMGVFKDENV-GMAYGMGLTAEKVANQWKITREMQDEFALQSHQRAIAG 185 Query: 214 QSRGCFH-----AEIVPVTTTVLNDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGG 268 Q G F EIV + + D K +V++DEG R + + LAKLKP F G Sbjct: 186 QQAGEFDNETTAVEIVDRVPNLATGEVDLKKRSVNRDEGARADSNLAALAKLKPVFAAKG 245 Query: 269 STTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAA 328 S TAGNSSQ SDGA A++L ++ L L S+AV GVPP++MGIGP AIP A Sbjct: 246 SVTAGNSSQTSDGAGALILVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPVA 305 Query: 329 LQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVV 388 + AG+T + +D E+NEAFA+Q++ ++ L + KVNP+GGAIALGHPLG TGA + Sbjct: 306 CRAAGITQDQLDWIELNEAFAAQSLAVIKDLDLDPAKVNPIGGAIALGHPLGATGAIRSA 365 Query: 389 TLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 T+++ L+RR + YG+V+MC+GTGMGAA +FE Sbjct: 366 TVIHALRRRNLK-YGMVTMCVGTGMGAAGIFE 396 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: 435 Number of extensions: 13 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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