Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >FitnessBrowser__HerbieS:HSERO_RS01265 Length = 398 Score = 312 bits (800), Expect = 1e-89 Identities = 185/392 (47%), Positives = 246/392 (62%), Gaps = 10/392 (2%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELL-SAVLTAVLQDVKLKPEQLGDISVGNVLQPG 95 D +V RTPIG+A RG FK+T PD+LL A+ +AV Q L P+ + D VG G Sbjct: 7 DAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFPEG 66 Query: 96 A-GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 A G MAR A L+G+P T+ T+NR C+SG+ A+A A IR G D+ +A G ESM+ Sbjct: 67 AQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAESMS 126 Query: 155 L-SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASA 213 + G H +I+ ++E MG+T+E VA+++ VSR+ QD F+LAS QKA +A Sbjct: 127 MVPMMGFHPSININAFKDENV-GMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQKAIAA 185 Query: 214 QSRGCF-----HAEIVPVTTTVLNDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGG 268 Q G F EIV + + D KT TVS DEG R + + LAKLKP F G Sbjct: 186 QEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADSNLAALAKLKPVFAAKG 245 Query: 269 STTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAA 328 S TAGNSSQ SDGA A+++ ++ L L S+AV GVPP++MGIGP AIPAA Sbjct: 246 SVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPAA 305 Query: 329 LQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVV 388 L+ GLT + ID E+NEAFA+QA+ + LG+ KVNP+GGAIALGHPLG TGA + Sbjct: 306 LKAGGLTQDQIDWIELNEAFAAQALAVIGDLGLDPSKVNPMGGAIALGHPLGATGAIRAA 365 Query: 389 TLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 T ++ L+R+ + YG+V+MC+GTGMGAA +FE Sbjct: 366 TTIHALRRKNLK-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: 411 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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 Sep 17 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