Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_065397667.1 BBI00_RS04610 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_001684965.1:WP_065397667.1 Length = 392 Score = 290 bits (743), Expect = 4e-83 Identities = 165/387 (42%), Positives = 238/387 (61%), Gaps = 8/387 (2%) Query: 40 VVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVL-QPGAG 97 +V G R+ +G+A +G + T PD + + V+ ++ ++ +L ++ D+ VGN + + G Sbjct: 6 IVKGFRSAVGKAPKGSLRFTRPDVMAATVIEKLMAELPQLDKNRIDDLIVGNAMPEAEQG 65 Query: 98 AIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTLSQ 157 +AR+ + + VP TVNR C+SG +A+A + I+ G D +A G ESM+ Sbjct: 66 LNVARLISLMGLNTDKVPGVTVNRYCASGSEAIAIASAKIQAGMADCIIAGGTESMSYIP 125 Query: 158 RGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQSRG 217 G + + + D MG T+E VA+++ +SR++QD FA S KA A G Sbjct: 126 MGGYKPVPETDIAKTNP-DYYWGMGYTAEEVAKQYNISREEQDQFAFESHMKALKANQEG 184 Query: 218 CFHAEIVPVTTTVL----NDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGGSTTAG 273 F +IVP+ N K K S DEG R T++ GLAKL+P F +GGS TAG Sbjct: 185 KFANQIVPIPVQYNFLDENQKMQTKKFDFSVDEGPRADTSLAGLAKLRPVFANGGSVTAG 244 Query: 274 NSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQKAG 333 NSSQ+SDGAA V++ +ELGL L +YA G+ P +MG+GP YAIP AL++AG Sbjct: 245 NSSQMSDGAAFVMVMSEEMVKELGLEPEARLVAYAAAGLEPRIMGMGPIYAIPKALKQAG 304 Query: 334 LTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLLNE 393 L + DID+ E+NEAFASQ+V ++LG+ E +N GGAIALGHPLGCTG + V LL+E Sbjct: 305 LELKDIDLIELNEAFASQSVAIKKELGLNPEILNVNGGAIALGHPLGCTGTKLTVQLLDE 364 Query: 394 LKRRGRRAYGVVSMCIGTGMGAAAVFE 420 ++RRG + YG+VSMC+GTG GAA++FE Sbjct: 365 MRRRGNK-YGMVSMCVGTGQGAASIFE 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: 396 Number of extensions: 15 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