Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8S4Y1 (403 letters) >NCBI__GCF_001418085.1:WP_055437058.1 Length = 392 Score = 444 bits (1141), Expect = e-129 Identities = 234/391 (59%), Positives = 292/391 (74%), Gaps = 3/391 (0%) Query: 11 RDVCIVGVARTPMGGFLGSLSSLPATKLGSLAIAAALKRANVDPALVQEVVFGNVLSANL 70 ++V IV ARTP+G FLG+LS++PA KLG++AI AL++ N++P LVQEV+ GNV+ A Sbjct: 3 KEVVIVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAGT 62 Query: 71 GQAPARQAALGAGIPNSVICTTVNKVCASGMKAVMIAAQSIQLGINDVVVAGGMESMSNT 130 GQAPARQAA+ AGIPN+V CTT+NKVCASGMK VM AAQSI LG ++VVAGGME+MS Sbjct: 63 GQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSLI 122 Query: 131 PKYLAEARKGSRFGHDSLVDGMLKDGLWDVYNDCGMGSCAELCAEKFQITREQQDDYAVQ 190 P Y AR ++FG ++VDGM KDGL DVY+ MG A+ CA K++ +RE QD YA+Q Sbjct: 123 PHYF-HARSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSREDQDAYAIQ 181 Query: 191 SFERGIAAQEAGAFTWEIVPVEVSGGRGRPSTIVDKDEGLGKFDAAKLRKLRPSFKENGG 250 S++R AA EAG F EIVPV V RG IV +DE K+ LR +F + G Sbjct: 182 SYKRSAAAWEAGKFNNEIVPVAVPQRRG-DDVIVTEDEEYKNVRMDKIPTLRAAFTKEG- 239 Query: 251 TVTAGNASSISDGAAALVLVSGEKALQLGLLVLAKIKGYGDAAQEPEFFTTAPALAIPKA 310 TVTA NAS+I+DGA A+VL+S EKA +LGL VLA IKGY DAA EPE+FTTAP++A+PKA Sbjct: 240 TVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAPSIALPKA 299 Query: 311 IAHAGLESSQVDYYEINEAFAVVALANQKLLGIAPEKVNVNGGAVSLGHPLGCSGARILI 370 + AGL+ VD++E NEAF++V LAN K+LG+ VNVNGGAVSLGHPLGCSG RILI Sbjct: 300 LNKAGLDIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLGCSGVRILI 359 Query: 371 TLLGILKKRNGKYGVGGVCNGGGGASALVLE 401 TLL +L++ + K G +CNGGGGASALVLE Sbjct: 360 TLLNVLEQNDAKIGAAAICNGGGGASALVLE 390 Lambda K H 0.316 0.134 0.382 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: 483 Number of extensions: 14 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: 403 Length of database: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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