Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_017599366.1 D471_RS0114985 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_000341125.1:WP_017599366.1 Length = 380 Score = 415 bits (1066), Expect = e-120 Identities = 216/391 (55%), Positives = 278/391 (71%), Gaps = 11/391 (2%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 MAEAYIV AVRT G K G L+ HPADL A VL LV RTG DPA VEDV+MGCV+Q G Sbjct: 1 MAEAYIVGAVRTPVGTKKGALAAVHPADLGAHVLKELVTRTGVDPAAVEDVVMGCVTQAG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 QA ++AR A L++ PESVPG ++DRQCGSSQQA+HFAAQ VMSG D+V+A+GVE+M Sbjct: 61 PQALDLARTAWLSAGFPESVPGVTIDRQCGSSQQAVHFAAQGVMSGTQDLVVASGVENMG 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 VPMG + Q NG G+ +E RY + SQF GA+++ K+ RE+L+ +AL+S Sbjct: 121 MVPMGANVQFAIDNGLGLYGEGWVE-RYGTQEISQFRGAQLMCEKWGYKREELERFALES 179 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGRV 240 HQRA A + GRF +I P+ G DEGVR D TLE + +K + EG + Sbjct: 180 HQRAARAIEDGRFDDQIAPLA-----GV-----ARDEGVRADTTLEKMAGLKPLREGWEL 229 Query: 241 TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALK 300 TAA ASQI GA +++ +E +++ G+ PLAR+ ++++G DPV ML AP+PAT +AL Sbjct: 230 TAAVASQISVGAGAVLLASERAVREHGLTPLARIVQLSLVGDDPVYMLTAPIPATRIALD 289 Query: 301 KAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTTL 360 KAGL I DID+ E+NEAFAPVP++W++ GADPA++N +GGAIALGHPLG +GA LMT L Sbjct: 290 KAGLTIDDIDVTEINEAFAPVPMSWIEELGADPAKVNPNGGAIALGHPLGATGAVLMTKL 349 Query: 361 VHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 V+ LH G RYGLQTMCEGGG ANVT++ER+ Sbjct: 350 VNELHRSGGRYGLQTMCEGGGQANVTVIERV 380 Lambda K H 0.317 0.132 0.379 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: 478 Number of extensions: 23 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: 391 Length of database: 380 Length adjustment: 30 Effective length of query: 361 Effective length of database: 350 Effective search space: 126350 Effective search space used: 126350 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 (21.7 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