Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_066919695.1 ACG33_RS06435 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_001579945.1:WP_066919695.1 Length = 395 Score = 424 bits (1089), Expect = e-123 Identities = 213/389 (54%), Positives = 284/389 (73%), Gaps = 1/389 (0%) Query: 6 DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65 + I IV+A RTP+G FQG L S+SAP LGAAA RAA++ +G+ A ++E + GCVL AG+ Sbjct: 6 EDIYIVAARRTPIGSFQGVLSSVSAPYLGAAAARAAIQDSGLDAGRIDEAIMGCVLMAGV 65 Query: 66 GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125 GQAPARQAAL AG+ + TT+NKMCGS ++A +LA D + AGSA +V+AGG+ESM+NA Sbjct: 66 GQAPARQAALAAGVPQKVPATTINKMCGSALKATMLAADQIAAGSARIVLAGGLESMTNA 125 Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185 PYLL +AR G RMGHG++LDHMF DGL+ A+D G+ MG FA+ A+ FTRE QD FA Sbjct: 126 PYLLPKARGGLRMGHGEILDHMFFDGLQSAFD-GKPMGFFADATAKKYSFTREQQDSFAA 184 Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245 S RA AI+ G F EI P+ + K ++ + DE P +++I LKPAF GTV Sbjct: 185 ESVRRALAAIEAGRFEPEIAPVIIKDRKGERTVAKDETPFNCDIERIPQLKPAFNKDGTV 244 Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305 TAA+SSSISDGAAA+++ + + L+PLA I GHA++A P F APVGAI+ +L Sbjct: 245 TAASSSSISDGAAAVVIAGAAAVREHDLRPLARIVGHASYAQAPEWFTTAPVGAIQSVLD 304 Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365 K GW EV+L+E+NEAFA V++ + L + H++VNV+GGACALGHPIGA+GARIL TL Sbjct: 305 KAGWRAAEVDLYEINEAFACVTMAAIHDLGLDHARVNVNGGACALGHPIGATGARILTTL 364 Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394 + L+++G KRG+A++CIGGGEA A+A+E Sbjct: 365 IHELKRRGQKRGIASLCIGGGEAAALAIE 393 Lambda K H 0.318 0.133 0.378 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: 487 Number of extensions: 13 Number of successful extensions: 2 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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