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 GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Phaeo:GFF3267 Length = 390 Score = 473 bits (1216), Expect = e-138 Identities = 240/387 (62%), Positives = 296/387 (76%), Gaps = 2/387 (0%) Query: 8 IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67 +VI A RTPMGGFQG ++A +LG +AIRAA+ AG A V+E+L GCVL AG GQ Sbjct: 4 VVIAGAARTPMGGFQGMYDGVAAAELGGSAIRAAL--AGAGATTVDEILMGCVLPAGQGQ 61 Query: 68 APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127 APARQA AGL + TTLNKMCGSGM+AA++A+D + G AD ++AGGMESM+NAPY Sbjct: 62 APARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAPY 121 Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187 LL + R+G R+GHG+V+DHMFLDGLEDAYDKGRLMGTFAEDCAE FTREAQDE+A+ S Sbjct: 122 LLPKMRNGARLGHGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREAQDEYALTS 181 Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247 + A A + G+F+AEI P+ V K + + DEQP A+ DKI +LKPAFR GTVTA Sbjct: 182 LSNALAAQESGAFDAEIAPVTVKTRKGETVTNADEQPKSARPDKIPTLKPAFRKDGTVTA 241 Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307 AN+SSISDGAAAL+L AE +GL A I GHA+ A PGLF APV A KKL+ + Sbjct: 242 ANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVPAAKKLMAQL 301 Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367 GW++ +V+L+EVNEAFAVV + M ++ +P KVNV+GGACALGHPIGASGARI+VTLL+ Sbjct: 302 GWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRDKVNVNGGACALGHPIGASGARIMVTLLN 361 Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394 AL ++ LKRG+AAICIGGGE TA+A+E Sbjct: 362 ALEKRNLKRGIAAICIGGGEGTAIAIE 388 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: 488 Number of extensions: 15 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: 390 Length adjustment: 31 Effective length of query: 366 Effective length of database: 359 Effective search space: 131394 Effective search space used: 131394 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 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