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 N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Dyella79:N515DRAFT_0938 Length = 394 Score = 442 bits (1138), Expect = e-129 Identities = 232/395 (58%), Positives = 298/395 (75%), Gaps = 3/395 (0%) Query: 3 MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62 MS +VI A RT +G F G+ + P LGA AI+AA+E+AG+AA V EVL GCVL Sbjct: 1 MSDVSVVIAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLP 60 Query: 63 AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122 A LGQAPARQAAL AGL + CTT+NK+CGSGM+A +L HD++ AGSA VVVAGGMESM Sbjct: 61 ANLGQAPARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESM 120 Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDE 182 +NAP++++ AR+G R G G+++DHM DGL + YD G+ MG F E CA+ FTRE QD Sbjct: 121 TNAPHMVN-ARTGIRYGDGQLVDHMAWDGLTNPYD-GKAMGVFGELCADKYHFTREEQDA 178 Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFR-D 241 FAI S RAQ A ++G+F EIVP+ V K ++ DEQP ++ + K+ SLKPAFR + Sbjct: 179 FAIESVKRAQAAQQNGAFAGEIVPVTVAGRKGDVVVDTDEQPGRSDIAKVPSLKPAFRKE 238 Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301 GT+TAA+SSSISDGAAA++L+ +A+ RGL+PLA I HA + P F APV AI+ Sbjct: 239 NGTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPEWFTTAPVSAIQ 298 Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361 K+L K GW +D+V+LFEVNEAFAVV++ M +L IPH+K+NV+GGACALGHPIGASG R+ Sbjct: 299 KVLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPHAKLNVNGGACALGHPIGASGTRL 358 Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVECL 396 +VTLL+AL+ +GLKRGVA++CIGGGEATA+AVE L Sbjct: 359 VVTLLNALQTRGLKRGVASLCIGGGEATAIAVELL 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: 466 Number of extensions: 15 Number of successful extensions: 4 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 Apr 09 2024. 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