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 7025620 Shewana3_2771 acetyl-CoA acetyltransferases (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__ANA3:7025620 Length = 396 Score = 470 bits (1210), Expect = e-137 Identities = 243/387 (62%), Positives = 294/387 (75%), Gaps = 1/387 (0%) Query: 8 IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67 IVIV+A RTPMGGFQG L + +P L A AI+A + VA D V+EVL GCVL AGLGQ Sbjct: 10 IVIVAAKRTPMGGFQGSLSGVMSPSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQ 69 Query: 68 APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127 APARQA LGAGL S TT+NK+CGSGM+ +LAHD+L AGSA +VVAGGMESMS APY Sbjct: 70 APARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLLKAGSAKLVVAGGMESMSQAPY 129 Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187 LLD+AR+G RMGHGKVLDHMFLDGLEDAY G MGTFA+ A+ G TRE D FA++S Sbjct: 130 LLDKARAGMRMGHGKVLDHMFLDGLEDAYTGGA-MGTFAQKTADEYGLTREQMDAFALSS 188 Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247 +A AI G+F AEIVP+ V + + DEQP A+ +KI +L+PAF GT+TA Sbjct: 189 LEKANAAINSGAFKAEIVPVTVSDRRGDVTVDTDEQPGNARPEKIPALRPAFAKDGTITA 248 Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307 ANSSSISDGAAAL+L R+ AE+ GL LA I GH A P LF APVGA+ KLL Sbjct: 249 ANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPSLFTTAPVGAMAKLLSNV 308 Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367 GWS DEV+LFE+NEAFA+V+++ +++L + +KVNV+GGACALGHPIG SGAR+LVTL+ Sbjct: 309 GWSKDEVDLFEINEAFAMVTMLAVSELGLDMAKVNVNGGACALGHPIGCSGARLLVTLIH 368 Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394 AL+ +GLKRGVA++CIGGGEATAMA+E Sbjct: 369 ALKARGLKRGVASLCIGGGEATAMAIE 395 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: 486 Number of extensions: 17 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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