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 3606642 Dshi_0074 acetyl-CoA acetyltransferase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Dino:3606642 Length = 392 Score = 458 bits (1179), Expect = e-133 Identities = 239/387 (61%), Positives = 286/387 (73%) Query: 8 IVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQ 67 + I A RTPMGGFQG +SA QLG AAI A+ AGVA V E+L GCVL AG GQ Sbjct: 4 VAICGAARTPMGGFQGVFSDVSAAQLGGAAIAGALADAGVAPAQVNELLMGCVLPAGQGQ 63 Query: 68 APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127 APARQA AGL + TTLNKMCGSGM+AA++A D + G +D+VVAGGMESM+NAPY Sbjct: 64 APARQAGYAAGLGDAVPATTLNKMCGSGMKAAMIACDQIALGQSDLVVAGGMESMTNAPY 123 Query: 128 LLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIAS 187 LLD+ R G R+GHG+V+DHMFLDGLEDAYDKGRLMGTFAEDCAEA FTR AQD +A+ S Sbjct: 124 LLDKMRGGARIGHGQVIDHMFLDGLEDAYDKGRLMGTFAEDCAEAFQFTRAAQDTYALGS 183 Query: 188 TTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTA 247 A A +F E+VP+ V K + ++ DEQP A+ +KI LKPAFR GTVTA Sbjct: 184 LENALAAEASEAFAMELVPVTVSGRKGETVVIRDEQPAAARPEKIPHLKPAFRKDGTVTA 243 Query: 248 ANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKT 307 ANSSSISDGAAAL+L +AE GL A + GHA+ A P LFP APV A +KLL + Sbjct: 244 ANSSSISDGAAALVLADAGQAEAHGLPVRARVLGHASHAQKPALFPTAPVPAARKLLDRL 303 Query: 308 GWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLS 367 GW + +V+L+EVNEAFAVV + M ++ +P K+NV+GGACALGHPIGASGARILVTLL+ Sbjct: 304 GWCVADVDLWEVNEAFAVVPMAFMHEMGVPREKMNVNGGACALGHPIGASGARILVTLLN 363 Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394 A+ + LKRGVAAICIGGGE TA+A+E Sbjct: 364 AMEARDLKRGVAAICIGGGEGTAIALE 390 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: 497 Number of extensions: 20 Number of successful extensions: 1 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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