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_041096886.1 SUTH_RS02650 acetyl-CoA C-acetyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_000828635.1:WP_041096886.1 Length = 393 Score = 550 bits (1417), Expect = e-161 Identities = 277/389 (71%), Positives = 322/389 (82%) Query: 6 DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65 DPIVI+SA RTPMGGFQG+ SL+ QLG+AAI+AAVERAG+A V+EV+ GCVL AG Sbjct: 3 DPIVIISAARTPMGGFQGDFNSLTCAQLGSAAIKAAVERAGLAPAQVDEVIMGCVLPAGQ 62 Query: 66 GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125 GQAPARQA+LGAGL + CTT+NKMCGSGM AA+ AHDMLLAGS DV+VAGGMESMSNA Sbjct: 63 GQAPARQASLGAGLPLAAGCTTVNKMCGSGMRAAMYAHDMLLAGSVDVMVAGGMESMSNA 122 Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185 PYLL +AR GYR+GHG+V DHMFLDGLEDAYDKGRLMGTFAEDCA + FTREAQD FA+ Sbjct: 123 PYLLPKARGGYRLGHGEVKDHMFLDGLEDAYDKGRLMGTFAEDCAGSYKFTREAQDAFAV 182 Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245 ASTTRA+QA DGSF EI P+ V K +I DEQP KA+L+KI +LKPAFR GTV Sbjct: 183 ASTTRAKQANTDGSFTWEIAPVTVSGRKGDVVIDKDEQPFKAQLEKIPTLKPAFRKDGTV 242 Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305 TAANSSSISDGAAAL++MR S A + GLKP+A I GH+ FA PGLF APVGA+KKLL Sbjct: 243 TAANSSSISDGAAALVMMRASTAARLGLKPIATIVGHSTFAQEPGLFTTAPVGAMKKLLA 302 Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365 K GWS D V+L+E+NEAFAVV++ M L++PH KVNVHGGACALGHPIGASGAR++VTL Sbjct: 303 KNGWSADSVDLWEINEAFAVVTMAAMHDLKLPHEKVNVHGGACALGHPIGASGARVIVTL 362 Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394 + ALR+ G KRGVA++CIGGGEATA+ +E Sbjct: 363 IGALRKYGKKRGVASLCIGGGEATAVGIE 391 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: 539 Number of extensions: 10 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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