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_011654330.1 RL_RS28905 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_000009265.1:WP_011654330.1 Length = 395 Score = 548 bits (1413), Expect = e-161 Identities = 274/389 (70%), Positives = 326/389 (83%) Query: 6 DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65 DPIVIV A RTP+G FQGELK +AP+LGA AIRAA++R+GV A +EEV+FGCVL AG Sbjct: 5 DPIVIVGAARTPIGSFQGELKEATAPELGATAIRAALQRSGVEAATIEEVVFGCVLPAGQ 64 Query: 66 GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125 GQAPARQAA+ AGL +T +T+NKMCGSGM+A ++AHD++ AGSA V VAGGMESM+NA Sbjct: 65 GQAPARQAAIHAGLPFATAASTVNKMCGSGMKAVMMAHDLIAAGSASVAVAGGMESMTNA 124 Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185 PYLLD+AR GYR+GHG+V+DHMFLDGLEDAYDKGRLMG+FAEDCAEA FTREAQD +AI Sbjct: 125 PYLLDKARGGYRLGHGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDSYAI 184 Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245 AS RAQ+AI +G F++EI + V K +++ + DEQP KAKLDKI +LKPAFR+GGTV Sbjct: 185 ASLARAQKAIAEGCFDSEIAAVTVKSSKVEQVASRDEQPGKAKLDKIPTLKPAFREGGTV 244 Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305 TAANSSSISDGAAAL+LMRRSEAE RGLKPLA I GHA + P LF AP+GA++KL Sbjct: 245 TAANSSSISDGAAALVLMRRSEAEHRGLKPLATILGHATHSQAPNLFATAPIGALQKLSD 304 Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365 +TG L EV+LFE+NEAFAVV++ M L +PH KVNVHGGACALGHPIGASGARILVTL Sbjct: 305 RTGLPLSEVDLFEINEAFAVVAMAAMRDLNLPHEKVNVHGGACALGHPIGASGARILVTL 364 Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394 L+AL + LKRG+AA+CIGGGEATA+A+E Sbjct: 365 LAALERYDLKRGMAALCIGGGEATAVAIE 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: 510 Number of extensions: 11 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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 24 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