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_004312070.1 C665_RS12455 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_000310185.1:WP_004312070.1 Length = 402 Score = 544 bits (1401), Expect = e-159 Identities = 271/392 (69%), Positives = 330/392 (84%), Gaps = 3/392 (0%) Query: 6 DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65 DP+VIVS RTP+GGFQG+L SL+ PQLG+ AI+AAVERAGVA V+EV+ GCVL AGL Sbjct: 3 DPVVIVSVARTPLGGFQGDLSSLTTPQLGSIAIKAAVERAGVAPAQVQEVIMGCVLPAGL 62 Query: 66 GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125 GQAPARQAALGAGL S CTT+NK+CGSGM+A +LAHD++LAGS +V+VAGGMESMSNA Sbjct: 63 GQAPARQAALGAGLPLSAGCTTINKVCGSGMKATMLAHDLILAGSNEVMVAGGMESMSNA 122 Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAY---DKGRLMGTFAEDCAEANGFTREAQDE 182 PYLL +AR+GYR+GHG++ DHMFLDGLED+Y +KGRLMGTFAEDCA FTR+AQDE Sbjct: 123 PYLLPKARAGYRLGHGQMFDHMFLDGLEDSYSKENKGRLMGTFAEDCAGHFNFTRQAQDE 182 Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDG 242 FAIASTTRAQ AI +G F+ E+VP+ V K ++ DEQP KA++DKI SLKPAF+ Sbjct: 183 FAIASTTRAQAAINNGDFSWEVVPVTVASRKGDVVVDKDEQPLKAQIDKIPSLKPAFKKD 242 Query: 243 GTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKK 302 GTVT ANSSSISDGAAAL+LMR+S AEK G+KP+A I GHA A P LF APVGA++K Sbjct: 243 GTVTPANSSSISDGAAALVLMRKSTAEKLGVKPVATIIGHATHAQEPALFTTAPVGAMQK 302 Query: 303 LLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARIL 362 +L K GWS ++V+L+E+NEAFAVV++ M ++++PH KVNV+GGACALGHPIGASGARIL Sbjct: 303 VLAKAGWSTEQVDLWEINEAFAVVTMAAMHEMKLPHDKVNVNGGACALGHPIGASGARIL 362 Query: 363 VTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 V+L+ ALR++GLKRGVA++CIGGGEATAMA+E Sbjct: 363 VSLIGALRKRGLKRGVASLCIGGGEATAMAIE 394 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: 523 Number of extensions: 13 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: 402 Length adjustment: 31 Effective length of query: 366 Effective length of database: 371 Effective search space: 135786 Effective search space used: 135786 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