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_013420948.1 RVAN_RS17080 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_000166055.1:WP_013420948.1 Length = 399 Score = 493 bits (1268), Expect = e-144 Identities = 246/397 (61%), Positives = 308/397 (77%), Gaps = 3/397 (0%) Query: 1 MTMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCV 60 M+ + D IVI S VRTP+G FQG SL+AP+LGA A+RA+VERAG+ A ++EV GCV Sbjct: 1 MSKNTDAIVIASVVRTPIGAFQGAFASLAAPELGAVALRASVERAGLTASDIDEVFMGCV 60 Query: 61 LSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGME 120 L AG+GQAPARQA+L A L S CTT+NK+CGSG++A +L HD +LAGSA VV AGGME Sbjct: 61 LGAGVGQAPARQASLRAKLPLSAGCTTINKVCGSGLKAVMLGHDAILAGSARVVSAGGME 120 Query: 121 SMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYD---KGRLMGTFAEDCAEANGFTR 177 SM+NAPYLL +AR G R+GH +VLD MF DGLEDAY KGRLMGTFAE+CA A GFTR Sbjct: 121 SMTNAPYLLPKARGGQRLGHDRVLDAMFFDGLEDAYGPETKGRLMGTFAEECAAAYGFTR 180 Query: 178 EAQDEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKP 237 + QD +A+AS TRA+ A++ G+F+ E VP+ V K ++ DEQP + + KI +LKP Sbjct: 181 DEQDAYAVASATRARAAVEGGAFDWETVPVTVETRKGAAIVERDEQPGRIDIAKIPTLKP 240 Query: 238 AFRDGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPV 297 AFR+GGTVTAANSSSISDGAAA+ LMRRS AE +G+ PLA I GH ++D P LFP AP+ Sbjct: 241 AFREGGTVTAANSSSISDGAAAVTLMRRSTAEAKGVAPLATILGHTTYSDEPRLFPTAPI 300 Query: 298 GAIKKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGAS 357 AI+ LL K GW +V+L+E+NEAFAVV++ M L +PH KVN+ GGACALGHPIGAS Sbjct: 301 HAIRALLDKLGWRAGDVDLYEINEAFAVVAMAAMRDLGLPHDKVNIGGGACALGHPIGAS 360 Query: 358 GARILVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 GAR+LV+L+ ALR+ G KRG+A++CIGGGEA A+A+E Sbjct: 361 GARVLVSLIGALRRTGAKRGIASLCIGGGEAVALAIE 397 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: 506 Number of extensions: 15 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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