Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_013418242.1 RVAN_RS02760 acetyl-CoA acetyltransferase
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_000166055.1:WP_013418242.1 Length = 403 Score = 263 bits (672), Expect = 7e-75 Identities = 167/414 (40%), Positives = 234/414 (56%), Gaps = 38/414 (9%) Query: 1 MAEAYIVAAVRT--AGGRKGGKLSGWHPADLAAQVLDALVERT-GADPALVEDVIMGCVS 57 M +AY+ AVRT G+K G L P LAAQ+LDA+ ER G D VEDVI+GCVS Sbjct: 1 MVDAYVFDAVRTPRGKGKKDGALHEVTPVKLAAQMLDAVQERNPGLDTRDVEDVILGCVS 60 Query: 58 QVGEQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVE 117 VGEQ ++AR+A L S ESVPG V+R C S +A++ AA VMSG ++ GVE Sbjct: 61 PVGEQGADIARSASLISGFDESVPGVQVNRFCASGLEAINMAAAKVMSGQSPFIVGGGVE 120 Query: 118 SMTRVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYA 177 SM+RVPM A +G P P + + Q A++IA K+ SR+ LDAY+ Sbjct: 121 SMSRVPM-------ASDGGAWPIDPAVA--FSTYFVPQGISADLIATKWGYSRDDLDAYS 171 Query: 178 LQSHQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK-LIAE 236 ++SH+RA + GRF I+PV+ D + DE +R DA+++S+G++K A+ Sbjct: 172 VESHKRATQSWAEGRFAKSIVPVK----DILGITLLDKDEMIRPDASMQSLGALKPSFAD 227 Query: 237 GGRV---------------------TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVH 275 G+ T ++S I DGAA ++ ++ +K G+KP AR+ Sbjct: 228 MGKNYGFDGVALQKYPEIERIDHVHTPGNSSGIVDGAAVALIGSKEAGEKAGIKPRARIR 287 Query: 276 AMTVIGHDPVVMLEAPLPATEVALKKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPAR 335 + IG +P +ML P A E AL KAG+ DIDL+E+NEAFA V L + + Sbjct: 288 SFASIGSEPTIMLTGPSFAAERALAKAGMTKADIDLWELNEAFASVVLRFRDLLDIADDK 347 Query: 336 LNVHGGAIALGHPLGGSGAKLMTTLVHALHTHGKRYGLQTMCEGGGLANVTIVE 389 LNV+GGAIA+GHPLG +GA ++ TL+ + G GL T+C G G+ TI+E Sbjct: 348 LNVNGGAIAMGHPLGATGAMVLGTLLDEMERRGAATGLVTLCIGAGMGTATILE 401 Lambda K H 0.317 0.132 0.379 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: 422 Number of extensions: 18 Number of successful extensions: 5 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: 391 Length of database: 403 Length adjustment: 31 Effective length of query: 360 Effective length of database: 372 Effective search space: 133920 Effective search space used: 133920 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