Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate SMc02228 SMc02228 acetyl-CoA acetyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >FitnessBrowser__Smeli:SMc02228 Length = 402 Score = 270 bits (690), Expect = 5e-77 Identities = 162/407 (39%), Positives = 232/407 (57%), Gaps = 20/407 (4%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M + + D +R+P GR K A E+ + L A+V++ + +RN LD VDDVI GCV Sbjct: 1 MTKVFVYDHVRTPRGRGKKDGALHEVPSVRLAAKVLEAVRDRNGLDTSTVDDVIMGCVDP 60 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 + A + A AG+ P I R C S AV+F A I GA DIVIA G+ES Sbjct: 61 VMDAGAVIPKAAAFEAGYSTRAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVES 120 Query: 121 MSRVPMGSARIGQNPYGPSME--ARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHE 178 MSRV +G + G PS+ A + P QGV+A+L+A KY SR D+D+Y+ S + Sbjct: 121 MSRVGLGMSG-GAWFMDPSVNLPAYFMP----QGVSADLIATKYGFSRDDVDAYAVESQK 175 Query: 179 LAATARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFRNDELSARFPQ 236 AA A E G F+ ++ + NGLV ++DE +RPGT ++ L +L SF+ F Sbjct: 176 RAANAWEKGYFKNSVVPVKDQNGLVILDRDEHMRPGTDMQALASLNPSFQMPGEMGGFEA 235 Query: 237 IGWNVT-----------AGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDP 285 +G AGN+S I DGA+A+L+ S++ + +GLKPRAR AF G DP Sbjct: 236 VGIQAHPEIERINYVHHAGNSSGIVDGAAAVLIGSKAGGEAMGLKPRARIRAFANIGSDP 295 Query: 286 VMMLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIA 345 +MLT P+ +++ +K++ +KL ID +E+NEAFA V L + +A ++N GGAIA Sbjct: 296 ALMLTGPVDVTEKLLKRADMKLSDIDLFELNEAFAAVVLRYCQAFDIPHDKINVNGGAIA 355 Query: 346 LGHPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 +GHPLGA+G ++ T+L LE L ++C GM ATIIER+ Sbjct: 356 MGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATIIERV 402 Lambda K H 0.318 0.132 0.384 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: 440 Number of extensions: 20 Number of successful extensions: 4 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: 392 Length of database: 402 Length adjustment: 31 Effective length of query: 361 Effective length of database: 371 Effective search space: 133931 Effective search space used: 133931 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 17 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