Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_033101535.1 JG50_RS0112880 thiolase family protein
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000763315.1:WP_033101535.1 Length = 384 Score = 331 bits (849), Expect = 2e-95 Identities = 187/395 (47%), Positives = 256/395 (64%), Gaps = 22/395 (5%) Query: 2 QQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQA 61 Q AVI+DA R+P+GR K + + + EL A +++ LVERN+LDP ++D+ GCVTQ Sbjct: 4 QDAVIIDAARTPIGRKK--GSLSGIRPDELAAFLLQKLVERNQLDPAEIEDIKMGCVTQT 61 Query: 62 GEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESM 121 GEQ GR+A L AGFP V +++R C SS + + A IMAG D VIA G+ESM Sbjct: 62 GEQGYNIGRLAGLIAGFPVEVCGVSVNRMCASSLETLAQGAHAIMAGMSDCVIAAGVESM 121 Query: 122 SRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAA 181 +RVPMGS + + R+ +V QG++AEL+A K++LSR ++D +S SH+ A Sbjct: 122 NRVPMGS---DGGSFSDQLLNRF--NIVPQGISAELIAEKWQLSREELDQFSLSSHQKAL 176 Query: 182 TARESGAFRREILGIS--TPNG---LVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQ 236 A+ F+ EI+ + TP+G ++ DET RP T++E L +L SF D Sbjct: 177 KAQSENRFQNEIIPVKAQTPSGETIQLQTDETPRPDTNLEALLSLPPSFLPDG------- 229 Query: 237 IGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPAS 296 +TAGN+SQISDG +A+LL S A+ LGLKPRA+ A + G DP +MLT IPA+ Sbjct: 230 ---KITAGNSSQISDGVAAVLLASRRKAEELGLKPRAKVRATAIAGVDPEIMLTGIIPAT 286 Query: 297 QRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGVR 356 Q+ +K++GL LD ID +E+NEAFA V LAWQR LG ++NP GGAIALGHPLGASG R Sbjct: 287 QKVLKRAGLTLDDIDLFEVNEAFASVVLAWQRELGVPSHKINPNGGAIALGHPLGASGAR 346 Query: 357 LMTTMLHALEDSGQRYGLQSMCEAGGMANATIIER 391 ++ T+L+ LE +R+GL +MC GMA+A IIER Sbjct: 347 IVATLLNELERQEKRFGLIAMCIGFGMASAIIIER 381 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: 410 Number of extensions: 21 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: 392 Length of database: 384 Length adjustment: 30 Effective length of query: 362 Effective length of database: 354 Effective search space: 128148 Effective search space used: 128148 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