Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_015798780.1 AFER_RS07055 acetyl-CoA C-acyltransferase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000023265.1:WP_015798780.1 Length = 399 Score = 332 bits (850), Expect = 2e-95 Identities = 180/393 (45%), Positives = 254/393 (64%), Gaps = 7/393 (1%) Query: 7 LVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKRAGIKAEQIDEVIFGCVLQAGL-GQN 65 LVG RTP G +GG L V L A V+ A++R GI E IDEV+ GC QAG +N Sbjct: 5 LVGGVRTPFGRYGGQLASVRPDDLLATVLAGAVERVGIPVEAIDEVVAGCANQAGEDNRN 64 Query: 66 VARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPFI 125 VAR + AG + V A T+N++C SGL A+ AA+ I G+AD+++AGG E+M +APF+ Sbjct: 65 VARMSTLLAGFGEGVPAVTVNRLCASGLEAIVDAARRIAVGEADVVVAGGVESMSRAPFV 124 Query: 126 LPNARWGYRMSMPKGDLID--EMVWGGLTDVFNGYHMGITAENINDMYGITREEQDAFGF 183 +P A + S D V L + F MG TAEN+ + + +TRE+QD F Sbjct: 125 MPKAEAAFARSATVYDTTIGWRFVNPRLAERFGVDSMGETAENVAEEFKVTREDQDRFAL 184 Query: 184 RSQTLAAQAIESGRFKDEIVPV-VIKGKKGDIVFDTDEHPRKSTPEAMAKLAPAFKKGGS 242 RS T A A SGRF EIVPV V++G+ ++V + DEHPR+++ EA+A+L PAF+ GG+ Sbjct: 185 RSHTRALAAQRSGRFAAEIVPVRVVRGRSEEVV-ELDEHPRETSLEALARLRPAFRVGGT 243 Query: 243 VTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASRKAL 302 VTAGNASG+ND A+AV+V S G++P ++V + GV P +MG+GP+PASR+ L Sbjct: 244 VTAGNASGVNDGASAVVVASDAALARYGLEPWCEIVGGQTAGVPPRIMGIGPVPASRRLL 303 Query: 303 EKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEK--VNVNGGAIAIGHPIGSSGAR 360 E+ GL + D+D++E NEAFAAQS+A +LG + VN NGGAIA+GHP+G+SGAR Sbjct: 304 ERFGLGVADLDVVELNEAFAAQSLACLGELGLPTDPDDDLVNPNGGAIALGHPLGASGAR 363 Query: 361 ILVTLLYEMQKRGSKKGLATLCIGGGMGTALIV 393 + +T +E++ R + L T+C+G G G A ++ Sbjct: 364 LALTAAHELRARDGRYALVTMCVGVGQGVAALL 396 Lambda K H 0.317 0.135 0.387 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: 452 Number of extensions: 23 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: 396 Length of database: 399 Length adjustment: 31 Effective length of query: 365 Effective length of database: 368 Effective search space: 134320 Effective search space used: 134320 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