Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_073035813.1 BUB04_RS00235 acetyl-CoA C-acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_900129305.1:WP_073035813.1 Length = 391 Score = 278 bits (710), Expect = 3e-79 Identities = 158/405 (39%), Positives = 249/405 (61%), Gaps = 20/405 (4%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M +A I A+RTP+G + G L + A LGAV I+ ++R G++ V++VI G Sbjct: 1 MREAVIVSAVRTPLGSFNGTLSGIGATALGAVVIEEAVKR-AGIEKADVNEVIMGQVLPC 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 G +N A+ +A+ AG+P +A TIN++CGSG+ AV AA+AI+ G+A +++AGG+E+M Sbjct: 60 GY-GQNPAKQAAVKAGMPWEAECLTINKVCGSGLKAVMLAAQAIQTGDADVVVAGGMENM 118 Query: 121 TRAPFVMGKAASAFT------RQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQF 174 + AP+ + KA + + IHD W VN M + E +E++ Sbjct: 119 SMAPYFLDKARFGYRMGHGQLKDHMIHDGL--WDIVNDF--------HMGISNELCSERY 168 Query: 175 GISRADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESL 234 G+SR DQD +A S ++A A G EIV V + Q+KGD + DE PRETS E L Sbjct: 169 GVSREDQDRYAAESYRRALEAIATGKFQDEIVPVPVPQRKGDPVMFDRDECPRETSYELL 228 Query: 235 ARLKGVVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIM 294 A++K + G TAGNAS ++DGA A+++ +++ AE G R A V A+AG++ + + Sbjct: 229 AKMKPAFKEGGVTTAGNASVISDGAAAVVVMAREKAEALGCRILATVGAQASAGIDMKYV 288 Query: 295 GIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIAL 354 + P A K L++ G+ L+ +D+ E+NEAF+ +AVL+ L L D +VN NGG+++L Sbjct: 289 LVAPIWAIPKCLKKEGIGLEDVDLYEVNEAFSGSTVAVLKELNL--DPAKVNVNGGSVSL 346 Query: 355 GHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399 GHP+GASGAR++ T LH++ R++ + L ++C+G G+ +ALV++R Sbjct: 347 GHPIGASGARVLVTLLHEMIRTDKKIGLASLCLGGGEAVALVVKR 391 Lambda K H 0.319 0.134 0.386 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: 372 Number of extensions: 17 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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