Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_015448186.1 R2APBS1_RS12475 acetyl-CoA C-acyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000230695.2:WP_015448186.1 Length = 394 Score = 239 bits (610), Expect = 1e-67 Identities = 155/399 (38%), Positives = 225/399 (56%), Gaps = 17/399 (4%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 V I A RT IG F G V L A ++A +E++ V + + EV +GC A Sbjct: 6 VVIVGAKRTAIGSFLGQFTGVPTPKLGATAIRAALEQSG-VAPADVGEVIMGCVLPANL- 63 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 + AR A L A LP T+N++C SGM A+ I +G A +V+AGG+ESM+ A Sbjct: 64 GQAPARQASLGADLPAGTGCTTINKVCGSGMKAIMLGHDLIKAGSAAIVVAGGMESMTNA 123 Query: 125 PY-VMGKADSAFGRGQKIEDTTIGWRFI-NPLMKAQYGVDAMPETADNVADDYKVSRADQ 182 P+ V + +G GQ ++ + W + NP Y AM + AD Y +R Q Sbjct: 124 PHMVQARTGIRYGDGQLVDH--MAWDGLTNP-----YDGKAMGVFGELCADKYHFTREAQ 176 Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHL-RPDTTLEALAKLKPV 241 DAFA+ S A AQ G FA EIVPV + G+KG+ VVD DE R D + LKP Sbjct: 177 DAFAIESVNRAKAAQQNGAFAGEIVPVTVSGRKGDVVVDTDEQPGRSDVA--KIPSLKPA 234 Query: 242 NGPDK-TVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300 + T+TA ++S ++DG+ A++L SA+ K GLK A+++ A+ P PV Sbjct: 235 FRKENGTITAASSSSISDGAAAVVLLSADDANKRGLKPLARIVAHATHSQEPEWFTTAPV 294 Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360 A++K+L++ V + D+ E+NEAFA + +ELGI A++N NGGA ALGHP+G Sbjct: 295 GAIQKVLDKAGWKVDEVDLFEINEAFAVVAMTPMKELGI--QHAKLNVNGGACALGHPIG 352 Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 ASGARLV+T ++ L+ G +RG+ ++C+G G+ A+AVE Sbjct: 353 ASGARLVVTLLNALKVRGLKRGVASLCIGGGEATAIAVE 391 Lambda K H 0.317 0.134 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: 394 Number of extensions: 24 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: 401 Length of database: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 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 (21.6 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