Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_053939433.1 WG78_RS19070 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_001294205.1:WP_053939433.1 Length = 393 Score = 319 bits (817), Expect = 1e-91 Identities = 185/400 (46%), Positives = 256/400 (64%), Gaps = 9/400 (2%) Query: 3 REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62 +E+ I A RT IG FGG+LA+V A DL A +K L++R+ + Q+ EV +G AG Sbjct: 2 QEIAIVAAGRTAIGNFGGALASVSAPDLGATVIKGLLQRSG-ISADQISEVMMGNVLTAG 60 Query: 63 EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122 +N AR A AG+PD+VPG+T+N++C SG+ AV ++I +G+ ++VIAGG E+MS Sbjct: 61 L-GQNPARQASRKAGVPDAVPGLTVNQVCGSGLKAVALGVQSILAGDNQIVIAGGQENMS 119 Query: 123 RAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQ 182 AP+++ + F G + T+ + + Y M TA+N+A Y +SRA+Q Sbjct: 120 AAPHLLPGSRDGFRMG----NATLVDSMVYDGLTDVYHQYHMGVTAENIARKYGISRAEQ 175 Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDA-DEHLRPDTTLEALAKLKPV 241 D A SQ A A+ AG FA+EI+ V + +KG+ + DE +RP TT+E LA+L+P Sbjct: 176 DELAATSQMRAAAAREAGRFADEIIAVPVPQRKGDPIAFLEDEFIRPGTTVETLARLRPA 235 Query: 242 NGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVP 301 + TVTAGNASG+NDG+ +IL S E + GL A + ASAGV P +MG+GPVP Sbjct: 236 FDKEGTVTAGNASGINDGAAGVILMSRERAAELGLPILAIIRAAASAGVDPALMGMGPVP 295 Query: 302 AVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGA 361 A ++ L R S+ D+IE NEAFAAQ L V REL D RVN NGGAIALGHP+GA Sbjct: 296 ATQRALARAGWSLDSLDLIEGNEAFAAQALGVAREL--RWDMQRVNVNGGAIALGHPIGA 353 Query: 362 SGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 SGAR+++T +H++ + QRGL T+C+G G GVALAVERV Sbjct: 354 SGARVLVTLLHEMARRDAQRGLATLCIGGGMGVALAVERV 393 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: 464 Number of extensions: 19 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: 401 Length of database: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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