Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000018545.1:WP_012709751.1 Length = 393 Score = 319 bits (818), Expect = 8e-92 Identities = 177/397 (44%), Positives = 255/397 (64%), Gaps = 9/397 (2%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 + I A RT +G F G+ A +L A +KA++ER VD +++DEV LG AGE Sbjct: 6 IVIASAARTAVGSFNGAFGNTPAHELGATVIKAVLER-AGVDAAEVDEVILGQVLPAGE- 63 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 +N AR A + AG+P +N+LC SG+ AV + IA+G+A +++AGG+ESMS A Sbjct: 64 GQNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMA 123 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184 P+ K+ DT I + L A YG M TA+NVA ++++R +QD Sbjct: 124 PHCAHLRGGVKMGDYKMIDTMIK----DGLTDAFYGYH-MGTTAENVARKWQLTREEQDE 178 Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244 FALRSQ A AQ AG FA+EIVP ++K +KG+ VD DE++R TLE++AKL+P Sbjct: 179 FALRSQNKAEAAQKAGRFADEIVPFIVKTRKGDVTVDQDEYIRHGATLESIAKLRPAFDK 238 Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304 + TVTAGNASG+NDG+ A +L + K G++ A+++ A+AGV P++MG GP+PA R Sbjct: 239 EGTVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPIPASR 298 Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364 K LE+ + D +++E NEAFAAQ AV ++LG D + VN NGGAIA+GHP+GASGA Sbjct: 299 KALEKAGWPIGDVELVEANEAFAAQACAVNKDLGW--DPSIVNVNGGAIAIGHPIGASGA 356 Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 R++ T + ++++ G +GL T+C+G G GVA+ VER+ Sbjct: 357 RVLNTLLFEMKRRGVSKGLATLCIGGGMGVAMCVERL 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: 446 Number of extensions: 18 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 Apr 09 2024. 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