Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_017599812.1 D471_RS0117455 acetyl-CoA C-acyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000341125.1:WP_017599812.1 Length = 402 Score = 395 bits (1014), Expect = e-114 Identities = 217/402 (53%), Positives = 282/402 (70%), Gaps = 5/402 (1%) Query: 2 SREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61 +R+VY+ DAVRTP+GR+ G+LAAVR DDLAA V+AL+ER P +D ++ +VYLG AN A Sbjct: 3 TRDVYVVDAVRTPVGRYDGALAAVRPDDLAAHTVRALLERTPDLDPDRIGDVYLGNANGA 62 Query: 62 GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121 GE+NRNV RMA LLAGLP SVPGVT+NRLCASG++AV A RAIA G+A +++AGGVESM Sbjct: 63 GEENRNVGRMAALLAGLPTSVPGVTVNRLCASGLEAVVQAARAIALGDASVLVAGGVESM 122 Query: 122 SRAPYVMGKADSAFGRGQ-KIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 +RAPYV+ K+D AF G ++ TT+GWR +NP M+ ++ V + E+A+ +AD++ ++R Sbjct: 123 TRAPYVLPKSDRAFPAGHAELYSTTLGWRMVNPAMEPRWTV-PLGESAELIADEHGITRE 181 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETV-VDADEHLRPDTTLEALAKLK 239 QD FAL S A AQ G F E VPV + ++G V VD DE +RPD +LEA+A+L+ Sbjct: 182 RQDEFALESHLKAAAAQEQGLFDAETVPVRVPRRRGGAVTVDRDEGVRPDASLEAMARLR 241 Query: 240 P-VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298 P D TVTAGNAS ++DG+ AL+LA E V+ G A++ A + V P G+G Sbjct: 242 PSFRAEDGTVTAGNASPLSDGAAALLLADEEGVRATGRAPLARISASAVSAVEPHWFGLG 301 Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358 PV AV + L R S+ D DV+ELNEAFAAQ L E D A +NP GGAIALGHP Sbjct: 302 PVEAVNRALSRAGRSLTDVDVLELNEAFAAQVLGCLAEWP-EFDRAVLNPLGGAIALGHP 360 Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 LGASGARL T HQL ++G G+ +CVGVGQG+AL +ER Sbjct: 361 LGASGARLAGTVAHQLARAGSGTGVAALCVGVGQGLALVLER 402 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: 501 Number of extensions: 22 Number of successful extensions: 6 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: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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