Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_068004809.1 PsAD2_RS08250 thiolase family protein
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_001623255.1:WP_068004809.1 Length = 383 Score = 157 bits (396), Expect = 6e-43 Identities = 135/406 (33%), Positives = 193/406 (47%), Gaps = 35/406 (8%) Query: 4 EVYICDAVRTPIGRFG--GSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61 + YI DAVRT G+ G LAAV+ D+L A A+ +R Q + + + LG Q Sbjct: 2 QTYIYDAVRTARGKAKPEGGLAAVKPDELVAALSDAITDRVGQF---KPEALLLGSVGQV 58 Query: 62 GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121 G N+A ++ A LPD T+N CASG+ A+G A +A+G+A V+AGGVE M Sbjct: 59 GAQGGNIALVSKFRAKLPDETVAWTINNFCASGLTAIGQASSMVATGQANRVLAGGVEMM 118 Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRAD 181 S P++ AD A DTT+ R +Y + A+ AD +A+D +SRA+ Sbjct: 119 SCVPFM---ADDA----HYYVDTTLPERH-------RYLLVAL--AADKLAEDLDISRAE 162 Query: 182 QDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPV 241 D ALRS A G A I ++ G E +H A A L P Sbjct: 163 MDTAALRSHAQALLGDDNGKNASRI---IVNGLNREECAKKMDHESIAALQPAFAALAPQ 219 Query: 242 NGP------DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVM 295 D T +A + DG+ ++ + A+ RA+++ A G P V Sbjct: 220 YAQVLGRKVDHRHTIAHAPPMTDGAGLAMVGTYGAI---DAPPRAQIVAFAEVGGDPAVS 276 Query: 296 GIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIAL 355 A+ ++L + LS+ D D IE EAFA + R+ +D RVN +GG +A Sbjct: 277 LGAGFAAMDQVLAKSELSLEDMDRIEFMEAFAVTIVKFLRDHPHLED--RVNTSGGHLAK 334 Query: 356 GHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 GHPLGASGA LV T + L+ G+ GL G G A+ V+R+ Sbjct: 335 GHPLGASGAILVSTLLDTLDMVQGRYGLVVASGAEGIGSAMIVKRM 380 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: 372 Number of extensions: 20 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: 383 Length adjustment: 31 Effective length of query: 370 Effective length of database: 352 Effective search space: 130240 Effective search space used: 130240 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