Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_027457980.1 K420_RS0110260 acetyl-CoA C-acyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000519045.1:WP_027457980.1 Length = 393 Score = 303 bits (776), Expect = 6e-87 Identities = 176/401 (43%), Positives = 248/401 (61%), Gaps = 8/401 (1%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 MS++V + AVR+P+G FGGSLA + DL + +K + R+ VD Q++ V +G Sbjct: 1 MSKDVVVLSAVRSPVGAFGGSLADMDPCDLGGIVMKEAIARSG-VDPQQINYVTVGTTMP 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 V+R+A + AGL + ++RLCASG+ A+ T + I G+AE I GGVE Sbjct: 60 VDSRYAYVSRVASIQAGLSMDSVAMQVSRLCASGLQAIVTTAQNIMLGDAEYGIGGGVEV 119 Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 MS+ Y+M A G ++ DT + ++ +GV M TA+N+A + +R Sbjct: 120 MSKVAYLM----PALRSGARMGDTKAIDAMV-AVLTDPFGVGHMGITAENLAAKHGFTRE 174 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240 DQDAFA+ SQ+ A A AGYF +I+P+V + KKGE V D DEHL+ TT+E+LAK+KP Sbjct: 175 DQDAFAVESQRRAAAAIDAGYFKSQILPIVKQTKKGEVVFDTDEHLKRGTTMESLAKMKP 234 Query: 241 VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300 D TVTAGNASG+ND + +LA A G K A+++ A AGV VMG GP+ Sbjct: 235 AFKKDGTVTAGNASGINDAAAFFVLADAAKAAAAGQKPIARMVSYAVAGVPNDVMGEGPI 294 Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360 PA + L++ L++ DVIE NEAFAAQ L V++ LG+ D A+ NPNGGAIALGHP+G Sbjct: 295 PATKLALKKAGLTLDQMDVIESNEAFAAQALTVSKCLGL--DPAKTNPNGGAIALGHPVG 352 Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 SGA + A++++ + GG+ L TMC+G GQG+A+ ERV Sbjct: 353 CSGAFIATKAIYEMNRIGGKYCLVTMCIGGGQGIAVIFERV 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: 408 Number of extensions: 22 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: 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