Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_012759437.1 RLEG_RS20540 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000023185.1:WP_012759437.1 Length = 393 Score = 318 bits (815), Expect = 2e-91 Identities = 182/396 (45%), Positives = 258/396 (65%), Gaps = 11/396 (2%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 + I A RT +G F G+ A V A +L A +K +ER VD ++DEV LG AGE Sbjct: 6 IVIASAGRTAVGAFNGAFATVLAHELGAAVIKGALER-AGVDAGEVDEVILGQVLAAGE- 63 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 +N AR A + AG+P +N+LC SG+ AV + IA+G+A++++AGG ESMS A Sbjct: 64 GQNPARQAAMKAGIPQEATAWGVNQLCGSGLRAVALGMQQIATGDAKIIVAGGQESMSMA 123 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184 P+ K+ DT I + L A +G M TA+NVA +++SR DQD Sbjct: 124 PHAAHLRGGVKMGDMKMIDTMIK----DGLTDAFHGYH-MGITAENVARQWQLSRDDQDQ 178 Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244 FA+ SQ A AQ AG F +EI+P VIK +KG+ VDADE++R T+EA+ KL+P Sbjct: 179 FAVSSQNKAEAAQKAGRFVDEIIPYVIKTRKGDVTVDADEYIRHGATIEAMGKLRPAFDK 238 Query: 245 DKTVTAGNASGVNDG-SVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAV 303 D TVTA NASG+NDG +VA++++ AEAV++ G++ A+++ A+AGV P++MG GP+PA Sbjct: 239 DGTVTAANASGLNDGAAVAVLMSEAEAVRR-GVQPLARIVSWATAGVDPQIMGTGPIPAS 297 Query: 304 RKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASG 363 RK LE+ SV D D++E NEAFAAQ AVT++LG D + VN NGGAIA+GHP+GASG Sbjct: 298 RKALEKAGWSVNDLDLVEANEAFAAQACAVTKDLGW--DPSIVNVNGGAIAIGHPIGASG 355 Query: 364 ARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 AR++ T + ++++ G ++GL T+C+G G GVA+ E Sbjct: 356 ARVLNTLLFEMKRRGAKKGLATLCIGGGMGVAMCFE 391 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: 448 Number of extensions: 20 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