Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_002117405.1:WP_085770214.1 Length = 391 Score = 320 bits (819), Expect = 6e-92 Identities = 178/400 (44%), Positives = 259/400 (64%), Gaps = 9/400 (2%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 M+ ++ I A RT +G F G+ V A +L A VK+ +ER +V S++ EV LG Sbjct: 1 MTTDIVIVSAARTAVGSFNGAFGGVPAHELGAAAVKSALER-AKVAPSEVCEVILGQVLG 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 A + +N AR A + AG+PDS +N++C SG+ AV A + I +G+A++V+AGG ES Sbjct: 60 AAQ-GQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQES 118 Query: 121 MSRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180 MS + + + G K+ + I + + M TA+NVA +++SRA Sbjct: 119 MSLSTHA-----AHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRA 173 Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKP 240 +QDAFA+ SQ A AQ AG F +EI+P I +KG+ VVD+DE+++ TLE+++KL+P Sbjct: 174 EQDAFAVASQNKAEAAQKAGKFKDEILPYTISTRKGDVVVDSDEYVKHGVTLESVSKLRP 233 Query: 241 VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300 D TVTA NASG+NDG+ AL++ SA KK GL+ A++ A+AGV P +MG GP+ Sbjct: 234 AFTKDGTVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPI 293 Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360 PA RK LE+ V+D +++E NEAFAAQ +AV ++LG D A VN NGGAIA+GHP+G Sbjct: 294 PATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLGW--DPAIVNVNGGAIAIGHPIG 351 Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 ASGAR++ T +++L++ GG +GL T+C+G G G+ALAVER Sbjct: 352 ASGARILTTLLYELKRRGGGKGLATLCIGGGMGIALAVER 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: 412 Number of extensions: 12 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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