Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_036258927.1 DL86_RS05200 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000746085.1:WP_036258927.1 Length = 391 Score = 334 bits (856), Expect = 3e-96 Identities = 185/401 (46%), Positives = 258/401 (64%), Gaps = 11/401 (2%) Query: 1 MSREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQ 60 MSRE+ I A RT +G F G+ AA A +L A +KA ++R ++D + +DEV LG Sbjct: 1 MSREIVIVSAARTAVGSFNGAFAATPAHELGAAAIKAALDR-AKIDAADVDEVILGQVLT 59 Query: 61 AGEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVES 120 AG+ +N AR A + AG+P LN++C SG+ AV A + IA+G+AE+V+AGG ES Sbjct: 60 AGQ-GQNPARQAAIKAGIPQEKTAFGLNQVCGSGLRAVALAAQQIATGDAEIVVAGGQES 118 Query: 121 MSRAPYVMGKADSAFGR-GQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSR 179 MS++ + A+ R G K+ D + + + M +TA+NVA ++++R Sbjct: 119 MSQSQH------GAYLRSGVKMGDLKFVDTMLRDGLTDVFNGYHMGQTAENVAAKWQITR 172 Query: 180 ADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLK 239 +QD FAL SQ A AQ G F EEI P + +KG+ V+DADE++R TL+ LAKLK Sbjct: 173 DEQDRFALASQNKAEAAQKEGRFKEEIAPFTVTSRKGDVVIDADEYIRLGATLDGLAKLK 232 Query: 240 PVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299 P D TVTAGNASG+NDG AL+L SA+ GL A++ ASAGV P +MG GP Sbjct: 233 PAFAKDGTVTAGNASGINDGGAALVLMSAKDAAARGLTPLARIASWASAGVDPALMGSGP 292 Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359 +PA RK LE+ V D D++E NEAFAAQ LAV +++G D A VN NGGAIA+GHP+ Sbjct: 293 IPASRKALEKAGWKVKDLDLVEANEAFAAQALAVNKDMGW--DPAIVNVNGGAIAIGHPI 350 Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 GASGAR+++T +H++++ G ++GL T+C+G G G+AL VER Sbjct: 351 GASGARVLITLLHEMQRRGAKKGLATLCIGGGMGIALTVER 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: 425 Number of extensions: 22 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: 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