Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__PV4:5209189 Length = 396 Score = 269 bits (687), Expect = 1e-76 Identities = 162/401 (40%), Positives = 236/401 (58%), Gaps = 15/401 (3%) Query: 2 SREVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61 ++E+ I A RTP+G F GSL++V + LAA +K L++ V ++EV +GC A Sbjct: 7 NQEIVIVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDA-AGVQGGDVNEVLMGCVLPA 65 Query: 62 GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121 G + AR A L A LP SV T+N++C SGM V A I +G A++VIAGG+ESM Sbjct: 66 GL-GQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESM 124 Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRAD 181 S+APY++ KA G + F++ L A G AM A ADD+ ++R Sbjct: 125 SQAPYLLDKARGGMRMGH---GKVLDHMFLDGLEDAYTG-GAMGTFAQKTADDFGITREA 180 Query: 182 QDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADE---HLRPDTTLEALAKL 238 D FAL S Q A A +G F EIVPV + +KG+ VVD DE + RP E + L Sbjct: 181 MDNFALSSLQKANAAIESGAFKAEIVPVTVASRKGDLVVDTDEQPGNARP----EKIPTL 236 Query: 239 KPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298 +P D T+TA N+S ++DG+ L++ SA+ K GL+ A + G + P + Sbjct: 237 RPAFAKDGTITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTA 296 Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358 PV A+ KLL+++N S + D+ E+NEAFA + ELG+ D+A+VN NGGA ALGHP Sbjct: 297 PVGAMNKLLDKVNWSKDEVDLFEINEAFAMVTMLAISELGL--DEAKVNVNGGACALGHP 354 Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 +G SGAR+++T +H L+ G +RG+ ++C+G G+ A+A+E Sbjct: 355 IGCSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395 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: 398 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 370 Effective length of database: 365 Effective search space: 135050 Effective search space used: 135050 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 17 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