Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate 6937205 Sama_1375 Acetyl-CoA C-acetyltransferase (RefSeq)
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__SB2B:6937205 Length = 392 Score = 259 bits (662), Expect = 9e-74 Identities = 162/399 (40%), Positives = 231/399 (57%), Gaps = 15/399 (3%) Query: 4 EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63 ++ I A RT +G F GSL+ V + LAA VKAL++ + +D +++DE+ +GC AG Sbjct: 5 DIVIVAAKRTAMGGFQGSLSEVPSPKLAATAVKALLD-DTGLDGARVDELLMGCVLPAGL 63 Query: 64 DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123 + AR A L AGLP SV T+N++C SGM V A I +G A++VIAGG+ESMS+ Sbjct: 64 -GQAPARQAALGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQ 122 Query: 124 APYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQD 183 APY++ KA G + F++ L A G AM A ADDY ++R D Sbjct: 123 APYLLDKARGGMRMGH---GKVLDHMFLDGLEDAYTG-GAMGTFAQKTADDYGLTRESMD 178 Query: 184 AFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADE---HLRPDTTLEALAKLKP 240 AFAL S + A A +G F EIVPV + +KG+ V DE + RP E + L+P Sbjct: 179 AFALSSLEKANAAINSGAFEAEIVPVTVSSRKGDVEVKVDEQPGNARP----EKIPTLRP 234 Query: 241 VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300 D T+TA N+S ++DG+ AL+L S + GLK A + G + P + PV Sbjct: 235 AFAKDGTITAANSSSISDGAAALMLMSRDQADALGLKVLATIKGHTTHAQEPAMFTTAPV 294 Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360 A+ KLL + S + D+ E+NEAFA + EL + D ARVN NGGA ALGHP+G Sbjct: 295 GAMTKLLSNVGWSKDEVDLFEINEAFAMVTMLAISELKL--DAARVNVNGGACALGHPIG 352 Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399 SGAR+++T +H L+ G +RG+ ++C+G G+ A+A+E Sbjct: 353 CSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 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: 387 Number of extensions: 19 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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