Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__azobra:AZOBR_RS28180 Length = 397 Score = 267 bits (683), Expect = 4e-76 Identities = 162/396 (40%), Positives = 227/396 (57%), Gaps = 8/396 (2%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 V I A RTP+GRF G L+A+ A L A V+A + R ++DEV LGC AG+ Sbjct: 8 VVIVSAARTPLGRFQGELSALPAHALGAHAVRAALSRAGLAP-ERVDEVLLGCVLPAGQ- 65 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 + AR A AGLPD+ T+N++C SGM A A I +G A+LV+AGG+ESMS A Sbjct: 66 GQAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESMSNA 125 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184 PY++ KA + G D + ++ L A G M + + AD Y +RA+QDA Sbjct: 126 PYLLAKARGGYRIGH---DRILDHLMLDGLEDAYEGGRPMGDFGEATADLYGFTRAEQDA 182 Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244 +A+ + A A A+G F EI PV + K GE V AD+ E + LKP Sbjct: 183 YAVETLTRARAAIASGAFTAEIAPVTLAVKGGERTV-ADDENPLKVAPEKIPALKPAFRR 241 Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304 D T+TA ++S DG+ AL+L ++ GL A +LG A+ P P+PA+R Sbjct: 242 DGTITAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWFTTAPIPAIR 301 Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364 KLL+R+ + D D+ E+NEAFA +A R+LGI D +N NGGA ALGHP+GA+GA Sbjct: 302 KLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRD--ALNVNGGACALGHPIGATGA 359 Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 RL++T +H L G +RG+ ++C+G G+ A+AVER Sbjct: 360 RLIVTLLHALAARGLRRGVASLCIGGGEATAIAVER 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: 428 Number of extensions: 22 Number of successful extensions: 6 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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