Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__Phaeo:GFF329 Length = 391 Score = 298 bits (762), Expect = 2e-85 Identities = 168/396 (42%), Positives = 246/396 (62%), Gaps = 9/396 (2%) Query: 5 VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64 V I A RT +G FGG+ A A DL A ++A+VER +D S++ E LG A + Sbjct: 4 VVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVER-AGIDKSEVSETILGQVLTAAQ- 61 Query: 65 NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124 +N AR A + AGLP +LN++C SG+ AV A + I G+A +V AGG E+M+ + Sbjct: 62 GQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTLS 121 Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184 P+ G K+ D + I + + M +TA+NVA+ +++SR QD Sbjct: 122 PHAAN-----LRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDE 176 Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244 FA+ SQ A AQ AG FA+EI +K +KG+ +VD DE++R T+EA+ KL+P Sbjct: 177 FAVASQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAK 236 Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304 D +VTA NASG+NDG+ A +L SA+ +K G++ A++ A+AG+ P +MG+GP+ A R Sbjct: 237 DGSVTAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASR 296 Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364 K LE+ SV D D++E NEAFAAQ AV +++G D A VN NGGAIA+GHP+GASG Sbjct: 297 KALEKAGWSVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAIGHPIGASGC 354 Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 R++ T + ++++ ++GL T+C+G G GVA+ VER Sbjct: 355 RVLNTLLFEMKRRDAKKGLATLCIGGGMGVAMCVER 390 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: 381 Number of extensions: 18 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 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