Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate HSERO_RS01180 HSERO_RS01180 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__HerbieS:HSERO_RS01180 Length = 391 Score = 315 bits (806), Expect = 2e-90 Identities = 177/398 (44%), Positives = 258/398 (64%), Gaps = 10/398 (2%) Query: 4 EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63 +V I A RT IG+FGG+L+ + A DL A +KAL+ + + + EV LG AG Sbjct: 3 DVVIVAAQRTAIGKFGGALSKIAAADLGAQVIKALLAKTG-IKPEAISEVILGQVLTAGL 61 Query: 64 DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123 +N AR +++ +GLPD VP + ++C SG+ AV A +AI G+A++VIAGG E+MS Sbjct: 62 -GQNPARQSVIKSGLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENMSA 120 Query: 124 APYVMGKADSAFGRGQ-KIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQ 182 +P+V+ + F G K+ DT I ++ L Y M TA+NVA +++SR +Q Sbjct: 121 SPHVLNNSRDGFRMGDAKLTDTMI----VDGLWDV-YNQYHMGITAENVAKKFEISREEQ 175 Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVN 242 DAFA SQ A AQ AG F +EIVP+ IKGKK V D DE ++ T E+LA L+P Sbjct: 176 DAFAAASQNKAEAAQKAGKFKDEIVPIEIKGKKETVVFDTDEFVKHGVTAESLATLRPAF 235 Query: 243 GPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPA 302 TVTAGNASG+NDG+ A+++ SA+ + GL AK+ +SAG+ P +MG+GPVPA Sbjct: 236 DKAGTVTAGNASGINDGAAAVVVTSAKLAAELGLPVLAKIKAYSSAGLDPSIMGMGPVPA 295 Query: 303 VRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGAS 362 + L++ + D D++E+NEAFAAQ +AV +++G D +++N NGGAIALGHP+GAS Sbjct: 296 SQLTLKKAGWTPQDLDLMEINEAFAAQAIAVNKQMGW--DTSKINVNGGAIALGHPIGAS 353 Query: 363 GARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 G R+++T +H++ + ++GL ++C+G G GVALAVER Sbjct: 354 GCRVLVTLLHEMVRRDAKKGLASLCIGGGMGVALAVER 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: 401 Number of extensions: 14 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