Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011427695.1 RHE_RS23190 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000092045.1:WP_011427695.1 Length = 395 Score = 258 bits (659), Expect = 2e-73 Identities = 153/396 (38%), Positives = 229/396 (57%), Gaps = 8/396 (2%) Query: 4 VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63 + I A RTPIG F G L A +L A ++A +E + V + V+EV FGC AG Sbjct: 7 IVIVGAARTPIGSFQGELKEATAPELGATAIRAALERS-RVPAEAVEEVVFGCVLPAGL- 64 Query: 64 NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123 + AR A + AGLP + T+N++C SGM A+ A IA+G +A+AGG+ESM+ A Sbjct: 65 GQAPARQAAISAGLPFATGSTTVNKMCGSGMKAVMMAHDLIAAGNASVAVAGGMESMTNA 124 Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183 P+++ +A GY + F++ L + M A++ A+ YQ +R QD Sbjct: 125 PYLLDRARGGYRLG---HGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDN 181 Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243 +A+ S +A A A G F EIV V + K E + RDE + ++ + LKP Sbjct: 182 YAIASLTRAQKAIADGCFESEIVAVTVKSGKAEQVASRDEQ-PGKAKIDKIPTLKPAFRD 240 Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303 TVTA N+S ++DGAAAL+L + GL P A VLG A+ AP + P+ A++ Sbjct: 241 GGTVTAANSSSISDGAAALVLMRRSEAEHRGLVPLATVLGHATHSQAPNLFATAPIGALQ 300 Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363 KL++R G+A+SD D+ E+NEAFA +A +R+L + + +VN +GGA ALGHP+G SG Sbjct: 301 KLSDRTGLALSDVDLFEINEAFAVVAMAAMRDLDLPHE--KVNVHGGACALGHPIGASGG 358 Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 R+++T L LE+ ++G+A +C+G G+ A+AIER Sbjct: 359 RILVTLLSALERYDLKRGMAALCIGGGEATAVAIER 394 Lambda K H 0.318 0.134 0.383 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: 372 Number of extensions: 19 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: 400 Length of database: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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