Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011427695.1 RHE_RS23190 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000092045.1:WP_011427695.1 Length = 395 Score = 254 bits (648), Expect = 4e-72 Identities = 153/394 (38%), Positives = 223/394 (56%), Gaps = 8/394 (2%) Query: 6 ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65 I A RTPIG + G LK+ A +LGA I+A ++R+ V AV++V++GC AG + Sbjct: 9 IVGAARTPIGSFQGELKEATAPELGATAIRAALERSR-VPAEAVEEVVFGCVLPAGL-GQ 66 Query: 66 NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125 AR +A+ AGLP T+N++CGSGM AV A I AG A + +AGG+ESMT AP+ Sbjct: 67 APARQAAISAGLPFATGSTTVNKMCGSGMKAVMMAHDLIAAGNASVAVAGGMESMTNAPY 126 Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185 ++ +A + H + F++ L M AE+ AE + +R QD +A Sbjct: 127 LLDRARGGYRLG---HGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDNYA 183 Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245 +AS +A +A DG EIV V + K + + + DE P + ++ + LK R G Sbjct: 184 IASLTRAQKAIADGCFESEIVAVTVKSGKAEQV-ASRDEQPGKAKIDKIPTLKPAFRDGG 242 Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305 TVTA N+S ++DGA AL++ + AE GL A V+G AT P + P A QKL Sbjct: 243 TVTAANSSSISDGAAALVLMRRSEAEHRGLVPLATVLGHATHSQAPNLFATAPIGALQKL 302 Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365 + G+ L +D+ E+NEAFA +A +R L L + +VN +GGA ALGHP+GASG R+ Sbjct: 303 SDRTGLALSDVDLFEINEAFAVVAMAAMRDLDLPHE--KVNVHGGACALGHPIGASGGRI 360 Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399 + T L LER + + + +CIG G+ A+ IER Sbjct: 361 LVTLLSALERYDLKRGMAALCIGGGEATAVAIER 394 Lambda K H 0.319 0.134 0.386 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: 358 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: 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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