Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_035238344.1 Q366_RS09305 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000745975.1:WP_035238344.1 Length = 391 Score = 259 bits (661), Expect = 1e-73 Identities = 150/404 (37%), Positives = 240/404 (59%), Gaps = 17/404 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 MN+A+I+ A RTP+G + G+L+ + A LG + ++ I R ++ + VD+ I G Sbjct: 1 MNKAVIVSATRTPLGSFGGSLSGMGATTLGGLVIREAI-RRADIEDAVVDECIMGMVLPC 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N + A + +GLP V T+N++CGS L AV AA+A++CG+A +++AGG+E+M Sbjct: 60 GY-GQNPGKQAVVKSGLPWEVEAITINKVCGSSLKAVMLAAQAIQCGDADVVVAGGMETM 118 Query: 121 SRAPFVMGKSEQAF----GRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNI 176 S AP+ M K+ GR + W VN M + E + ++ + Sbjct: 119 SMAPYYMDKARWGHRMGPGRIEDHMVHDGLWDIVNDF--------HMGMSNELCSERWEV 170 Query: 177 SRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLA 236 +R DQD FA RS +A A+A GR EI+ V I QRKG KI + DE P+ +T+ E L+ Sbjct: 171 TREDQDRFAARSYERANKAVAQGRFKDEIMPVSIPQRKGDPKIFDTDECPQ-ETSFEFLS 229 Query: 237 KLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMG 296 K+ F++ G TAGNAS + DGA A+++ S A+ G A + A+ G++ + + Sbjct: 230 KMKPAFKKDGVGTAGNASIIADGASAVVMMSESKAKALGCTVMAEIGAQASYGIDMKYVL 289 Query: 297 IGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALG 356 + P+ A KVL+ G+++ D+ + E+NEAFA + + L L D E+VN NGG++ALG Sbjct: 290 MAPIYAIPKVLKKQGISINDVGLFEINEAFAGTSAGINKVLEL--DPEKVNVNGGSVALG 347 Query: 357 HPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 HP+G SGAR++TT L+E+ +R + L ++C+G G+ +AL++ R Sbjct: 348 HPIGASGARVLTTLLYEMAKRDVKTGLASLCLGGGEAVALVVNR 391 Lambda K H 0.319 0.134 0.384 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: 397 Number of extensions: 15 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: 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 ( 7.4 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 Sep 24 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