Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_066917847.1 ACG33_RS00350 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_001579945.1:WP_066917847.1 Length = 384 Score = 259 bits (663), Expect = 7e-74 Identities = 167/406 (41%), Positives = 233/406 (57%), Gaps = 28/406 (6%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M EA I+DA+R+P GR G+LA V DLGA +KAL+ R+ + + DDVI+GC + Sbjct: 1 MPEAFIVDALRSPTGRRGGSLAQVHGADLGAHVIKALVERNA-VPAAEYDDVIFGCVDTI 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G ++AR A L+AG+P++VPGTT++R CGS AV AA+A+ G ++LAGGV++M Sbjct: 60 GALAGDIARTAWLVAGMPLNVPGTTIDRQCGSSQQAVHFAAQAVMSGTQDVVLAGGVQTM 119 Query: 121 SRAPFVMGKSEQAFGRSAEI---FDTTIGW--RFVNKLMQQGFGIDSMPETAENVAAQFN 175 S P S GR F + GW RF + + Q + A+ +A +N Sbjct: 120 SSIPI---SSAMLAGRPLGFTTPFAESKGWQARFGDAPVNQFYA-------AQRIADHWN 169 Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235 ISR + FA S +A A+A GR +E+V A++ +TLE++ Sbjct: 170 ISREAMEIFAKESHDRALKAMAEGRFDREVVPFGEFLMDETARV----------STLEKM 219 Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295 A L +TA +S V D A A+L+ S A +R+GLK RAR+V ++ +P Sbjct: 220 ATLQPVDPAYPKITAAVSSSVCDAASAVLVVSEAALKRYGLKPRARIVHLSVLADDPIWH 279 Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355 P+PATR L+ G+ L D+D++E+NEAFA+ +A L+E G R+N NGGAIAL Sbjct: 280 LTAPIPATRNALKKAGMKLEDIDLVEINEAFASVVMAWLQETGYPH--ARINVNGGAIAL 337 Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 GHPLG SG +L+TT LHELE GRY L TMC G GQ IIER+ Sbjct: 338 GHPLGASGTKLMTTLLHELERTGGRYGLQTMCEGGGQANVTIIERM 383 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: 393 Number of extensions: 16 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: 384 Length adjustment: 31 Effective length of query: 370 Effective length of database: 353 Effective search space: 130610 Effective search space used: 130610 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