Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF49 HP15_49 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Marino:GFF49 Length = 391 Score = 328 bits (842), Expect = 1e-94 Identities = 193/407 (47%), Positives = 259/407 (63%), Gaps = 23/407 (5%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M + +I+DAVRTP+GR+ G+LA VRAD LGA+ L L+ R+ L ++DDV++GC Q Sbjct: 1 MKDVVIVDAVRTPVGRFRGSLAGVRADHLGALVLNELLYRNG-LAAESIDDVVFGCVTQI 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GE + N+AR + L AG P SVPG T++R CGSG AV A A+ G A +++AGG E+M Sbjct: 60 GEQSANIARTSLLGAGWPTSVPGLTIDRKCGSGEAAVHCAFGAIAAGSAEIVVAGGAENM 119 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SR P MG + G + L+ + + S E AE VA ++N+ R Sbjct: 120 SRVP--MGSNRDLHGEA------------FGHLVSDRYEMTSQGEAAERVAEKWNLDREQ 165 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQ-RKGPAKIVEH----DEHPRGDTTLEQL 235 DAFAL S +AA A +G EIV V +A R+ A+ VE DE R DT+LE+L Sbjct: 166 LDAFALESHRRAAVAADSGYFKSEIVPVPVADYRENGAEKVEGKFAADETIRRDTSLEKL 225 Query: 236 AKLGTPFR-QGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRI 294 A L T FR + G +TAGN+S ++DG ALLL SS+ A+ GLK +AR+ + T G +P + Sbjct: 226 ATLKTSFRKENGRITAGNSSQISDGCSALLLMSSDVARNLGLKPKARIRAVTTVGADPTL 285 Query: 295 MGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIA 354 M GP+ ATRKVL GL L ++D+ E+NEAFA+ LA ++E+G D ER+N NGGAIA Sbjct: 286 MLTGPIGATRKVLAKAGLELDEIDLFEINEAFASVPLAWMKEVGA--DPERLNVNGGAIA 343 Query: 355 LGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 LGHPLG SGAR++T+ L+ELE R+GRYAL +C G G A IIERI Sbjct: 344 LGHPLGASGARIMTSMLNELERRRGRYALQAICCAGGMGTATIIERI 390 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: 411 Number of extensions: 16 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: 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 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