Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Dsui_0317 Dsui_0317 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__PS:Dsui_0317 Length = 399 Score = 308 bits (789), Expect = 2e-88 Identities = 186/410 (45%), Positives = 244/410 (59%), Gaps = 24/410 (5%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 + +A I+ A R P+ + G + R DD+ A LK+++A+ PQLD + V+DVI GCA Sbjct: 5 IQDAYIVAATRLPVAKRNGMFKTTRPDDMLAHALKSVMAQVPQLDPALVEDVIVGCAMPE 64 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 E NVAR+ LLAGLP +VPG T+NR C SG+ AV AA +R GEA +MLA G E+M Sbjct: 65 AEQGMNVARIGLLLAGLPDTVPGLTINRFCSSGVQAVADAAARIRLGEADVMLAAGTETM 124 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 S +MG + IF+ + N + G G+ TAE VA ++ ISR D Sbjct: 125 SLMSQMMGNKVSL---NPAIFE-----KDENVAIAYGMGL-----TAEKVAQKWGISRDD 171 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQ-----RKGPAKIVEH----DEHPRGDTT 231 QDAFA+ S KA AAIA G+ EI + + G +IVE DE PR D++ Sbjct: 172 QDAFAVASHQKAVAAIAAGKFKDEISPYTVRAHLPDLKSGTVRIVEKVCDTDEGPRPDSS 231 Query: 232 LEQLAKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVE 291 L+ LAKL F GSVTAGN+S ++DGA A+LL S + ++ L+ AR G + AGV Sbjct: 232 LQGLAKLKPVFNARGSVTAGNSSQMSDGAGAVLLVSEKILKQFNLQPLARFAGFSVAGVP 291 Query: 292 PRIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGG 351 P IMGIGP+ A KVL G+ D+D IELNEAFAAQ LAV RELGL D ++NP GG Sbjct: 292 PEIMGIGPIAAIPKVLAQAGIKQDDLDWIELNEAFAAQALAVTRELGL--DPAKINPQGG 349 Query: 352 AIALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 AIALGHPLG +GA T +H + ++ + TMCIG G G A + E + Sbjct: 350 AIALGHPLGATGAIRTATLVHGMRRENKKWGMVTMCIGTGMGAAGLFEAL 399 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: 414 Number of extensions: 20 Number of successful extensions: 4 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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