Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate CCNA_00544 CCNA_00544 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Caulo:CCNA_00544 Length = 391 Score = 320 bits (819), Expect = 6e-92 Identities = 185/406 (45%), Positives = 261/406 (64%), Gaps = 20/406 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M+E +I+ A RTP+G + GALAS+ A +LG ++A ++R + S VD+VI G QA Sbjct: 1 MSEIVIVSAARTPVGSFNGALASLPASELGKAVIEAAVSR-AGIAPSDVDEVILGQVLQA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + AR A++ AG+PV P +LN+LCGSGL AV AA+ + G A +++AGG ESM Sbjct: 60 AA-GQGPARQASVKAGIPVEAPAWSLNQLCGSGLRAVALAAQQIADGSAKVVVAGGQESM 118 Query: 121 SRAPFVMG-KSEQAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQFN 175 S+AP + Q G +FV+ +++ G F M +TAEN+A+++ Sbjct: 119 SQAPHAQNLRGGQKMG----------DLQFVDTMIKDGLWDAFHGYHMGQTAENIASRWQ 168 Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235 I+R DQD FA+ SQ++A AA G+ EIV + I RKG IV+ DE R T+E + Sbjct: 169 ITREDQDKFAVTSQNRAEAAQKAGKFDDEIVPITIKGRKGDT-IVDKDEFIRHGATIESV 227 Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295 L F + GSVTA NASG+NDGA AL+L S+E A + GLK AR+ A AGVEP IM Sbjct: 228 QGLKPVFNKEGSVTAANASGLNDGAAALVLMSAEEAAKRGLKPLARIASWANAGVEPEIM 287 Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355 G GP+PA++K LE G +++D+D++E NEAFAAQ L V+RELGL D +VN NGGAIA+ Sbjct: 288 GTGPIPASKKALEKAGWSVSDLDLVESNEAFAAQALCVVRELGL--DPAKVNVNGGAIAI 345 Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 GHP+G SGAR++TT +HE++ + L T+C+G G G+A+ +E + Sbjct: 346 GHPIGASGARILTTLVHEMKRSGAKKGLATLCVGGGMGVAMCVEAV 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: 419 Number of extensions: 17 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 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