Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate AO353_27945 AO353_27945 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27945 Length = 393 Score = 333 bits (853), Expect = 7e-96 Identities = 192/401 (47%), Positives = 261/401 (65%), Gaps = 10/401 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M + +I+ A RT IG + G+LAS+ A +LGA ++ L+A+ L VD+VI G A Sbjct: 1 MQDVVIVAATRTAIGSFQGSLASIPAPELGAAVIRQLLAK-TGLAADQVDEVILGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N AR A++LAGLP +VP TLN++CGSGL A+ A+A+RCG+A +++AGG+E+M Sbjct: 60 GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118 Query: 121 SRAPFVMGKSEQAFGRS-AEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179 S AP+V+ + A++ D+ I + GI TAEN+ +++++R Sbjct: 119 SLAPYVLPAARTGLRMGHAKMVDSMISDGLWDAFNDYHMGI-----TAENLVDKYHLTRE 173 Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239 +QDAFA SQ KA AAIA GR A EI + I QRKG DE PR +TT E LAKL Sbjct: 174 EQDAFAAASQQKATAAIAAGRFADEITPILIPQRKGEPLSFTVDEQPRAETTAESLAKLK 233 Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299 F++ GSVTAGNAS +NDGA A+LL S++ A++ GL A++ A AGV+P IMGI P Sbjct: 234 PAFKKDGSVTAGNASSLNDGAAAVLLMSADKAKQLGLPVLAKIAAYANAGVDPAIMGIAP 293 Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPL 359 V ATR+ L+ G L +D+IE NEAFAAQ LAV +EL D +VN NGGAIALGHP+ Sbjct: 294 VSATRRCLDKAGWNLDQLDLIEANEAFAAQSLAVGKELEW--DASKVNVNGGAIALGHPI 351 Query: 360 GMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 G SG R++ + LHE+ +R + L T+CIG GQG+AL IER Sbjct: 352 GASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALAIER 392 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: 399 Number of extensions: 15 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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 Apr 09 2024. 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