Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Smeli:SMc00966 Length = 397 Score = 253 bits (645), Expect = 9e-72 Identities = 171/400 (42%), Positives = 227/400 (56%), Gaps = 35/400 (8%) Query: 5 LIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYG-CANQAGED 63 ++I A+RTP+GR G+LA+V L A+ ++ +IA +D + +DDV+ G AN AG Sbjct: 12 VVIAALRTPVGRVNGSLAAVEPARLAALLIERIIA-DTGIDRAEIDDVLVGNAANSAG-- 68 Query: 64 NRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSRA 123 N+AR+AAL AGLPV++PG T++R CGSGL+A+ AAR ++ G LAGG ES SRA Sbjct: 69 --NLARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRA 126 Query: 124 ------PFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNIS 177 P G+ Q R+ ++ G M AENVA IS Sbjct: 127 HIRLRPPLTRGEEPQPVKRA--------------RMAPDSIGDPDMGVAAENVATACGIS 172 Query: 178 RADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAK 237 R QD FAL S +A AA A GR ++EIV V + GP + DE PR + + E L++ Sbjct: 173 RERQDRFALESHRRAVAAEAEGRFSREIVPVPTPE--GP---IARDECPRANASAETLSR 227 Query: 238 LGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297 L F GG+VTAGNA VNDGA +L+ + A++ G + ATAGVEP+++G+ Sbjct: 228 LRPVFVAGGTVTAGNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGL 287 Query: 298 GPVPATRKV-LELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALG 356 GPVPA K+ L +A +D IE NEAFA+Q L L +L +A ERVN +GGAIALG Sbjct: 288 GPVPAMAKLRARNPALDVARVDFIEFNEAFASQVLGSLDQLDIA--PERVNRDGGAIALG 345 Query: 357 HPLGMSGARLVTTALHE-LEERQGRYALCTMCIGVGQGIA 395 HP G SGA LV + L L M IG G GIA Sbjct: 346 HPYGASGAILVVRLFSQMLAASSPAEGLAMMGIGGGMGIA 385 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: 428 Number of extensions: 25 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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