Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2303 Length = 392 Score = 310 bits (794), Expect = 5e-89 Identities = 177/404 (43%), Positives = 253/404 (62%), Gaps = 17/404 (4%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M D+ I A RT +G+FGGALA A +L A+ ++ I + DQ+ EV G A Sbjct: 1 MEDIVIVSAARTAVGKFGGALAKTPASELGAIVIREAIA-RAGLSSDQIGEVIMGQVLAA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR A + AG+ + P +T+N +C SG+ A+ A +A+A G+ ++ +AGG E+M Sbjct: 60 GV-GQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENM 118 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQ----YGVDSMPETADNVADDYQV 176 S AP V+ + G ++ D W+ ++ ++ Y M TA+NVA Y + Sbjct: 119 SLAPHVLNGSRDG----QRMGD----WKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGI 170 Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALT 235 +R QDA AL SQQKAAAAQ AG FA+EIV V +A KKG+ I+ DE+L +T EAL Sbjct: 171 TRDMQDALALGSQQKAAAAQDAGKFADEIVGVSLAQKKGDPILFNADEYLNRKTNAEALA 230 Query: 236 KLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295 L+P +VTAGNASG+NDGAAA+++ SA+ GL P AR+ + G+ P MG Sbjct: 231 GLRPAFDKAGSVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMG 290 Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALG 355 +GPVPA RK +R G +D D+ ELNEAFA+Q AV +EL + D +VN NGGAIA+G Sbjct: 291 MGPVPASRKALQRAGWNAADVDLFELNEAFAAQACAVNKELAI--DPAKVNVNGGAIAIG 348 Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 HP+G SG R+++T LH++++ +KGLA +C+G G G++LA+ER Sbjct: 349 HPIGASGCRILVTLLHEMQRRDAKKGLAALCIGGGMGVSLALER 392 Lambda K H 0.318 0.134 0.383 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: 20 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: 400 Length of database: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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