Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2303 Length = 392 Score = 310 bits (794), Expect = 5e-89 Identities = 179/404 (44%), Positives = 250/404 (61%), Gaps = 16/404 (3%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M + I RT +G++GGAL+ A +L AI +RE + R L ++ I +VI+G A Sbjct: 1 MEDIVIVSAARTAVGKFGGALAKTPASELGAIVIREAIAR-AGLSSDQIGEVIMGQVLAA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G +N AR A++ AG+ + TIN +CGSGL A+ AA+A+ GD D+++AGG E+M Sbjct: 60 GV-GQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENM 118 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQ----FGTDSMPETAENVAELLKI 176 S AP V+ SR + W+ V+ ++ + M TAENVA+ I Sbjct: 119 SLAPHVLNG-----SRDGQRMGD---WKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGI 170 Query: 177 SREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLR 236 +R+ QD+ AL SQQ+ A AQ +G A+EIV V L KKG DE+L +T E L Sbjct: 171 TRDMQDALALGSQQKAAAAQDAGKFADEIVGVSLAQKKGDPILFNADEYLNRKTNAEALA 230 Query: 237 GLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296 GL+ F G +TAGNASG+NDGAAA+++ S + AAA GL P ARI A T+G++P MG Sbjct: 231 GLRPAFDKAGSVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATMG 290 Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALG 356 +GPVPA+R+ L+RAG + D+D+ ELNEAFAAQA V +EL + D VN NGGAIA+G Sbjct: 291 MGPVPASRKALQRAGWNAADVDLFELNEAFAAQACAVNKELAI--DPAKVNVNGGAIAIG 348 Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400 HP+G SG R+ + HE+ RR+ + L +CIG G G+++ LER Sbjct: 349 HPIGASGCRILVTLLHEMQRRDAKKGLAALCIGGGMGVSLALER 392 Lambda K H 0.319 0.135 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: 431 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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