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_1916 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_1916 Length = 399 Score = 295 bits (755), Expect = 2e-84 Identities = 181/409 (44%), Positives = 235/409 (57%), Gaps = 27/409 (6%) Query: 1 MREAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 +++A+I RTPIGR G G + R DDL ++ +++ P LD + I+D I+GC+ Sbjct: 6 VQDAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGCSFP 65 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 GE N+AR+A LA V G T+NR C SG+ AL AA I+ G+ D+LIAGG ES Sbjct: 66 EGEQGMNMARIAVGLA-FNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGGAES 124 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 MS P MG +F+ + D +G + M TAE VA+ KISRE Sbjct: 125 MSLVP--MGGNKPSFNAEVFARDEDVGIAY------------GMGLTAEKVAQQWKISRE 170 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKK-----GVVTE----IQHDEHLRPET 230 QD+FAL S R KAQ +G +EI P + + G V E + DE RP+T Sbjct: 171 AQDAFALESHLRAIKAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDT 230 Query: 231 TLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGV 290 +LE L LK F A G +TAGN+S +DGA ALI+ASE+ GLTP AR V+ A GV Sbjct: 231 SLEGLAKLKPVFAARGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGV 290 Query: 291 EPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNG 350 P +MG+GP+ A L AGL D+ ELNEAFAAQ+L V+ LGL + +VNP G Sbjct: 291 PPEIMGIGPIEAIPAALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGL--NPANVNPMG 348 Query: 351 GAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 GAIALGHPLG +GA A H L R +Y + TMC+G GQG A I+E Sbjct: 349 GAIALGHPLGATGAIRAATVVHALRRHKLKYGMVTMCVGTGQGAAGIIE 397 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: 414 Number of extensions: 22 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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