Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_026127547.1 D471_RS0108850 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000341125.1:WP_026127547.1 Length = 399 Score = 295 bits (755), Expect = 2e-84 Identities = 170/404 (42%), Positives = 243/404 (60%), Gaps = 24/404 (5%) Query: 2 REAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 R+ DG+RTP G+ G G + RADD+ +RELL RNP L E +D+V + Q Sbjct: 6 RDVVFVDGVRTPFGKSGKGLYAETRADDMVVRVIRELLRRNPGLPPERVDEVAIAATTQI 65 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G+ + R A +LAGLPQSV G I+R+C L A+ + I G D++IAGGVE M Sbjct: 66 GDQGLTIGRSAAILAGLPQSVPGYAIDRMCAGALTAVTTSGAGISFGAYDVVIAGGVEHM 125 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLK-ISRE 179 R P MG+ R + + V+P M TAEN+ + I++E Sbjct: 126 GRHP--MGEGVDPNPR-------FLSEKLVDPSALV------MGNTAENLHDRYPTITKE 170 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKK---GVVTEIQHDEHLRPETTLEQLR 236 D++A+RSQ++ AKA + G + +++V +V+++ + G+ TE DE RP TT+E L Sbjct: 171 RADAYAVRSQEKVAKAYADGKIQQDLVEMVVRSLEKGWGLATE---DEPPRPGTTMESLA 227 Query: 237 GLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296 GLK PFR++G +T GNA+G+NDGA ++A+E +AA GL R R+V + AGV+P +MG Sbjct: 228 GLKTPFRSHGNVTPGNAAGLNDGATGALLAAEDVAAELGLDARMRLVDFSFAGVDPAVMG 287 Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALG 356 +GPVPAT ++ R G+SI D+ +IE+NEAFA Q L L G+ DD VNP GGAIA+G Sbjct: 288 VGPVPATEKLFARQGISIDDIGIIEINEAFAVQVLAFLEHFGVADDDARVNPWGGAIAVG 347 Query: 357 HPLGMSGARLALAASHEL-HRRNGRYALCTMCIGVGQGIAMILE 399 HPL SG RL + + + R + RY L TMC+G+G G ++ E Sbjct: 348 HPLASSGVRLMMQLARQFAERPDVRYGLTTMCVGLGMGGTILWE 391 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: 490 Number of extensions: 22 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: 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 24 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