Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AO356_02325 AO356_02325 3-ketoacyl-CoA thiolase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02325 Length = 391 Score = 301 bits (772), Expect = 2e-86 Identities = 177/405 (43%), Positives = 244/405 (60%), Gaps = 24/405 (5%) Query: 2 REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 R+ I D RTP+GR GG + RA+D++A + +LL RN ++D ++DVI GC NQ Sbjct: 6 RDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQT 65 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 E N+ARMA+L+ +P + +G T++RLCGS + AL AA+AI G+GD+ + GGVE M Sbjct: 66 LEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHM 125 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKISR 178 + G NP M+ S M TAE + ++ ISR Sbjct: 126 GHVSMMHGVDP-------------------NPHMSLYAAKASGMMGLTAEMLGKMHGISR 166 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 E QD+F +RS Q KA G +EI+P+ ++ G + +DE +RPETTLE L L Sbjct: 167 EQQDAFGVRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAAL 226 Query: 239 KAPFRANG-VITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297 K F G +TAG +S + DGA+ +I+ S Q A G+ P A I +MA AGV+P +MG Sbjct: 227 KPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGY 286 Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDA-PHVNPNGGAIALG 356 GPVPAT++ L+RAGL I D+D ELNEAFAAQAL VL++L + D VN +GGAIALG Sbjct: 287 GPVPATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALG 346 Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 HP G SGAR++ + + + G + + TMCIG+GQGIA + ERV Sbjct: 347 HPFGCSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 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: 433 Number of extensions: 17 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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 Apr 09 2024. 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