Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate PP_1617 PP_1617 S-formylglutathione hydrolase / S-lactoylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__Putida:PP_1617 Length = 284 Score = 350 bits (897), Expect = e-101 Identities = 167/269 (62%), Positives = 201/269 (74%), Gaps = 3/269 (1%) Query: 8 RCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP-PVLYWLSGLTCNDENFTTKAGAQ 66 + F GW +R+RH S L C M F+++LPP + PVLYWLSGLTC DENF KAGAQ Sbjct: 10 KSFGGWHKRYRHHSKVLGCDMVFAVYLPPQAEQGEKLPVLYWLSGLTCTDENFMQKAGAQ 69 Query: 67 RVAAELGIVLVMPDTSPRGEKVAND-DG-YDLGQGAGFYLNATQPPWATHYRMYDYLRDE 124 R+AAELG+++V PDTSPRGE+V D DG +D G GAGFYLNATQ PWA HYRM+DY+ +E Sbjct: 70 RLAAELGLIIVAPDTSPRGEQVPGDPDGAWDFGLGAGFYLNATQQPWAQHYRMHDYVVEE 129 Query: 125 LPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVPWGIKAF 184 LPAL+++ F S +ISGHSMGGHGAL+ AL+NPG+Y SVSAF+PI NP PWG KAF Sbjct: 130 LPALIEAHFPASGERSISGHSMGGHGALVCALRNPGRYRSVSAFSPISNPMDCPWGEKAF 189 Query: 185 SSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEAARQKAW 244 S YLGED+ W EWD+ L+ + A P L+DQGD D FL QL+P L +AAR+ Sbjct: 190 SRYLGEDRGRWREWDASVLLAETPAGQCPPLLVDQGDRDDFLEKQLKPEALEQAARKGGH 249 Query: 245 PMTLRIQPGYDHSYYFIASFIEDHLRFHA 273 MTLR+QPGYDHSYYFIASFIE+HLR HA Sbjct: 250 AMTLRMQPGYDHSYYFIASFIEEHLRHHA 278 Lambda K H 0.320 0.136 0.441 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: 349 Number of extensions: 15 Number of successful extensions: 3 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: 278 Length of database: 284 Length adjustment: 26 Effective length of query: 252 Effective length of database: 258 Effective search space: 65016 Effective search space used: 65016 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: 47 (22.7 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