Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate GFF2760 Psest_2815 S-formylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__psRCH2:GFF2760 Length = 281 Score = 370 bits (950), Expect = e-107 Identities = 180/279 (64%), Positives = 215/279 (77%), Gaps = 5/279 (1%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP-PVLYWLSGLTCNDENF 59 +E++ ++ F GW +R+RH SS+LNC M F++FLPP + PVLYWLSGLTC DENF Sbjct: 3 LEIVSSNKSFGGWHKRYRHRSSSLNCDMVFAVFLPPQAEQGEKLPVLYWLSGLTCTDENF 62 Query: 60 TTKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DG-YDLGQGAGFYLNATQPPWATHYRM 117 KAGA R+AAELG+++V PDTSPRG V +D DG +D G GAGFYLNATQ PWA HYRM Sbjct: 63 MQKAGALRMAAELGLIIVAPDTSPRGAGVPDDPDGAWDFGLGAGFYLNATQEPWAQHYRM 122 Query: 118 YDYLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSV 177 YDY+ DELPALV++ F VSDR ISGHSMGGHGALI ALKNPG+Y SVSAFAPI NP + Sbjct: 123 YDYVVDELPALVEANFPVSDRRGISGHSMGGHGALICALKNPGRYLSVSAFAPISNPLNC 182 Query: 178 PWGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAE 237 PWG KAFS YLGE+++ W EWD+CAL+ + A + +P L+DQGD D F+ QL+P L Sbjct: 183 PWGEKAFSRYLGEERSRWREWDACALI--AEAGEKLPLLVDQGDRDDFMEGQLKPQALQA 240 Query: 238 AARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYL 276 AA P+TLRIQPGYDHSYYFIASFI+DHLR HAQ L Sbjct: 241 AAAAAGHPLTLRIQPGYDHSYYFIASFIDDHLRHHAQAL 279 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: 337 Number of extensions: 15 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: 278 Length of database: 281 Length adjustment: 26 Effective length of query: 252 Effective length of database: 255 Effective search space: 64260 Effective search space used: 64260 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