Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate GFF3109 PGA1_c31600 S-formylglutathione hydrolase FghA
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__Phaeo:GFF3109 Length = 277 Score = 302 bits (773), Expect = 6e-87 Identities = 151/279 (54%), Positives = 196/279 (70%), Gaps = 4/279 (1%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPPPVLYWLSGLTCNDENFT 60 ME + E+ F G Q +RH SS+ NC MTF +FLP P P+L++LSGLTC EN Sbjct: 1 METVSENAAFGGVQGVYRHASSSTNCDMTFGLFLPEEVADGPVPLLWYLSGLTCTHENAM 60 Query: 61 TKAGAQRVAAELGIVLVMPDTSPRGEKVANDDGYDLGQGAGFYLNATQPPWATHYRMYDY 120 TKAGAQ AE GI +V PDTSPRGE VA+D+ YDLGQGAGFY+NATQ PWA H++M+DY Sbjct: 61 TKAGAQAWCAEQGIAMVFPDTSPRGEGVADDEAYDLGQGAGFYVNATQAPWAPHFQMWDY 120 Query: 121 LRDELPALVQSQFNVS-DRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVPW 179 + ++LPAL+ +F + DR +I+GHSMGGHGAL MA+ PG++ SVSAFAPI NP + W Sbjct: 121 ITEDLPALLGERFALDMDRQSITGHSMGGHGALTMAMSLPGRFRSVSAFAPICNPSASDW 180 Query: 180 GIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEAA 239 G K ++YLG D+ AW D+ +M S P LID G +DQFL D L+P LA+AA Sbjct: 181 GRKQLTAYLGADEAAWARHDATLMMQDSGFDG--PILIDTGTSDQFL-DLLKPEALAQAA 237 Query: 240 RQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYLLK 278 + LR+QPGYDHSY+F+++F+EDH+ FHA+ L + Sbjct: 238 AARRQQAVLRMQPGYDHSYFFVSTFMEDHVSFHAEALYR 276 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: 264 Number of extensions: 10 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: 277 Length adjustment: 25 Effective length of query: 253 Effective length of database: 252 Effective search space: 63756 Effective search space used: 63756 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