Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate BPHYT_RS21055 BPHYT_RS21055 S-formylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__BFirm:BPHYT_RS21055 Length = 276 Score = 338 bits (868), Expect = 6e-98 Identities = 157/274 (57%), Positives = 205/274 (74%), Gaps = 3/274 (1%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPP-PVLYWLSGLTCNDENF 59 ME +E+H + G+Q+ W+H SSTL C M F ++LP PVLYWLSGLTC ++NF Sbjct: 1 MERIEQHASYGGYQEVWKHASSTLGCEMRFGLYLPNAALRGQKCPVLYWLSGLTCTEQNF 60 Query: 60 TTKAGAQRVAAELGIVLVMPDTSPRGEKVANDDGYDLGQGAGFYLNATQPPWATHYRMYD 119 TKAGAQR AAE G+++V PDTSPRG+ V +D GYDLG+GA FY+NA Q PWATHYRMYD Sbjct: 61 ITKAGAQRYAAEHGLIIVAPDTSPRGDDVPDDPGYDLGKGASFYINAAQEPWATHYRMYD 120 Query: 120 YLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVPW 179 Y+ DELPALV+++F + AISGHSMGGHGAL +AL+NPG+Y SVSAF+PIV P VPW Sbjct: 121 YVVDELPALVEAEFPANGARAISGHSMGGHGALTIALRNPGRYRSVSAFSPIVAPTEVPW 180 Query: 180 GIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEAA 239 G KAF +YLGED+ W ++D+ L+ +A + +P L+DQG+ D+FL +QL+P +L A Sbjct: 181 GRKAFRAYLGEDREVWKQYDTVELL--KSAVERLPLLVDQGEGDEFLEEQLKPQLLRAAC 238 Query: 240 RQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHA 273 A P+ L ++PGYDHSYYFI++FI +H+ HA Sbjct: 239 EAAAHPLRLNLRPGYDHSYYFISNFIGEHIAHHA 272 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: 294 Number of extensions: 8 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: 276 Length adjustment: 25 Effective length of query: 253 Effective length of database: 251 Effective search space: 63503 Effective search space used: 63503 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