Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate WP_086511895.1 BZY95_RS21310 S-formylglutathione hydrolase
Query= BRENDA::P33018 (278 letters) >NCBI__GCF_002151265.1:WP_086511895.1 Length = 284 Score = 335 bits (860), Expect = 5e-97 Identities = 158/279 (56%), Positives = 201/279 (72%), Gaps = 3/279 (1%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPPPVLYWLSGLTCNDENFT 60 +E + ++ F GW +R+RH S L+C M F+I+LPP + PVL+WLSGLTC DENF Sbjct: 7 LEPISSNKSFGGWHKRYRHRSRALDCEMEFAIYLPPQAETERVPVLWWLSGLTCTDENFM 66 Query: 61 TKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DGYDLGQGAGFYLNATQPPWATHYRMYD 119 KAGA RVAAELGI ++ PDTSPRG + + D YD G GAGFY+NATQ PW HYRMYD Sbjct: 67 QKAGAHRVAAELGIAIICPDTSPRGTDLPGEHDSYDFGSGAGFYVNATQEPWKKHYRMYD 126 Query: 120 YLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVPW 179 Y+ +ELP++V+ F ++ R AISGHSMGGHGALI+AL+ PG Y SVSAF+PIVNP PW Sbjct: 127 YVAEELPSVVRQHFPLNGREAISGHSMGGHGALILALRRPGHYRSVSAFSPIVNPTQCPW 186 Query: 180 GIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEAA 239 G KAF YLG+D W ++D+C L+ + + IDQG+ DQFL +QL+P L Sbjct: 187 GRKAFRGYLGDDPGEWTQYDACELVAKGASTQHL--FIDQGEADQFLEEQLKPERLEAVC 244 Query: 240 RQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYLLK 278 + P+TLR QPGYDHSY+FIASFIE+HLR+HA++L K Sbjct: 245 EEHDHPLTLRRQPGYDHSYFFIASFIEEHLRYHAEHLSK 283 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: 335 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: 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 24 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