Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate SM_b20171 SM_b20171 carboxylesterase
Query= BRENDA::P33018 (278 letters) >FitnessBrowser__Smeli:SM_b20171 Length = 280 Score = 297 bits (761), Expect = 1e-85 Identities = 149/276 (53%), Positives = 189/276 (68%), Gaps = 3/276 (1%) Query: 1 MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPPPVLYWLSGLTCNDENFT 60 ME++ + +CF G Q +RH S MTF +++PP P+L++LSGLTC EN Sbjct: 5 MELVTQSQCFGGTQSVYRHASEVCGVEMTFGLYMPPQARTRSVPLLWYLSGLTCTHENAM 64 Query: 61 TKAGAQRVAAELGIVLVMPDTSPRGEKVANDDGYDLGQGAGFYLNATQPPWATHYRMYDY 120 KAG QR AAE G+ LV PDTSPRGE VA+D+ YDLGQGAGFY+NATQ PW+ HYRMYDY Sbjct: 65 IKAGLQRHAAEQGLALVFPDTSPRGEGVADDEAYDLGQGAGFYVNATQKPWSPHYRMYDY 124 Query: 121 LRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVPWG 180 + ELPAL+Q Q ++ I+GHSMGGHGAL +A +NP + SVSAFAPIVNP WG Sbjct: 125 IVTELPALLQEQLPLNGVNGITGHSMGGHGALTIAFRNPELFRSVSAFAPIVNPTRSDWG 184 Query: 181 IKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEAAR 240 K FS+YLG+D+ W +D+C L+ I LIDQG DQFL D+LQP +A Sbjct: 185 RKQFSAYLGDDEADWGSYDACLLLGELGWHGDI--LIDQGAADQFL-DELQPEAMARLLA 241 Query: 241 QKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYL 276 ++ +R+Q GYDHSYYF+ASF EDH+R+HA+ L Sbjct: 242 ERRQAGVVRLQAGYDHSYYFVASFGEDHVRWHAERL 277 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: 286 Number of extensions: 14 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: 280 Length adjustment: 26 Effective length of query: 252 Effective length of database: 254 Effective search space: 64008 Effective search space used: 64008 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