Align Putative sugar lactone lactonase; EC 3.1.1.- (characterized, see rationale)
to candidate WP_011650656.1 RL_RS04775 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:Q92RN9 (294 letters) >NCBI__GCF_000009265.1:WP_011650656.1 Length = 295 Score = 380 bits (976), Expect = e-110 Identities = 173/293 (59%), Positives = 221/293 (75%), Gaps = 1/293 (0%) Query: 1 MTDLVPFSGRTLSEAASELGEGPTFDPGTGTAWWFNITGRELHELHLESGRKAIHPLPFL 60 MTD+ F G+TL S LGEGPT+DP + T WWFNI G+ELHEL+L + K +HPLP + Sbjct: 1 MTDIYEFEGKTLCNTNSVLGEGPTYDPDSNTVWWFNILGKELHELNLSTAAKKVHPLPVM 60 Query: 61 GSVLAVIDPLRQLIASDQGLFVRDTESSKLGHFATLE-EKPGNRSNDGRIHPCGALWIGT 119 SVLA ID RQLIA+++GLFVRD S L +A LE ++P NRSNDGR HP GALWIGT Sbjct: 61 ASVLARIDAGRQLIATEEGLFVRDVASGNLTFYAALENDRPENRSNDGRTHPSGALWIGT 120 Query: 120 MGRSAEKHAGAIYHVAGSRVTKLYSNITIPNAICFSPDGATAYFTDTDVNQLMRVDIDPA 179 M + AE AGAIYHVA +VTK+++ I+IPN+ICFSPDG Y+TD+ +N+LMRV +DP Sbjct: 121 MSKRAENQAGAIYHVASGKVTKIFNGISIPNSICFSPDGTIGYYTDSRINRLMRVMVDPL 180 Query: 180 TALPTGDPVLLSDESTSPGGVDGAVCDADGLIWNARWGASAVEVYKPDGQKVARYAVPAT 239 T LP+G+P++L D PG +DG+V DADG +WNARWGA V+ Y PDG +++RY VPA Sbjct: 181 TGLPSGEPIVLVDSMDEPGSIDGSVVDADGYLWNARWGAGVVDRYSPDGLRISRYMVPAV 240 Query: 240 QPSCPAFVGAKAERLLVTSAWQGMDDAARAADPHAGKTFELGIEVKGRFEPAF 292 QPSCPAF+G A+RL VT+AW+G+D+ AR+A P AG ELGI+VKG F+P + Sbjct: 241 QPSCPAFIGVNADRLAVTTAWEGLDEDARSAQPSAGALLELGIDVKGVFDPVY 293 Lambda K H 0.317 0.135 0.418 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: 324 Number of extensions: 7 Number of successful extensions: 2 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: 294 Length of database: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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