Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate SMa0060 SMa0060 gluconolactonase
Query= BRENDA::Q64374 (299 letters) >FitnessBrowser__Smeli:SMa0060 Length = 311 Score = 130 bits (327), Expect = 4e-35 Identities = 83/278 (29%), Positives = 138/278 (49%), Gaps = 10/278 (3%) Query: 17 GESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALRQLGGYVATIGTK 76 GES +W ++L +VDI K I R + + + V+S+ +R+ GG++ + Sbjct: 16 GESILWCGDEKALYWVDIVGKRIHRLEPENGRHDTWPTPDFVTSIGMRKDGGFIVGLSRN 75 Query: 77 FCALNWENQSVFV-LAMVDEDKKNNRFNDGKVDPAGRYFAGTMAEET----APAVLERHQ 131 C W F AM + D NR N+G+V P G ++ TM +P ++R Sbjct: 76 VCL--WTPDGPFEEFAMPEPDLPENRLNEGRVAPDGSFWVATMQSNLDAGGSPKDMDRQS 133 Query: 132 GSLYSLFPDHSVKKYF-DQVDISNGLDWSLDHKIFYYIDSLSYTVDAFDYDLQTGQISNR 190 G++Y + P V + ++ I+N + W+ D++ F++ D+L+ + FD DL +I NR Sbjct: 134 GAVYRIDPTGHVSQLTPNEYGITNTMGWTRDNR-FFFADTLANEIYMFDCDLAARRIDNR 192 Query: 191 RIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPETGKRLQTVKLPVDKTTSCCF 250 R + +PDG C+DA+ +LW GG + G+ + ++LP TSC F Sbjct: 193 RTIVAGFA-RGLPDGSCLDADDRLWNCRVAGGAAVAGFDGAGRLMHLIELPASWPTSCTF 251 Query: 251 GGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLG 288 GG S +YVT AR + + L P G +F + G+G Sbjct: 252 GGPVLSTLYVTSARFTMTGDHLDMHPLEGGLFAVEGVG 289 Lambda K H 0.319 0.137 0.419 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: 271 Number of extensions: 21 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: 299 Length of database: 311 Length adjustment: 27 Effective length of query: 272 Effective length of database: 284 Effective search space: 77248 Effective search space used: 77248 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: 48 (23.1 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