Align galactaro-1,5-lactonase (characterized)
to candidate SMa0060 SMa0060 gluconolactonase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Smeli:SMa0060 Length = 311 Score = 127 bits (318), Expect = 4e-34 Identities = 92/299 (30%), Positives = 131/299 (43%), Gaps = 22/299 (7%) Query: 5 LIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAG 64 L++DA++ VGE +W E ALYWVDI + R G W P + I G Sbjct: 7 LLLDAKDIVGESILWCGDEKALYWVDIVGKRIHRLEPENGRHDTWPTPDFVTSIGMRKDG 66 Query: 65 NWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNM-- 122 ++ G+ TP DG + + + P + RLN+GR G FW +M N+ Sbjct: 67 GFIVGLSRNVCLWTP--DGPFEEFAMPEPDLP--ENRLNEGRVAPDGSFWVATMQSNLDA 122 Query: 123 -----GLNAAEGTLYRY-TSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWA 176 ++ G +YR +G + + N + ++ D R +A L +I+ Sbjct: 123 GGSPKDMDRQSGAVYRIDPTGHVSQLTPNEYGITNTMGWTRDNRFFFAD---TLANEIYM 179 Query: 177 FDYDIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAG-LIHRFSPDGRLDRS 235 FD D+ NRR V G PDG+ +DAD W C G + F GRL Sbjct: 180 FDCDLAARRIDNRRTIVAGFAR-GLPDGSCLDADDRLWNCRVAGGAAVAGFDGAGRLMHL 238 Query: 236 LTVPVKKPTMCAFGGSRLDTLFVTSIR-----DDQSEQSLSGGVFALNPGVVGLPEPTF 289 + +P PT C FGG L TL+VTS R D L GG+FA+ G+ EP F Sbjct: 239 IELPASWPTSCTFGGPVLSTLYVTSARFTMTGDHLDMHPLEGGLFAVEGVGHGVEEPKF 297 Lambda K H 0.321 0.137 0.443 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: 369 Number of extensions: 28 Number of successful extensions: 6 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: 291 Length of database: 311 Length adjustment: 27 Effective length of query: 264 Effective length of database: 284 Effective search space: 74976 Effective search space used: 74976 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