Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate SMc01698 SMc01698 oxidoreductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Smeli:SMc01698 Length = 251 Score = 148 bits (374), Expect = 1e-40 Identities = 87/247 (35%), Positives = 135/247 (54%), Gaps = 6/247 (2%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKAD 78 L+ K+ ++TGA GIG A+ + A ++++D A+ +VAA R G D Sbjct: 5 LEGKIAIVTGAGSGIGAAVSRQLGGEGAEVIVADRDADAARSVAAEIRSAGGRARDFTVD 64 Query: 79 VSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAWYGC 137 V++ + M V G + + VN AG+ R + EDWRR ++L+G +Y Sbjct: 65 VTDAGAVEQMVAFTVRECGGLHLAVNNAGIEGPRQATADYPLEDWRRLIEVNLNGVFYCM 124 Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197 K + M+ +G G+I+N++S + +P Y AKHG++GLT+A GIEYA G+R+NA Sbjct: 125 KYEIAAMLGKGGGAIVNMSSILGAVALPTASAYTAAKHGVVGLTKAAGIEYARMGIRINA 184 Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 + PG+IET L +G ++ A+ +R L P R G+P EVA FL S++A FI Sbjct: 185 VGPGWIETPL----LSGHSE-LAKTRRLEALQPLGRRGKPEEVAALVCFLLSEQASFITG 239 Query: 258 SCITIDG 264 S +DG Sbjct: 240 SYHPVDG 246 Lambda K H 0.321 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: 156 Number of extensions: 5 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: 272 Length of database: 251 Length adjustment: 25 Effective length of query: 247 Effective length of database: 226 Effective search space: 55822 Effective search space used: 55822 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