Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_085218502.1 B9N75_RS09070 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::B8H1Z0 (248 letters) >NCBI__GCF_900177405.1:WP_085218502.1 Length = 258 Score = 77.0 bits (188), Expect = 3e-19 Identities = 58/181 (32%), Positives = 87/181 (48%), Gaps = 5/181 (2%) Query: 15 VITGGGSGIGAGLTAGFARQGAEVIFL-DIADEDSRALEAELAGSPIPPVYKRCDLMNLE 73 ++TG +GIG L A G ++I D A+ +S A G + PV + DL + Sbjct: 8 IVTGASTGIGFELAKCCAADGYDLIIAADEAEIESAAETLRATGVWVQPV--QADLGTPD 65 Query: 74 AIKAVFAEIGD--VDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQAVAPGMK 131 + + AEIGD VD L+ NAG H D I VN+ + Q V GM+ Sbjct: 66 GVDKLIAEIGDRPVDALLANAGRGLGHAFLDQDFDEIAAVIGVNVTGTVALVQQVGRGMR 125 Query: 132 KRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVVPGNVKT 191 R G ++ GSI+ +L +Y KA ++ + AL EL +I VTC++PG +T Sbjct: 126 DRNKGRILITGSIAGYLPGSFQAVYNGTKAFLDSFSYALGNELKDTEITVTCLMPGATET 185 Query: 192 K 192 + Sbjct: 186 E 186 Lambda K H 0.319 0.137 0.416 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: 136 Number of extensions: 5 Number of successful extensions: 1 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: 248 Length of database: 258 Length adjustment: 24 Effective length of query: 224 Effective length of database: 234 Effective search space: 52416 Effective search space used: 52416 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 (21.7 bits) S2: 46 (22.3 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