Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_012468563.1 GLOV_RS02315 NAD-dependent epimerase
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000020385.1:WP_012468563.1 Length = 337 Score = 152 bits (384), Expect = 1e-41 Identities = 101/335 (30%), Positives = 159/335 (47%), Gaps = 35/335 (10%) Query: 1 MNILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNAL----------FYEQ 50 M ILVTG AGFIG H+ +L+ G V+ +DNL+S +L + L F + Sbjct: 1 MRILVTGAAGFIGFHLCRRLLARGDAVLGLDNLNSYYDVSLKQARLAQLQPHPGFSFVQA 60 Query: 51 SIEDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVK 110 + D ME++FS+ + + V HLAAQA V S+ P +N+ G + +LE GVK Sbjct: 61 DLADRPAMEQLFSVEQFDIVIHLAAQAGVRYSLENPHAYVDSNLTGFMNILEGCRHTGVK 120 Query: 111 KFIFSSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRY 170 +F+S+ ++YG N + + + HP+S Y K + E+ +A + L T LR Sbjct: 121 HLVFASS-SSVYGANTAIPFSIHQNVDHPVSLYAATKKANELMAHSYASLFNLPVTGLRL 179 Query: 171 ANVYGPRQDPYGEAGVVAI-FTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEK- 228 VYG P+G + FT +L G ++IF G RD+ YVDD+V + EK Sbjct: 180 FTVYG----PWGRPDMAYFSFTRAILEGRPINIFNRGRMQRDFTYVDDIVEGIVRIAEKP 235 Query: 229 ------------------GDNEVFNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGD 270 ++NIG + + Q ++L++ G + + P + GD Sbjct: 236 AEKNPTWSGTQPDPGTSFAPYRIYNIGNNKPVELLQFIEILEQQLGITAQKNFLPMQAGD 295 Query: 271 VRKSILDYTKAKEKLGWEPKVSLEEGLKLTVEYFR 305 V + D + G+ P SLE+G+ V +FR Sbjct: 296 VPATFADIDELAAATGFRPATSLEDGIARFVAWFR 330 Lambda K H 0.318 0.139 0.396 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: 254 Number of extensions: 15 Number of successful extensions: 5 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: 309 Length of database: 337 Length adjustment: 28 Effective length of query: 281 Effective length of database: 309 Effective search space: 86829 Effective search space used: 86829 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 (21.6 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