Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate Ac3H11_1900 UDP-glucose 4-epimerase (EC 5.1.3.2)
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1900 Length = 287 Score = 161 bits (407), Expect = 2e-44 Identities = 88/240 (36%), Positives = 138/240 (57%), Gaps = 3/240 (1%) Query: 68 EYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVK-KFIFSSTGGAIYGENV 126 + + HLA+ A + +P +DA+TN++G+L LL+ + G + + +F+S+GGA+YG Sbjct: 46 DVIVHLASSTVPATASEDPVQDAQTNLVGTLRLLQALRQKGARPRLLFASSGGAVYGRPQ 105 Query: 127 KVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGPRQDPYGEAGV 186 V P ET P+ YG K + E +L ++GL +LR +N YG Q P+G GV Sbjct: 106 FV-PLSETHPTMPMGAYGATKLAIEHHLRIEEAQHGLPSRILRLSNPYGEWQQPHGVQGV 164 Query: 187 VAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANL-LAMEKGDNEVFNIGTGRGTTVN 245 +A+F R L G V ++GDG VRD+VY DV RA + A +G FN+G G G +VN Sbjct: 165 IAVFAHRALHGHSVDVWGDGSVVRDFVYAADVGRAFVSAARHEGPTRTFNVGGGTGHSVN 224 Query: 246 QLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLEEGLKLTVEYFR 305 + L+ + G E P R D ++LD +A+E+L W P ++ EEG+ ++V++ R Sbjct: 225 DIIHTLERLLGKAVERRVFPARPFDPPVNVLDIQRAQEELLWTPAMAFEEGVAMSVQWLR 284 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: 204 Number of extensions: 9 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: 309 Length of database: 287 Length adjustment: 26 Effective length of query: 283 Effective length of database: 261 Effective search space: 73863 Effective search space used: 73863 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 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