Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate GFF4358 HP15_p187g66 UDP-glucose 4-epimerase
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Marino:GFF4358 Length = 343 Score = 200 bits (509), Expect = 3e-56 Identities = 126/326 (38%), Positives = 179/326 (54%), Gaps = 30/326 (9%) Query: 4 LVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERIFS 63 L+TG AGFIGS++++ L++ VI +DN ++G NL+ +S+ E R+ S Sbjct: 24 LITGAAGFIGSNLLEHLLKLNQHVIALDNFATGHQSNLDE-----VRSLVSTEQWTRLQS 78 Query: 64 LH----RPE----------YVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGV 109 + PE YV H AA SV S+ +P NI G L +L + GV Sbjct: 79 IEGDIRNPEDCARACEGVDYVLHQAALGSVPRSLNDPITTNAANITGFLNMLVAARDAGV 138 Query: 110 KKFIFSSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLR 169 K F ++++ YG++ P E +I P+SPY + K+ E+Y E FAR YG K LR Sbjct: 139 KSFTYAASSST-YGDH-PALPKVEEKIGKPLSPYAVTKHVNELYAEVFARSYGFKAIGLR 196 Query: 170 YANVYGPRQDPYGE-AGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEK 228 Y NV+G RQDP G A V+ +T M+RGE+V I GDGE RD+ ++++ V+ANLLA Sbjct: 197 YFNVFGKRQDPNGAYAAVIPKWTAAMVRGEDVFINGDGETSRDFCFIENAVQANLLAATA 256 Query: 229 GD---NEVFNIGTGRGTTVNQLFKLLKEITG-----YDKEPVYKPPRKGDVRKSILDYTK 280 D NEV+N+ G TT+N LF LK YDK PVY+ R GDVR S D K Sbjct: 257 EDSARNEVYNVAVGDRTTLNDLFAALKSALAENGVVYDKAPVYRDFRPGDVRHSQADIGK 316 Query: 281 AKEKLGWEPKVSLEEGLKLTVEYFRK 306 A +LG+ P+ + EG+ + ++ K Sbjct: 317 ASSRLGYNPEFRIVEGIAKAMPWYLK 342 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: 280 Number of extensions: 10 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: 343 Length adjustment: 28 Effective length of query: 281 Effective length of database: 315 Effective search space: 88515 Effective search space used: 88515 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