Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate 350587 BT1059 putative UDP-glucose 4-epimerase (NCBI ptt file)
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Btheta:350587 Length = 309 Score = 146 bits (368), Expect = 7e-40 Identities = 99/321 (30%), Positives = 165/321 (51%), Gaps = 35/321 (10%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLN-----------RNALFYEQS 51 ILV+GGAGFIGSH+ +L+ G+ VI +DN +G +N+ R+ + Y S Sbjct: 4 ILVSGGAGFIGSHLCTRLVNEGHDVICLDNFFTGSKDNIKHLMGNHHFEVVRHDVTYPYS 63 Query: 52 IEDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKK 111 E +E +++LA AS +P + AKT+++G++ +L +++ K Sbjct: 64 AEVDE-------------IYNLACPASPIHYQHDPIQTAKTSVMGAINMLGLAMRLDAK- 109 Query: 112 FIFSSTGGAIYGENVKVFPTPETEIPH--PI---SPYGIAKYSTEMYLEFFAREYGLKYT 166 I ++ +YG+ + + P PE+ + P+ S Y K E + R+ + Sbjct: 110 -ILQASTSEVYGDPI-IHPQPESYWGNVNPVGYRSCYDEGKRCAETLFMDYYRQNQTRIK 167 Query: 167 VLRYANVYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAM 226 ++R N YGPR P + VV+ F + L E++ I+GDG+ R + Y+DD++ + M Sbjct: 168 IIRIFNTYGPRMLP-NDGRVVSNFIIQALNNEDITIYGDGKQTRSFQYIDDLIEGMVRMM 226 Query: 227 EKGDNEV--FNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEK 284 + D+ NIG V +L + + +TG + V+KP D ++ D AKEK Sbjct: 227 DTEDDFTGPINIGNPNEFPVLELAERVIRMTGSTSKIVFKPLPTDDPKQRQPDIKLAKEK 286 Query: 285 LGWEPKVSLEEGLKLTVEYFR 305 LGW+P V LE+GLK +EYF+ Sbjct: 287 LGWQPTVELEDGLKRMIEYFK 307 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: 245 Number of extensions: 16 Number of successful extensions: 4 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: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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