Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_013537555.1 THEAM_RS04055 epimerase
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000185805.1:WP_013537555.1 Length = 314 Score = 231 bits (590), Expect = 1e-65 Identities = 135/306 (44%), Positives = 200/306 (65%), Gaps = 12/306 (3%) Query: 1 MNILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENL--NRNALFYEQSIEDEEMM 58 M++LVTGGAGFIGSH+V+ L+ G V+V+D+LS+GK+ NL + + F + S+ DEE++ Sbjct: 1 MSVLVTGGAGFIGSHLVEVLLSQGREVVVLDDLSTGKLSNLPDSSSLEFVKGSVTDEELV 60 Query: 59 ERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTG 118 R+F VFHLAA ASV SV EP + N G+L LL+ ++ GVK+FIF+S+ Sbjct: 61 RRLFEEFNFSSVFHLAAVASVQRSVEEPLYCHRVNCDGTLYLLQSAVSRGVKRFIFASS- 119 Query: 119 GAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVYGPRQ 178 A+YG+ + P E P++PY + KY++E Y+ R YGL+ LR+ NV+G RQ Sbjct: 120 AAVYGD-LPQLPKREEMPVSPLTPYAVDKYASERYVVNSFRLYGLEGVALRFFNVFGERQ 178 Query: 179 DPYGE-AGVVAIFTERM---LRGE--EVHIFGDGEYVRDYVYVDDVVRANLLAMEKG-DN 231 DP +GV++IF +R+ L GE V IFGDG RD++YV DVV A L+A E+G Sbjct: 179 DPSSPYSGVISIFIDRVKRYLTGEPVTVDIFGDGRQTRDFIYVKDVVSALLIAEERGVPG 238 Query: 232 EVFNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKV 291 EV+N+GTG+ T++ +L +++I G E + P R GD+++S+ D +K EKLG+ P+ Sbjct: 239 EVYNVGTGKETSLLELLDYIRDIVGTLPEIRFLPERPGDIKRSVADISKL-EKLGFSPRF 297 Query: 292 SLEEGL 297 S++EGL Sbjct: 298 SVKEGL 303 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: 271 Number of extensions: 18 Number of successful extensions: 6 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: 314 Length adjustment: 27 Effective length of query: 282 Effective length of database: 287 Effective search space: 80934 Effective search space used: 80934 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