Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate BPHYT_RS23350 BPHYT_RS23350 NAD-dependent epimerase/dehydratase
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS23350 Length = 343 Score = 185 bits (470), Expect = 1e-51 Identities = 119/319 (37%), Positives = 184/319 (57%), Gaps = 20/319 (6%) Query: 4 LVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLN--RNALFYEQ-----SIEDE- 55 L+TG AGFIGS++++ L++ V+ +DN S+G NL+ R+ + EQ IE + Sbjct: 20 LITGVAGFIGSNLLEALLKLDQTVVGLDNFSTGYQRNLDEVRSVVSPEQWKRFRFIEGDI 79 Query: 56 -EMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIF 114 + + + ++H ++V H AA SV SV +P + NI G L +L + V F + Sbjct: 80 RRLEDCVSAVHGVDHVLHEAALGSVPRSVADPIATHEVNISGFLNMLVAARDAQVSSFTY 139 Query: 115 SSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYANVY 174 +++ YG+++ + P E +I P+SPY + KY+ E+Y FAR YG K LRY N + Sbjct: 140 AASSST-YGDHLGL-PKVEDQIGQPLSPYAVTKYANELYASVFARAYGFKTIGLRYFNAF 197 Query: 175 GPRQDPYGE-AGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAM---EKGD 230 G RQDP G A V+ +T ++ G++V I GDGE RD+ +VD+VV+AN+LA E Sbjct: 198 GKRQDPDGAYAAVIPKWTAALIAGDDVLINGDGETSRDFCFVDNVVQANILAAMSDETAR 257 Query: 231 NEVFNIGTGRGTTVNQLFKLLKEI-----TGYDKEPVYKPPRKGDVRKSILDYTKAKEKL 285 NEV+N+ G TT+ QL+ L+ + DK PV+ P R GDVR S + KA+ L Sbjct: 258 NEVYNVAVGDRTTLIQLYDGLRAVLTDNGVRCDKRPVFGPFRAGDVRHSQANVDKAERLL 317 Query: 286 GWEPKVSLEEGLKLTVEYF 304 G+E ++S EGL + ++ Sbjct: 318 GYENRISFVEGLSRAMPWY 336 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: 262 Number of extensions: 17 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