Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_092486399.1 BM299_RS15450 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_900115975.1:WP_092486399.1 Length = 322 Score = 181 bits (459), Expect = 2e-50 Identities = 112/311 (36%), Positives = 167/311 (53%), Gaps = 15/311 (4%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSS--------GKVENLNR--NALFYEQSI 52 ILVTG AGFIGS V + L+ GY VI +DNL+ +++NL + N FY+ I Sbjct: 4 ILVTGAAGFIGSKVSELLLTQGYNVIGIDNLNEYYDVRLKLWRLDNLKKYTNFKFYQVDI 63 Query: 53 EDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKF 112 E+ E ++ I+ LH + V + AA+A V S+ P TN G L +LE +Y V KF Sbjct: 64 ENVEALKIIYQLHCLDAVINEAARAGVRYSLENPHIYFSTNAAGCLNILELCREYKVPKF 123 Query: 113 IFSSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYAN 172 I +ST G+ + + + PISPY +K S E + YGL TVLRY Sbjct: 124 ILASTSSLYAGQETPFYE--DLPVNTPISPYAASKKSAEAMAYTYHYLYGLDVTVLRYFT 181 Query: 173 VYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGDNE 232 VYGP P F + ++ G + I+GDG RD+ Y+DD+ R + A++ + Sbjct: 182 VYGPAGRPDMS---YFRFIKWIMEGSPLEIYGDGSQSRDFTYIDDIARGTINALKPMGYK 238 Query: 233 VFNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVS 292 V N+G ++++ +L+++ TG YK K D+ + D +KA+ LGWEP +S Sbjct: 239 VINLGNSNPDRLSRMIQLIEKYTGNKARFKYKEFHKADMSATWADISKARLVLGWEPMIS 298 Query: 293 LEEGLKLTVEY 303 LEEG+K TV++ Sbjct: 299 LEEGIKNTVDW 309 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: 255 Number of extensions: 12 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: 322 Length adjustment: 27 Effective length of query: 282 Effective length of database: 295 Effective search space: 83190 Effective search space used: 83190 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