Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate WP_084260329.1 Q394_RS0103155 Vi polysaccharide biosynthesis UDP-N-acetylglucosaminuronic acid C-4 epimerase TviC
Query= BRENDA::Q9WYX9 (309 letters) >NCBI__GCF_000621325.1:WP_084260329.1 Length = 344 Score = 177 bits (450), Expect = 2e-49 Identities = 118/325 (36%), Positives = 179/325 (55%), Gaps = 30/325 (9%) Query: 4 LVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNR-----------NALFYEQSI 52 LVTG AGFIGS++++ L++ V+ +DN ++G NL+ N F I Sbjct: 21 LVTGVAGFIGSNLLETLLKLNQRVVGLDNFATGHQHNLDEVQSLVNREQWANFRFIRGDI 80 Query: 53 EDEEMMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKF 112 ++ + + +YV H AA SV S+ +P TNI G L +L + VK+F Sbjct: 81 R--QLSDCQAACEGVDYVLHQAALGSVPRSLEDPITTNGTNIDGFLNMLVAARDAQVKRF 138 Query: 113 IFSSTGGAIYGENVKVFPTPETEIPHPISPYGIAKYSTEMYLEFFAREYGLKYTVLRYAN 172 +++++ YG++ P E I P+SPY + KY E+Y + FAR YG LRY N Sbjct: 139 VYAASSST-YGDH-PALPKIEENIGKPLSPYAVTKYVNELYADVFARTYGFNTIGLRYFN 196 Query: 173 VYGPRQDPYGE-AGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLA--MEKG 229 ++G RQDP G A V+ + M++ E V+I GDGE RD+ Y+D+ V+ANLLA E Sbjct: 197 IFGKRQDPDGAYAAVIPKWIASMIKNEPVYINGDGETSRDFCYIDNAVQANLLAATAENT 256 Query: 230 D--NEVFNIGTGRGTTVNQLFKLLKE--------ITGYDKEPVYKPPRKGDVRKSILDYT 279 D N+V+N+ G TT+N+LF L E + G+ EP Y+ R GDVR S+ D + Sbjct: 257 DATNQVYNVAVGDRTTLNELFWHLHENLLPRFAHLQGF--EPNYRDFRAGDVRHSLADMS 314 Query: 280 KAKEKLGWEPKVSLEEGLKLTVEYF 304 KA++ LG++ + EGL T+ ++ Sbjct: 315 KAQQLLGYQATHRIGEGLVTTMPWY 339 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: 17 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: 344 Length adjustment: 28 Effective length of query: 281 Effective length of database: 316 Effective search space: 88796 Effective search space used: 88796 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