Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate Echvi_3799 Echvi_3799 Nucleoside-diphosphate-sugar epimerases
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Cola:Echvi_3799 Length = 314 Score = 140 bits (352), Expect = 5e-38 Identities = 100/316 (31%), Positives = 169/316 (53%), Gaps = 17/316 (5%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIEDEEMMERIF 62 ILVTGG+GF+GSH+ D+L++ G V+ VDNL +G+ N++ L E++ E + F Sbjct: 4 ILVTGGSGFLGSHLCDRLLKEGNEVLCVDNLFTGRKSNIHH--LLDEKNFEFLR-HDITF 60 Query: 63 SLH-RPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGAI 121 L+ + +++LA AS +P + AKT++IG++ +L + + V+ I ++ + Sbjct: 61 PLYVEVDEIYNLACPASPVHYQFDPVQTAKTSVIGAINMLGLAKRLKVR--ILQASTSEV 118 Query: 122 YGENVKVFPTPETEIPHPISPYGI------AKYSTEMYLEFFAREYGLKYTVLRYANVYG 175 YG+ ++ P PE+ ++ GI K E + R++G+ V+R N YG Sbjct: 119 YGD-PELHPQPES-YKGSVNTTGIRACYDEGKRCAETLFFDYHRQHGVDIKVMRIFNTYG 176 Query: 176 PRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRA--NLLAMEKGDNEV 233 PR P + VV+ F + L+GE++ IFGDG R + YV+D++ L+ G Sbjct: 177 PRMHP-NDGRVVSNFIVQALKGEDITIFGDGLQTRSFCYVEDLIEGMYRLMNSRDGFTGP 235 Query: 234 FNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSL 293 NIG T+ +L + + ++ G + + P + D + AK++LGWEPKV L Sbjct: 236 VNIGNPGEFTMLELAQEILDLVGSGSQLKFLPLPQDDPMQRQPIIHMAKKELGWEPKVRL 295 Query: 294 EEGLKLTVEYFRKTLE 309 EGL T+ YF + L+ Sbjct: 296 REGLIETINYFDRILK 311 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: 260 Number of extensions: 12 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: 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 Apr 09 2024. 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