Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate Ga0059261_3117 Ga0059261_3117 UDP-glucuronate decarboxylase
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Korea:Ga0059261_3117 Length = 310 Score = 150 bits (378), Expect = 5e-41 Identities = 105/319 (32%), Positives = 165/319 (51%), Gaps = 23/319 (7%) Query: 2 NILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENL-----NRNALFYEQSIEDEE 56 ++LVTGG+GF+GSH+ D+L+E G V+ VDN +G N+ N N + Sbjct: 3 HVLVTGGSGFLGSHLCDRLLERGNDVLCVDNFFTGAKRNIAHLLGNPNFELLRHDVTWPL 62 Query: 57 MMERIFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSS 116 +E + +++LA AS +P + KT++ G++ +L + +K I + Sbjct: 63 YVE-------VDQIYNLACPASPIHYQHDPVQTTKTSVHGAINML--GLAKRLKARIMQA 113 Query: 117 TGGAIYGENVKVFPTPETEIP--HPISP---YGIAKYSTEMYLEFFAREYGLKYTVLRYA 171 + +YG+ +V P E+ +PI P Y K E + R++ L V+R Sbjct: 114 STSEVYGDP-EVHPQRESYWGRVNPIGPRSCYDEGKRCAETLFFDYYRQHQLDVKVVRIF 172 Query: 172 NVYGPRQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAM--EKG 229 N YGPR P + VV+ F + LRGE++ I+G+G R + YVDD++ L M E+G Sbjct: 173 NTYGPRMHP-NDGRVVSNFIVQALRGEDITIYGEGHQSRSFCYVDDLLEGFLAMMDSEEG 231 Query: 230 DNEVFNIGTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEP 289 N+G T+ +L + + G + V++P D ++ D T AK KLGWEP Sbjct: 232 FAGPVNLGNPGEFTMLELADKVLSLVGSKSKMVFQPLPVDDPKQRQPDITLAKSKLGWEP 291 Query: 290 KVSLEEGLKLTVEYFRKTL 308 KVSLE+GLK T+ YFR+ L Sbjct: 292 KVSLEDGLKETIAYFRQVL 310 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: 254 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: 310 Length adjustment: 27 Effective length of query: 282 Effective length of database: 283 Effective search space: 79806 Effective search space used: 79806 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