Align UDP-glucose 4-epimerase (EC 5.1.3.2); UDP-N-acetylglucosamine 4-epimerase (EC 5.1.3.7) (characterized)
to candidate CA265_RS25425 CA265_RS25425 NAD-dependent dehydratase
Query= BRENDA::Q9WYX9 (309 letters) >FitnessBrowser__Pedo557:CA265_RS25425 Length = 342 Score = 151 bits (382), Expect = 2e-41 Identities = 99/309 (32%), Positives = 162/309 (52%), Gaps = 11/309 (3%) Query: 3 ILVTGGAGFIGSHVVDKLIENGYGVIVVDNLSSGKVENLNRNALFYEQSIE--DEEMMER 60 IL+TG AGF+GSH+ D+ ++ GY VI +DNL +G + N+ LF ++ E + ++ + Sbjct: 19 ILITGAAGFLGSHLCDRFVKEGYHVIGMDNLITGDMANIEH--LFKLENFEFYNHDVSKF 76 Query: 61 IFSLHRPEYVFHLAAQASVAISVREPARDAKTNIIGSLVLLEKSIKYGVKKFIFSSTGGA 120 + + Y+ H A+ AS ++ P + K +G+ LL + + I S++ Sbjct: 77 VHIPGKLHYILHFASPASPIDYLKIPIQTLKVGSLGTHNLLGLARNKNARMLIASTS--E 134 Query: 121 IYGE-NVKVFPTPETEIPHPISPYGI---AKYSTEMYLEFFAREYGLKYTVLRYANVYGP 176 +YG+ NV P +P+ P G+ AK E + +G++ ++R N YGP Sbjct: 135 VYGDPNVNPQPEEYWGNVNPVGPRGVYDEAKRFQEAITMAYHTFHGVETRIVRIFNTYGP 194 Query: 177 RQDPYGEAGVVAIFTERMLRGEEVHIFGDGEYVRDYVYVDDVVRANLLAMEKGDNEVFNI 236 R + V+ F + LRGE++ IFGDG R + YVDD++ + + NI Sbjct: 195 RMR-LNDGRVLPAFIGQALRGEDLTIFGDGSQTRSFCYVDDLIEGIYRLLMSDYAQPVNI 253 Query: 237 GTGRGTTVNQLFKLLKEITGYDKEPVYKPPRKGDVRKSILDYTKAKEKLGWEPKVSLEEG 296 G T+ Q + + ++TG ++ VYK + D ++ D TKA+ LGWEPKV EG Sbjct: 254 GNPDEITIKQFCEEIIKLTGTTQKIVYKELPQDDPKQRRPDITKARTILGWEPKVGRAEG 313 Query: 297 LKLTVEYFR 305 LK+T EYF+ Sbjct: 314 LKITYEYFK 322 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: 275 Number of extensions: 13 Number of successful extensions: 3 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: 342 Length adjustment: 28 Effective length of query: 281 Effective length of database: 314 Effective search space: 88234 Effective search space used: 88234 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