Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_038017848.1 G579_RS15595 NAD-dependent dehydratase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000423825.1:WP_038017848.1 Length = 663 Score = 153 bits (386), Expect = 1e-41 Identities = 104/331 (31%), Positives = 169/331 (51%), Gaps = 35/331 (10%) Query: 3 LVTGGAGFIGSHIVDKLIENNYDVIILDNLTT-GNKNNIN-------PKAEFVNADIRDK 54 L+TGGAGFIG+++ +L+ V+ILDNL G + N+ +A F AD+RD Sbjct: 316 LITGGAGFIGTNLAHRLLGMGRPVLILDNLARPGVERNLQWLRDTHGERARFQLADMRDA 375 Query: 55 DLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIVFAS 114 + + E V H AAQ+ V S+ NP++D +N LGTIN+LE +R D V + Sbjct: 376 GAVREAVAR-AEQVYHLAAQVAVTTSLVNPLHDFQVNALGTINLLEAVRAQDAPPPVLIT 434 Query: 115 SGGAVYGE----------PNYLP---------VDENHPINPLSPYGLSKYVGEEYIKLYN 155 S VYG Y P + E P++ SPYG SK ++Y+ Y Sbjct: 435 STNKVYGALEQVGLRLHGKRYEPEQDLLRGRGIGEEAPLDFHSPYGCSKGAADQYVLDYA 494 Query: 156 RLYGIEYAILRYSNVYGERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDV 215 R +G+ A+ R S +YG Q + G ++ F+ + +++Q ++GDG Q RD ++V D+ Sbjct: 495 RSFGLATAVFRMSCIYGPHQFGTEDQGWVAHFLIRAIEDQPITLYGDGMQVRDVLFVEDL 554 Query: 216 AKANLMALN----WKNEIVNIGTGKETSVN--ELFDIIKHEIGFRGEAIYDKPREGEVYR 269 A L+A+ + N+G G SV+ EL ++I G + + R G+ Sbjct: 555 VDALLLAMERMDALSGQAFNMGGGPANSVSLLELIELIAELHGGTPDYRFGPWRVGDQRY 614 Query: 270 IYLDIKKAE-SLGWKPEIDLKEGIKRVVNWM 299 D +K + + GW+P +D++ G++R+ W+ Sbjct: 615 YVSDTRKFQAATGWQPRVDVRTGVRRLYEWL 645 Lambda K H 0.317 0.140 0.405 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: 445 Number of extensions: 16 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: 305 Length of database: 663 Length adjustment: 33 Effective length of query: 272 Effective length of database: 630 Effective search space: 171360 Effective search space used: 171360 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: 51 (24.3 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