Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_011033111.1 MM_RS06035 UDP-glucose 4-epimerase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000007065.1:WP_011033111.1 Length = 334 Score = 212 bits (540), Expect = 8e-60 Identities = 120/317 (37%), Positives = 180/317 (56%), Gaps = 18/317 (5%) Query: 2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTTG-----NKNNIN-----PKAEFVNADI 51 I++TGGAGFIGSHI + L ++ ++++I+DNL K N+N A F+NAD+ Sbjct: 4 IVITGGAGFIGSHIAENLAKDGHEIVIVDNLDPYYSVDLKKKNLNIALNSGDATFINADV 63 Query: 52 RDKDLDEKINFKDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYDIDKIV 111 D + + V+ V H+AAQ VR SVE+P D+NV GT+N+L+ + K++ Sbjct: 64 TDLSGIKDVIDSTVDYVYHEAAQAGVRISVEDPFKPNDVNVHGTLNVLKASLDAGVKKVI 123 Query: 112 FASSGGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVY 171 ASS +VYG+ YLP DE HP P+SPYG+SK E Y +++ +YG+ LRY VY Sbjct: 124 NASSS-SVYGKVKYLPFDEQHPTEPVSPYGVSKLAAEHYCRVFYEVYGLPTTSLRYFTVY 182 Query: 172 GERQDPKGEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMALNWK---NE 228 G R P ISIF KML N+ +FGDG QTRDF Y+ DV +AN L + + Sbjct: 183 GPRMRPD---LAISIFTRKMLANEPITVFGDGEQTRDFTYIEDVVEANKRLLYNRATDGK 239 Query: 229 IVNIGTGKETSVNELFDIIKHEIGFRGEAIYDKPREGEVYRIYLDIKKAES-LGWKPEID 287 ++NIG G SVN L + ++ G E I ++G+ ++ + +G+ P + Sbjct: 240 VLNIGGGNRISVNNLIENLRFITGSTSEIINADKQKGDTEDTLANVDLGNNMIGYTPLFN 299 Query: 288 LKEGIKRVVNWMKNNNR 304 + +G+ + V+W K N+ Sbjct: 300 INKGLNKFVDWFKTENQ 316 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: 343 Number of extensions: 22 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: 305 Length of database: 334 Length adjustment: 28 Effective length of query: 277 Effective length of database: 306 Effective search space: 84762 Effective search space used: 84762 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