Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_044408414.1 NA59_RS04185 epimerase
Query= curated2:Q56623 (328 letters) >NCBI__GCF_000934765.1:WP_044408414.1 Length = 345 Score = 246 bits (628), Expect = 6e-70 Identities = 147/339 (43%), Positives = 204/339 (60%), Gaps = 35/339 (10%) Query: 12 ILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNK-DDGLLFEVGDINASTDFELP--- 67 + LTG+TGFVG+ L+ S + V++ VR ++ D + VGD+ D E Sbjct: 3 VFLTGATGFVGSALL-SRFVADGVSVRALVRRRLDGLPDAVEQVVGDLLGFVDVESSPSP 61 Query: 68 ----------LKNTTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKR 117 K VVVH AARAH+M D+ A+PL YR+VN T+ LA+ A +GV R Sbjct: 62 QPSPIEGEGAFKGVDVVVHVAARAHIMRDEVADPLAEYRKVNRGATLALARLAAQAGVGR 121 Query: 118 FIFISSIKVNGEGT----LVGCP------------FKTEDNHAPEDDYGLSKSEAEKQLV 161 F+F+SS+KVNGE T L P F+ +D P D YGLSK EAE+ L+ Sbjct: 122 FVFVSSVKVNGEMTFSHSLSPSPQPSPIEGEGVTKFRPDDKFVPTDPYGLSKYEAEQGLL 181 Query: 162 ALAKDSSMEVVIIRPTIVYGPGVKANFASLMRLVSKGIPLPFGSITQNKRSLVSINNLVD 221 A+A+++ +EVVIIRP +VYGP VK NFAS++ V KG+PLP G++ N RSLV+++NLVD Sbjct: 182 AIARETGVEVVIIRPPLVYGPNVKGNFASMVNWVKKGVPLPLGAVC-NLRSLVALDNLVD 240 Query: 222 LIVTCIDH---PKAANQVFLVSDGHDVSTAEMVRELAIALDKPTWQLPVPIWCYKLFGKL 278 I C D PKAAN+VFL+SDG DVST++++R++A A + LPVP+ + K Sbjct: 241 FIALCADRERSPKAANEVFLISDGVDVSTSDLLRKVAKACGVKSRLLPVPVGLMRFAAKA 300 Query: 279 FGKSDIVDRLTGTLQVDISHTKETLGWKPPQTLQEGFKQ 317 K + DRL G LQVD S ++ LGW+P T+ E ++ Sbjct: 301 LSKGAVADRLFGNLQVDSSKAQDLLGWQPVVTMDEALER 339 Lambda K H 0.318 0.134 0.388 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: 279 Number of extensions: 15 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: 328 Length of database: 345 Length adjustment: 28 Effective length of query: 300 Effective length of database: 317 Effective search space: 95100 Effective search space used: 95100 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 (21.7 bits) S2: 49 (23.5 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