Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate GFF1784 Psest_1823 Nucleoside-diphosphate-sugar epimerases
Query= curated2:Q56623 (328 letters) >FitnessBrowser__psRCH2:GFF1784 Length = 313 Score = 315 bits (807), Expect = 9e-91 Identities = 162/307 (52%), Positives = 215/307 (70%), Gaps = 1/307 (0%) Query: 11 SILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLKN 70 ++LLTG+ GF+G +V L + + AVR + + F VGD+ + D+ PL Sbjct: 2 NVLLTGANGFLGRAIVAHLCRQDRITLSCAVRSPLAQVRFATFAVGDLCGANDWSQPLLG 61 Query: 71 TTVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGEG 130 VV+H AARAH+M D+ A+PL+ YR VN GT+NLA+QA +GV+RFI+ISSIKVNGE Sbjct: 62 QQVVIHAAARAHIMKDELADPLSEYRLVNVEGTLNLARQAAAAGVERFIYISSIKVNGES 121 Query: 131 TLVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFAS 190 T +G PF + D APED YGLSK EAE+ L+ LA ++ MEVVIIRP +VYGPGVK NFAS Sbjct: 122 TPLGKPFVSSDAPAPEDPYGLSKLEAEQGLMQLAAETGMEVVIIRPPLVYGPGVKGNFAS 181 Query: 191 LMRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQVFLVSDGHDVSTAEM 250 +++L+ +GIPLPFG+I NKRSLV ++NLVDLI+ C+DHP AANQ+FL DG D+ST E+ Sbjct: 182 MIKLIDRGIPLPFGAI-HNKRSLVGVDNLVDLIIRCVDHPAAANQIFLAGDGKDLSTTEL 240 Query: 251 VRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQT 310 + + A+DKP +P P +L L GK + RL G+LQVDIS T E L WKPP T Sbjct: 241 LLGVGKAMDKPAKLIPAPAGFLQLGATLLGKKAMAQRLLGSLQVDISKTCELLDWKPPYT 300 Query: 311 LQEGFKQ 317 ++EG ++ Sbjct: 301 VEEGLRR 307 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: 269 Number of extensions: 7 Number of successful extensions: 2 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: 313 Length adjustment: 28 Effective length of query: 300 Effective length of database: 285 Effective search space: 85500 Effective search space used: 85500 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: 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