Align Putative UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_012471395.1 GLOV_RS16655 NAD-dependent epimerase
Query= curated2:Q57664 (305 letters) >NCBI__GCF_000020385.1:WP_012471395.1 Length = 335 Score = 165 bits (417), Expect = 2e-45 Identities = 106/317 (33%), Positives = 171/317 (53%), Gaps = 19/317 (5%) Query: 2 ILVTGGAGFIGSHIVDKLIENNYDVIILDNLTT---GNKNNINPKAEFVNADIRDKDLDE 58 +L+TGG GFIGS++ +L++ V ++D+L GN NI P E V +I D + Sbjct: 9 VLITGGLGFIGSNLAIRLVQLGAQVTLVDSLIPEYGGNLWNIEPVKEQVRVNISDVRDEH 68 Query: 59 KINF--KDVEVVIHQAAQINVRNSVENPVYDGDINVLGTINILEMMRKYD-IDKIVFASS 115 + + + + + + A Q + +S++NP D +IN ++ILE R ++ K+VFAS+ Sbjct: 69 AMKYLIQGQDFLFNLAGQTSHLDSMQNPYPDLEINARAQLSILEACRHHNPAIKLVFAST 128 Query: 116 GGAVYGEPNYLPVDENHPINPLSPYGLSKYVGEEYIKLYNRLYGIEYAILRYSNVYGERQ 175 +YG P YLPVDE HP+ P+ G++K GE Y +YN +YGI ++LR +N YG R Sbjct: 129 R-QMYGAPRYLPVDEKHPLAPVDVNGINKMAGEWYHLVYNNVYGIRASVLRLTNTYGPRM 187 Query: 176 DPK-GEAGVISIFIDKMLKNQSPIIFGDGNQTRDFVYVGDVAKANLMAL---NWKNEIVN 231 K + I+I +L Q ++FGDG Q RDF YV DV +A L+ EI N Sbjct: 188 RVKDARQTFLGIWIRNILTGQPVLVFGDGRQVRDFNYVDDVVEAMLLCAASDAANGEIFN 247 Query: 232 IGTGKETSVNELFDIIKHEIGFRGEAIYDKPRE------GEVYRIYLDIKKAESLGWKPE 285 +G ++ + ++ G A+ P + G+ Y Y IK +LGW+P Sbjct: 248 LGADDPANLQDTAQLLVQAAGQGSFALVPFPPDRKAIDIGDYYADYGKIK--ATLGWQPA 305 Query: 286 IDLKEGIKRVVNWMKNN 302 + L+EG++R + + + + Sbjct: 306 VALQEGLQRTLAYYRTD 322 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: 271 Number of extensions: 11 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: 335 Length adjustment: 28 Effective length of query: 277 Effective length of database: 307 Effective search space: 85039 Effective search space used: 85039 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