Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_026606975.1 METAC_RS0110355 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000427445.1:WP_026606975.1 Length = 333 Score = 125 bits (315), Expect = 1e-33 Identities = 98/315 (31%), Positives = 144/315 (45%), Gaps = 19/315 (6%) Query: 2 RALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTAD 61 R LVTG AGF+GS L RLL GH V+ +DNF+TG N+E L + + + VT Sbjct: 7 RILVTGGAGFLGSHLCRRLLNQGHEVLCVDNFSTGTRRNIEELISDPRFELLRHN-VTFP 65 Query: 62 LHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSS 121 L +++ +++LA DP +V G + + A++ VR + +S Sbjct: 66 LFVEVDE-----IYNLACPASPIHYQFDPVQTTKTSVSGAINMLGLAKRLKVR--ILQAS 118 Query: 122 GGSIYGTPPEYPTPE-----TAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANV 176 +YG P +P E P S Y GK E + + + N Sbjct: 119 TSEVYGDPIVHPQTEDYWGNVNPIGSRSCYDEGKRCAETLFFDYHRQHKMSIKVARIFNT 178 Query: 177 YGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRV---SADVG 233 YGP P V QALL G+ +FG G TR + +V D++D R+ +V Sbjct: 179 YGPNMRPDDGRVVSNFICQALL-GEDITIFGRGEQTRSFCYVTDLIDGLDRLMNSPEEVT 237 Query: 234 GGLRFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRP 293 G + NIG E + R+L V A G P D K+ +I +AE++LGWRP Sbjct: 238 GPI--NIGNPGEFTIRELAEKVIALTGSQSKLVERPLPEDDPKQRQPNIEVAEKLLGWRP 295 Query: 294 QIELADGVRRTVEYF 308 I+L +G+ RT+ YF Sbjct: 296 TIKLDEGLVRTIAYF 310 Lambda K H 0.320 0.137 0.410 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: 251 Number of extensions: 9 Number of successful extensions: 3 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: 314 Length of database: 333 Length adjustment: 28 Effective length of query: 286 Effective length of database: 305 Effective search space: 87230 Effective search space used: 87230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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