Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_005454693.1 SACCYDRAFT_RS06500 NAD-dependent epimerase/dehydratase family protein
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000244975.1:WP_005454693.1 Length = 326 Score = 137 bits (346), Expect = 3e-37 Identities = 106/315 (33%), Positives = 144/315 (45%), Gaps = 15/315 (4%) Query: 4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTADLH 63 +V G AGF+GS + +RLL G+ V +D+ TG N+ L N+ VE D VT L Sbjct: 9 VVIGGAGFVGSHVCERLLRSGYRVTCVDSLVTGSVDNVSALRHNAGFRLVELD-VTRPLS 67 Query: 64 AILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKIVHTSSGG 123 E P V HLA+ + P V +GT E A + G R ++ ++S Sbjct: 68 EWPEMPAPGSVLHLASPASPKDYQRLPIETLRVGAVGTENALELATRHGARFLLTSTS-- 125 Query: 124 SIYGTPPEYPTPETA-----PTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANVYG 178 +YG P E+P E+ P P S Y K E + G D + N YG Sbjct: 126 EVYGDPAEHPQNESYWGNVNPIGPRSVYDEAKRYAEALTMAYHRQRGTDVAIARIFNTYG 185 Query: 179 PRQDPHGEAG-VVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRV-SADVGGGL 236 PR G+ G ++ F LSG P V G GT TR +VDD V + + +D+ G + Sbjct: 186 PRM--RGDDGRMIPNFITQALSGAPLTVAGTGTQTRSVCYVDDTVSGLLALWRSDLTGPV 243 Query: 237 RFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRPQIE 296 NIG E + R L V A G P + D +R C DI LA LGW P+ Sbjct: 244 --NIGNPHELTVRHLAEEVRAITGTASAITSVPGAVDDPRRRCPDITLARTKLGWEPETG 301 Query: 297 LADGVRRTVEYF-RH 310 L +G+ RTV +F RH Sbjct: 302 LREGLNRTVAWFARH 316 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: 252 Number of extensions: 11 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: 314 Length of database: 326 Length adjustment: 28 Effective length of query: 286 Effective length of database: 298 Effective search space: 85228 Effective search space used: 85228 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