Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_029000185.1 H537_RS0125960 NAD-dependent epimerase
Query= BRENDA::P9WN67 (314 letters) >NCBI__GCF_000430725.1:WP_029000185.1 Length = 335 Score = 144 bits (364), Expect = 2e-39 Identities = 106/334 (31%), Positives = 160/334 (47%), Gaps = 29/334 (8%) Query: 1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNF-----ATGRATNLEHLADNSAHVFVEA 55 M+ LVTGAAGFIG V RLL G VVG+DN + L+ L ++ F++ Sbjct: 1 MKVLVTGAAGFIGMATVLRLLERGDEVVGVDNLNDYYDVNLKLARLQQLQPHAGFRFLKL 60 Query: 56 DIV-TADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVR 114 DI A + + + R + V HLAAQ VR S+ +P N++G V + E R T V+ Sbjct: 61 DIADRAGMETLFKAERFDRVVHLAAQAGVRYSLLNPNAYVDSNLVGFVNVLEGCRHTQVQ 120 Query: 115 KIVHTSSGGSIYGTPPEYPTPETAPTD-PASPYAAGKVAGEIYLNTFRHLYGLDCSHIAP 173 +V+ SS S+YG + P E+ D P S YAA K A E+ +T+ HLY L + + Sbjct: 121 HLVYASS-SSVYGGNVKMPFSESDGVDHPVSLYAATKKANELMAHTYSHLYKLPTTGLRF 179 Query: 174 ANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRV----- 228 VYGP P +F +A+L +P VF G RD+ +VDD+V+ +RV Sbjct: 180 FTVYGPWGRPD---MAPILFTKAILENRPIDVFNQGRMRRDFTYVDDIVEGVIRVLDRAA 236 Query: 229 ---------SADVGGGLR----FNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDL 275 + D G NIG + S + + A+G D P + GD+ Sbjct: 237 TPDEGFDPHAPDPGRSHAPYRVVNIGNNEPVSLMEFIECIEQALGRQADKRMLPMQNGDV 296 Query: 276 KRSCLDIGLAERVLGWRPQIELADGVRRTVEYFR 309 + D+ + + + P+ + +GV R V ++R Sbjct: 297 PATYADVDALKAWVDFAPRTGIREGVARFVAWYR 330 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: 241 Number of extensions: 16 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: 314 Length of database: 335 Length adjustment: 28 Effective length of query: 286 Effective length of database: 307 Effective search space: 87802 Effective search space used: 87802 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