Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_020175422.1 A3OQ_RS0110900 dTDP-glucose 4,6-dehydratase
Query= BRENDA::F2NQX6 (314 letters) >NCBI__GCF_000385335.1:WP_020175422.1 Length = 355 Score = 137 bits (345), Expect = 4e-37 Identities = 108/335 (32%), Positives = 154/335 (45%), Gaps = 33/335 (9%) Query: 1 MRVLVTGGAGFIGSHLV-HALHQKGIPVAVLDDLS-TGKRAHIPP-----DVPLYQTDIR 53 MR+LVTGGAGFIGS H + + G V +D L+ G A + + + DI Sbjct: 1 MRILVTGGAGFIGSAFCRHLVKEIGADVLNIDKLTYAGNLASLREIDSNANYRFLKADIC 60 Query: 54 DLNAVLHAFQDFQPTHVAHQAAQASVKHSVQNPCKDAEINLLGGLNILEAMRA-----TG 108 D A+ AF FQP V H AA++ V S+ E N++G +LE RA G Sbjct: 61 DRAAIEEAFSSFQPDGVVHLAAESHVDRSITRSGDFVETNVVGTYQMLECARAYWSSLAG 120 Query: 109 TQKIVFAS---TGGAIYGEVPEGRRAPETWPPKPKSPYAASKAAFEHYLEVYRQTHGLTY 165 +K F + +YG + + ET P SPY+ASKAA +H + +T+GL Sbjct: 121 ERKAQFRFLHVSTDEVYGSLGQEGHFQETTAYDPSSPYSASKAAADHLASAWHRTYGLPV 180 Query: 166 TTLRYANVYGPRQDPHGEAGVVAIFTNRLLHAQPVTLYARKEPGDPGCIRDYIHVEDVTR 225 +N YGP P ++ + LH +P+ +Y GD G IRD++ V D R Sbjct: 181 IISNCSNNYGPYHFPE---KLIPLVILNALHGKPLPVY-----GDGGNIRDWLFVADHAR 232 Query: 226 ANLLALETNLEG-TYNVSTGQGRTTEDVLYTIARALG-----TTPR---VTYAPPRDGDL 276 A L G YNV R DV+ + L +PR ++Y R G Sbjct: 233 ALFTILTRGRPGEKYNVGGRNERRNIDVVLRVCETLDLHVPCASPRKSLISYVTDRPGHD 292 Query: 277 EVSVLDPTQLQAH-GWRPQVPFEEGIRRTVAWFRE 310 +D T+L+ GWR + FE GI +T+ W+ E Sbjct: 293 RRYAIDATKLETELGWRAEETFETGIEKTILWYLE 327 Lambda K H 0.318 0.135 0.411 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: 21 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: 355 Length adjustment: 28 Effective length of query: 286 Effective length of database: 327 Effective search space: 93522 Effective search space used: 93522 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: 49 (23.5 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