Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 3610730 Dshi_4115 dTDP-glucose 4,6-dehydratase (RefSeq)
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Dino:3610730 Length = 346 Score = 156 bits (394), Expect = 8e-43 Identities = 109/325 (33%), Positives = 158/325 (48%), Gaps = 20/325 (6%) Query: 1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRAT-NLEHLADNSAHVFVEADIVT 59 M+ LVTG AGFIGS +V + + DGH VV LD N+ +AD+ A+ F DI Sbjct: 1 MKLLVTGGAGFIGSAVVRQAIRDGHQVVNLDALTYAACLDNVASVADSPAYAFEHVDIRD 60 Query: 60 -ADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRK--- 115 A L + H P+ V HLAA+ V RS+ P N+ GT + EAAR V + Sbjct: 61 RAALDRVFATHAPDAVMHLAAESHVDRSIDGPGDFIETNITGTYNMLEAARSHWVGQGRP 120 Query: 116 ---IVHTSSGGSIYGT-PPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHI 171 H S ++G+ P E P DP SPY+A K A + + + YGL Sbjct: 121 EDFRFHHISTDEVFGSLGPTGQFTEETPYDPRSPYSASKAASDHLVRAWHETYGLPVVMT 180 Query: 172 APANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSAD 231 +N YGP P V+ + A L+G+P ++GDG+N RD+++V+D DA + V Sbjct: 181 NCSNNYGPFHFPEKLVPVIILKA---LAGEPLPIYGDGSNVRDWLYVEDHADALLLVVQK 237 Query: 232 VGGGLRFNIGTGKETSDRQLHSAVAAAVG----GP----DDPEFHPPRLGDLKRSCLDIG 283 G +NIG E ++ QL + + GP + F R G R +D Sbjct: 238 GVVGRSYNIGGENERTNLQLVQTLCGILDELRPGPRPYAEQISFVTDRPGHDARYAIDPT 297 Query: 284 LAERVLGWRPQIELADGVRRTVEYF 308 LGWRP + + +G+RRTV+++ Sbjct: 298 RIATELGWRPSVTVEEGLRRTVQWY 322 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: 268 Number of extensions: 15 Number of successful extensions: 6 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: 346 Length adjustment: 28 Effective length of query: 286 Effective length of database: 318 Effective search space: 90948 Effective search space used: 90948 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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