Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate Ga0059261_3099 Ga0059261_3099 dTDP-glucose 4,6-dehydratase (EC 4.2.1.46)
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Korea:Ga0059261_3099 Length = 352 Score = 152 bits (384), Expect = 1e-41 Identities = 112/327 (34%), Positives = 160/327 (48%), Gaps = 25/327 (7%) Query: 4 LVTGAAGFIGSTLVDRLLADGHSVVGLDNFA-TGRATNLEHLADNSAHVFVEADIVTADL 62 LVTG AGFIGS +V RL+ G VV LD G +L L +H FV DI A L Sbjct: 5 LVTGGAGFIGSAVVRRLVRKGLRVVNLDKLTYAGNRASLRELDAAPSHRFVHGDIADAPL 64 Query: 63 H-AILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAA-----RQTGVRKI 116 ++L + R + + HLAA+ V RS+A P NV+GT RL AA + G ++ Sbjct: 65 VLSLLREERADAIMHLAAESHVDRSIARPGTFVETNVVGTFRLLSAALDYWRKLKGAKRD 124 Query: 117 V---HTSSGGSIYGTPPEYPT--PETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHI 171 H S +YG P ET P P+SPY+A K AG+ ++ T+R YGL Sbjct: 125 TFRFHHISTDEVYGDLPYGGGMFTETTPYAPSSPYSASKAAGDHFVRTWRTTYGLPVVLS 184 Query: 172 APANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSAD 231 +N YGP Q P ++ + ++G+ V+G G N RD++ VDD DA RV Sbjct: 185 NCSNNYGPYQFPE---KLIPLTILNAITGRSLPVYGKGENVRDWLHVDDHADALERVLTG 241 Query: 232 VGGGLRFNIGTGKETSDRQLHSAVAAAV-------GG---PDDPEFHPPRLGDLKRSCLD 281 G +N+G G E ++ Q+ A+ + GG D F R G +R +D Sbjct: 242 GTVGESYNVGGGNERTNLQVVEAICDLIDARMPLPGGRSRRDLIRFVADRPGHDRRYAID 301 Query: 282 IGLAERVLGWRPQIELADGVRRTVEYF 308 E LGW+ Q+ G+ +TV+++ Sbjct: 302 PAKIESELGWKAQLHFDTGLAQTVDWY 328 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: 265 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: 352 Length adjustment: 28 Effective length of query: 286 Effective length of database: 324 Effective search space: 92664 Effective search space used: 92664 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