Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate 5211288 Shew_3704 dTDP-glucose 4,6-dehydratase (RefSeq)
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__PV4:5211288 Length = 356 Score = 129 bits (324), Expect = 1e-34 Identities = 102/331 (30%), Positives = 152/331 (45%), Gaps = 29/331 (8%) Query: 4 LVTGAAGFIGSTLVDRLLA-DGHSVVGLDNFA-TGRATNLEHLADNSAHVFVEADIVTAD 61 L+TG AGFIGS L+ L+A G VV D G +LE +A + F++ADI D Sbjct: 15 LITGGAGFIGSALIRHLIALGGCRVVNYDKLTYAGNLASLESIAQAPNYHFIQADINDGD 74 Query: 62 -LHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAAR--------QTG 112 L L Q++ ++V HLAA+ V RS+ P+ N++GT L + + Sbjct: 75 TLGGALRQYQIDLVIHLAAETHVDRSIEGPRAFIGTNIVGTFELLQQCLDYYRKLPIEIA 134 Query: 113 VRKIVHTSSGGSIYGTPPEYPT---PETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCS 169 R +H S ++G E +P P+SPY+A K A + + + YGL Sbjct: 135 ARFRLHHVSTDEVFGDLGSDEAGYFSEQSPYAPSSPYSASKAAADHLVRAWHRTYGLPVV 194 Query: 170 HIAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVS 229 +N YGP Q P V + A L GK V+GDG RD+++VDD A +V+ Sbjct: 195 LSNCSNNYGPYQYPEKLIPVTLLNA---LQGKLIPVYGDGKQIRDWLYVDDHAHALCQVA 251 Query: 230 ADVGGGLRFNIGTGKETSDRQLHSAVAAAVG--------GPDDPE----FHPPRLGDLKR 277 A G +NIG E ++ ++ S + + G D F R G R Sbjct: 252 ARGELGESYNIGGMNEMTNLEVVSLICDLLNQKVTEKPCGISDFRQLIGFVKDRPGHDTR 311 Query: 278 SCLDIGLAERVLGWRPQIELADGVRRTVEYF 308 +D R LGW+P A G+ +TV+++ Sbjct: 312 YAIDASKLSRTLGWQPSESFASGLEKTVDWY 342 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: 246 Number of extensions: 9 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: 356 Length adjustment: 28 Effective length of query: 286 Effective length of database: 328 Effective search space: 93808 Effective search space used: 93808 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