Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate PP_1785 PP_1785 dTDP-glucose 4,6-dehydratase 2
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Putida:PP_1785 Length = 366 Score = 135 bits (340), Expect = 1e-36 Identities = 105/340 (30%), Positives = 152/340 (44%), Gaps = 39/340 (11%) Query: 4 LVTGAAGFIGSTLVDRLLADGHS-VVGLDNFA-TGRATNLEHLADNSAHVFVEADIVTAD 61 LVTG AGFIGS V + A V+ LD G NL+ L N H FV+ +I A Sbjct: 3 LVTGGAGFIGSNFVLQWCAHNEEPVLNLDALTYAGNLANLQPLEGNPQHRFVQGNICDAA 62 Query: 62 LHA-ILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAAR---------QT 111 L + +HRP V H AA+ V RS+ P+ NV+GT RL EAAR + Sbjct: 63 LLTKLFAEHRPRAVVHFAAESHVDRSITGPEAFVETNVMGTFRLLEAARAHWNSLEGAEK 122 Query: 112 GVRKIVHTSSGGSIYGT--PPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCS 169 + +H S+ +YGT P + ET P P SPY+A K A + + ++ H YG+ Sbjct: 123 EAFRFLHVST-DEVYGTLGPNDPAFTETTPYAPNSPYSASKAASDHLVRSYFHTYGMPVL 181 Query: 170 HIAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVS 229 +N YGP P ++ + L+GK V+GDG RD+++V+D RV Sbjct: 182 TTNCSNNYGPLHFPE---KLIPLMIVNALAGKALPVYGDGQQIRDWLYVEDHCSGIRRVL 238 Query: 230 ADVGGGLRFNIGTGKETSDRQL----------------HSAVAAAVGGPDDP-----EFH 268 G +NIG E ++ + + G P + + Sbjct: 239 EAGAFGETYNIGGWNEKANIDIVRTLCSLLDEMAPAASRQVINQKTGEPVEQYAELIAYV 298 Query: 269 PPRLGDLKRSCLDIGLAERVLGWRPQIELADGVRRTVEYF 308 R G +R +D ER LGW+P G+R+TV ++ Sbjct: 299 TDRPGHDRRYAIDARKIERELGWKPAETFETGIRKTVAWY 338 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: 2 Number of HSP's successfully gapped: 2 Length of query: 314 Length of database: 366 Length adjustment: 28 Effective length of query: 286 Effective length of database: 338 Effective search space: 96668 Effective search space used: 96668 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