Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate N515DRAFT_4257 N515DRAFT_4257 UDP-glucuronate 4-epimerase
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Dyella79:N515DRAFT_4257 Length = 348 Score = 150 bits (380), Expect = 3e-41 Identities = 103/335 (30%), Positives = 166/335 (49%), Gaps = 30/335 (8%) Query: 1 MRALVTGAAGFIGSTLVDRLLADGHSVVGLDN----FATG-RATNLEHLADNSAHVFVEA 55 M+ LVTG AGFIGS + +LLA G V+GLDN + G + L + + V A Sbjct: 1 MKVLVTGTAGFIGSHVARKLLARGDEVIGLDNLNDYYDVGLKQARLARVQAYPGYTHVHA 60 Query: 56 DIVT-ADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVR 114 D+ A + + H+PE V +LAAQ VR + +P + NV G + + E RQ GV+ Sbjct: 61 DLADRAAVEKLFATHKPERVVNLAAQAGVRYAATNPHVYVSSNVTGFLHILEGCRQHGVQ 120 Query: 115 KIVHTSSGGSIYGTPPEYPTPETAPTD-PASPYAAGKVAGEIYLNTFRHLYGLDCSHIAP 173 +V S+ S+YG + P E P + P + YAA K A E +++ HLYG+ + + Sbjct: 121 HLVFASTS-SVYGANRDLPFSEHRPAEHPLTLYAATKKANEQMAHSYAHLYGVPATGLRF 179 Query: 174 ANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSADVG 233 VYGP P + +F QA+L+G+P RVF +G + R + ++DD+V+ VR V Sbjct: 180 FTVYGPWGRPDM---ALFLFTQAILAGEPIRVFNEGRHKRSFTYIDDIVEGVVRALDTVP 236 Query: 234 G---------------GLR----FNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGD 274 G G+ +NIG + + + +G E P + GD Sbjct: 237 GKDPAWDATQPDPSTSGVAPYRLYNIGNEQPVELLRYIEVLEQYLGRKATMELLPLQAGD 296 Query: 275 LKRSCLDIGLAERVLGWRPQIELADGVRRTVEYFR 309 + + D+ +G+RP++ + +G+ V+++R Sbjct: 297 VPETEADVSSLVAAVGYRPKVSVEEGIAAFVDWYR 331 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: 289 Number of extensions: 18 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: 348 Length adjustment: 28 Effective length of query: 286 Effective length of database: 320 Effective search space: 91520 Effective search space used: 91520 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