Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate GFF3941 PGA1_65p00440 UDP-glucuronate 5'-epimerase
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__Phaeo:GFF3941 Length = 336 Score = 137 bits (345), Expect = 4e-37 Identities = 105/334 (31%), Positives = 156/334 (46%), Gaps = 26/334 (7%) Query: 3 ALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEH-----LADNSAHVFVEADI 57 AL+TG+AGFIG L DRLLA G V+GLD + L+ LA+ + + + Sbjct: 4 ALITGSAGFIGYHLADRLLAAGWRVIGLDCLSPYYDVRLKECRHARLAEYAGFTPIIGKL 63 Query: 58 VTAD-LHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGVRKI 116 D L + H+P+ V HLAAQ VR S+ P+ N+IGT L EAAR + Sbjct: 64 EDPDRLMGLFATHKPDAVIHLAAQAGVRHSIDAPRDYLEANLIGTFELLEAARAHPPAHM 123 Query: 117 VHTSSGGSIYGTPPEYPTPETAPTD-PASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPAN 175 + +S S YG + P E D S YAA K AGE +++ HLYGL + Sbjct: 124 L-IASTSSAYGANTQMPFDERQQADHQMSFYAATKKAGETMAHSYAHLYGLPTTMFRFFT 182 Query: 176 VYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAFVRVSADVGGG 235 VYGP P + F QA+ +G+P V+ G +RD+ ++DD+V + V G Sbjct: 183 VYGPWGRPD---MALFKFTQAMQAGQPIDVYNHGRMSRDFTYIDDLVAGITGLIDAVPGD 239 Query: 236 LR---------------FNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCL 280 NIG + T + +A+ A+G + GD+ + Sbjct: 240 QPVSEQDNLSPVAPFRVVNIGASRPTPLMEYIAALETALGITAQKNLMEMQPGDVPATWA 299 Query: 281 DIGLAERVLGWRPQIELADGVRRTVEYFRHKHTD 314 D L ++ G+ PQ+ + +GV R V ++R + D Sbjct: 300 DTSLLNQLTGYEPQVPVEEGVARFVTWYRAYYGD 333 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: 262 Number of extensions: 14 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: 336 Length adjustment: 28 Effective length of query: 286 Effective length of database: 308 Effective search space: 88088 Effective search space used: 88088 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: 48 (23.1 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