Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate AO353_11885 AO353_11885 dTDP-glucose 4,6-dehydratase
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11885 Length = 360 Score = 149 bits (376), Expect = 1e-40 Identities = 109/335 (32%), Positives = 164/335 (48%), Gaps = 32/335 (9%) Query: 1 MRALVTGAAGFIGSTLVDRLLADG-HSVVGLDNFA-TGRATNLEHLADNSAHVFVEADIV 58 MR L+TG AGFIGS LV L+ H V+ LD G +L +A N+ + FV+ADIV Sbjct: 1 MRILITGGAGFIGSALVRHLIRHTEHEVLNLDKLTYAGNLESLSSIATNTRYEFVQADIV 60 Query: 59 T-ADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAAR-------- 109 A + A+L + +P + HLAA+ V RS+ P N++GT L EA R Sbjct: 61 DQATVSAVLARFQPHAIMHLAAESHVDRSIDGPSDFIQTNIVGTYSLLEATRAYWNSLAE 120 Query: 110 -QTGVRKIVHTSSG---GSIYGTPPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYG 165 + + H S+ G ++G + ET P P+SPY+A K A + + ++ YG Sbjct: 121 PEKSAFRFHHISTDEVYGDLHGVDDLF--TETTPYAPSSPYSASKAASDHLVRAWQRTYG 178 Query: 166 LDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSGKPTRVFGDGTNTRDYVFVDDVVDAF 225 L +N YGP P +V + A L+GKP V+G+G RD++FV+D A Sbjct: 179 LPVLLTNCSNNYGPFHFPEKLIPLVILNA---LAGKPLPVYGNGLQVRDWLFVEDHARAL 235 Query: 226 VRVSADVGGGLRFNIGTGKETSDRQLHSAVAAAVG--GPDDPE----------FHPPRLG 273 + V + G +NIG E + + ++ + + P PE F R G Sbjct: 236 LTVVTNGVVGETYNIGGHNEQKNIDVVRSICSLLEELAPQKPEGVAHFADLITFVQDRPG 295 Query: 274 DLKRSCLDIGLAERVLGWRPQIELADGVRRTVEYF 308 +R +D ER LGW P+ A G+R+TV+++ Sbjct: 296 HDQRYAIDASKIERELGWVPEETFASGLRKTVQWY 330 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: 281 Number of extensions: 18 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: 360 Length adjustment: 28 Effective length of query: 286 Effective length of database: 332 Effective search space: 94952 Effective search space used: 94952 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