Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_012590207.1 MSIL_RS06020 UDP-glucuronate 5-epimerase
Query= BRENDA::A3MUJ4 (312 letters) >NCBI__GCF_000021745.1:WP_012590207.1 Length = 337 Score = 126 bits (317), Expect = 6e-34 Identities = 104/333 (31%), Positives = 155/333 (46%), Gaps = 42/333 (12%) Query: 1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLS-------SGRREFV---NPSAELHVR 50 MRI+VTG AGFIG H+ +L+ G+EVV VD + RR + NP H Sbjct: 1 MRILVTGSAGFIGFHMAARLLADGHEVVGVDGFTHYYDPELKRRRNAILSQNPYFTSHAI 60 Query: 51 DLKDYS-----WGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGV 105 L+D S + AG D V+HFAA VR S P + + N+ FN+LE R+ Sbjct: 61 LLEDASALKRVYDAGF--DAVYHFAAQAGVRYSLENPRAYVDANLTGAFNLLELMREAPP 118 Query: 106 RTVVFASSSTVYGDADVIPTPE-EEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRY 164 + + AS+S+VYG IP E + P++ Y A K A E M +YA LF + +R+ Sbjct: 119 KHALMASTSSVYGANTKIPFHETDRADHPLTFYAATKKANEEMAHSYAHLFKIPVTMLRF 178 Query: 165 ANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKK----- 219 V GP R + + ++V G ++ + +V D VEA K Sbjct: 179 FTVYGPWGRPDMALFKFVDAMVEGRPIDVFNHGKMKRDFTFVGDLVEAMALLIDKAPPAP 238 Query: 220 ---------FEEMD--APFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRG 268 ++ + AP+ +N+G V ++D + + GL+ E + Sbjct: 239 DSRTSPTPDYDSLSPVAPWRIVNIGTERPVGLMDFIEAIETATGLKAERNYLEMQ----- 293 Query: 269 WPGDVKYMTLAVTKLM-KLTGWRPTMTSAEAVK 300 GDV +T A T+L+ +LTG+RP T AE VK Sbjct: 294 -KGDVP-LTFASTRLLFELTGYRPATTLAEGVK 324 Lambda K H 0.320 0.137 0.409 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: 276 Number of extensions: 19 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: 312 Length of database: 337 Length adjustment: 28 Effective length of query: 284 Effective length of database: 309 Effective search space: 87756 Effective search space used: 87756 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 24 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