Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate Synpcc7942_0061 Synpcc7942_0061 CDP-glucose 4,6-dehydratase
Query= BRENDA::P9WN67 (314 letters) >FitnessBrowser__SynE:Synpcc7942_0061 Length = 368 Score = 59.7 bits (143), Expect = 1e-13 Identities = 88/342 (25%), Positives = 137/342 (40%), Gaps = 39/342 (11%) Query: 2 RALVTGAAGFIGSTLVDRLLADGHSVVGL-----DNFATGRATNLEHLADNSAHVFVEAD 56 + L+TG GF GS L LL G V G + A +L + F Sbjct: 10 QVLITGHTGFKGSWLTLWLLMQGADVWGYALPPESERSLFTALDLANQRQAGWGYFQYRL 69 Query: 57 IVTADLHAI---LEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGV 113 D A+ +EQ +PEVVFHLAAQ VRRS ADP NV+G+++L EA + Sbjct: 70 GEMNDAEALRQWVEQAQPEVVFHLAAQPLVRRSYADPLGTWQTNVLGSLQLLEALKSLQH 129 Query: 114 RKIVHTSSGGSIYGTPP-EYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIA 172 + + +Y Y ET PY+A K A E+ + ++R + D +H Sbjct: 130 PCAMVMVTTDKVYENREWVYGYRETDCLGGHDPYSASKAAMELAVASWRSSFCGDAAHQT 189 Query: 173 P---------ANVYGPRQDPHGEAGVVAIFAQAL--LSGKPTRVFGDGTNTRDYVFVDDV 221 P NV G G+ V I A+ LS + +TR + V + Sbjct: 190 PYLAIATARAGNVIG-----GGDWAVDRIVPDAVRSLSAGAAIAVRNSHSTRPWQHVLEP 244 Query: 222 VDAFVRVSADV------------GGGLRFNIGTGKET--SDRQLHSAVAAAVGGPDDPEF 267 + ++ ++ + FN G E+ S ++L + V G + Sbjct: 245 LGGYLLLAQRLLEHQQSAEKTVNPFARAFNFGPAIESNRSVKELITTVLQHWPGQWVDQS 304 Query: 268 HPPRLGDLKRSCLDIGLAERVLGWRPQIELADGVRRTVEYFR 309 P + L A ++LGW+P+ + V RT+ ++R Sbjct: 305 DPTAPHEAGLLHLVSDQARQLLGWQPRWDFETTVSRTIHWYR 346 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: 247 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 314 Length of database: 368 Length adjustment: 28 Effective length of query: 286 Effective length of database: 340 Effective search space: 97240 Effective search space used: 97240 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