Align L-ribulose-5-phosphate 4-epimerase; Phosphoribulose isomerase; EC 5.1.3.4 (characterized)
to candidate WP_006749089.1 THITH_RS04255 methylthioribulose 1-phosphate dehydratase
Query= SwissProt::P94525 (229 letters) >NCBI__GCF_000227685.2:WP_006749089.1 Length = 207 Score = 67.8 bits (164), Expect = 2e-16 Identities = 54/177 (30%), Positives = 84/177 (47%), Gaps = 13/177 (7%) Query: 22 VTFTWGNVSGIDREKERIVIKPSGVEYSDLTADDLVVLNLDGEVVEGSLKPSSDTPTHVY 81 V T GN S E E+IVI SG L +V++L+G ++ PS++T H+ Sbjct: 28 VPATAGNFSARLNE-EQIVITVSGRHKGHLDDSGFMVVDLEGNILSPGKTPSAETFLHII 86 Query: 82 LYKAFPNIGGIVHTHSQWATSWAQSGRDIPPLGTTHADYFD-SAIPCTREMYDEEIIH-- 138 +Y+ P+IG ++HTHS AT ++ + P G T +DY A P DE +H Sbjct: 87 MYRRDPSIGAVLHTHSANATVLSR----LLPYGLTLSDYVVLKAFPAITS--DETSLHVP 140 Query: 139 --DYELNTGKVIAETFQHHN-YEQVPGVLVNNHGPFCWGTDALNAIHNAVVLETVAE 192 + ++ A+ H N + V G LV+ HG + WG A+ + E + E Sbjct: 141 VFPNTHDVPQLAAQVDDHMNRHPGVSGYLVSGHGLYTWGRSVEAAVQHVEAFEFLFE 197 Lambda K H 0.316 0.133 0.407 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: 123 Number of extensions: 8 Number of successful extensions: 2 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: 229 Length of database: 207 Length adjustment: 22 Effective length of query: 207 Effective length of database: 185 Effective search space: 38295 Effective search space used: 38295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 45 (21.9 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