Align L-ribulose-5-phosphate 4-epimerase UlaF; EC 5.1.3.4; L-ascorbate utilization protein F; Phosphoribulose isomerase (uncharacterized)
to candidate WP_010877018.1 MTH_RS06730 class II aldolase family protein
Query= curated2:A7ZV69 (228 letters) >NCBI__GCF_000008645.1:WP_010877018.1 Length = 191 Score = 84.0 bits (206), Expect = 2e-21 Identities = 64/200 (32%), Positives = 103/200 (51%), Gaps = 27/200 (13%) Query: 6 QQVFEANMDLPRYGLVTFTWGNVSAIDRERGLVVIKPSGVAYETMKADDMVVVDMSGKVV 65 ++V + ++ + R GLV+ GNVSA +R V I P+ V + ++V+VD++G+V+ Sbjct: 8 REVVDVSLHIYRTGLVSGIGGNVSARMGDR--VFITPTMVPLGEVSLRNVVLVDLNGRVI 65 Query: 66 EGEYRPSSDTATHLELYRRYPSLGGIVHTHSTHATAWAQAGLAIP------ALGTTHADY 119 G RPSS+ HLE+YR P +GGIVHTHS HA A++ AG+ I LG + Sbjct: 66 RGG-RPSSELGLHLEVYRARPDVGGIVHTHSPHARAFSIAGVQIEKMEGFMGLGRGYIPM 124 Query: 120 FFGDIPYTRGLSEEEVQGEYELNTGKVIIETLGNAEPLHTPGIVVYQHGPFAWGKDAHDA 179 P +R L+ E G+V+++ ++ HG G+ DA Sbjct: 125 VPYHPPGSRELAAE---------CGRVMVD---------EDAAILENHGVVCAGEGLRDA 166 Query: 180 VHNAVVMEEVAKMAWIARSI 199 + A +EE A+ +IA ++ Sbjct: 167 LLLAEFIEESARTQFIAETL 186 Lambda K H 0.318 0.134 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: 127 Number of extensions: 7 Number of successful extensions: 4 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: 228 Length of database: 191 Length adjustment: 21 Effective length of query: 207 Effective length of database: 170 Effective search space: 35190 Effective search space used: 35190 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 (21.7 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