Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_011912006.1 PST_RS04165 NAD-dependent dehydratase
Query= BRENDA::F6DEY6 (311 letters) >NCBI__GCF_000013785.1:WP_011912006.1 Length = 309 Score = 211 bits (538), Expect = 1e-59 Identities = 125/290 (43%), Positives = 177/290 (61%), Gaps = 14/290 (4%) Query: 3 VLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKG--VPFFQVDLRDKEEVER 60 +LVTGGAGFIGS++V+ LL RG + VLDNL+TGKREN+P+ V D+ D E V R Sbjct: 6 ILVTGGAGFIGSNLVDALLVRGYAIRVLDNLSTGKRENLPQDERVELIVGDVADAECVRR 65 Query: 61 AFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTGGA 120 + + R V H AA ASV+ SV+DP+ + NL+G LNL EA R+ GV++++FAS+ A Sbjct: 66 SVQGCRA--VVHLAAVASVQASVDDPLGTHQSNLIGTLNLCEAMREAGVKRVLFASSA-A 122 Query: 121 IYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQDP 180 +YG EG+ +E P +PYAA K A EHYL Y + +GL+ V R+ NVYGPRQDP Sbjct: 123 VYGNNGEGQAIDEGTAKAPLTPYAADKLASEHYLDFYRRQHGLEPVVFRFFNVYGPRQDP 182 Query: 181 HGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALALFSL---EG 236 +GV++IF ER G P+ ++ GD RD++YVGD+ E AL + EG Sbjct: 183 SSPYSGVISIFTERAQRGRPIAVF-----GDGEQTRDFIYVGDLVEVLVQALEAADAPEG 237 Query: 237 IYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLM 286 NVG + + ++L+A+ + G P+V R GD+ S + +L+ Sbjct: 238 AVNVGLNKATSLNQLLDAIGDVLGDLPEVSYQAARSGDIRHSRANNARLV 287 Lambda K H 0.318 0.138 0.411 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: 279 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: 311 Length of database: 309 Length adjustment: 27 Effective length of query: 284 Effective length of database: 282 Effective search space: 80088 Effective search space used: 80088 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: 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