Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate AO353_06770 AO353_06770 NAD-dependent dehydratase
Query= BRENDA::F6DEY6 (311 letters) >FitnessBrowser__pseudo3_N2E3:AO353_06770 Length = 309 Score = 204 bits (520), Expect = 2e-57 Identities = 120/291 (41%), Positives = 179/291 (61%), Gaps = 15/291 (5%) Query: 3 VLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVPFFQV---DLRDKEEVE 59 VL+TGGAGFIGSH+ + LLA+G V +LD+L+TGKR N+P P ++ D+ D V Sbjct: 6 VLITGGAGFIGSHLADALLAKGHSVRILDDLSTGKRSNLPLDNPRVELIEGDVADAALVA 65 Query: 60 RAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTGG 119 + + V+H AA ASV+ SV+DPV + N +G LN+ EA RQ GV++++FAS+ Sbjct: 66 KVM--LGCSAVAHLAAVASVQASVDDPVRTHQSNFIGTLNVCEAMRQAGVKRVLFASSA- 122 Query: 120 AIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQD 179 A+YG EGE +E P +PYAA K A E+YL Y + +GL+ R+ N++GPRQD Sbjct: 123 AVYGNNGEGESIDEETAKAPLTPYAADKLAGEYYLDFYRRQHGLEPAIFRFFNIFGPRQD 182 Query: 180 PHGE-AGVVAIFAERVLNGLPVTLYARKTPGDEGCVRDYVYVGDVAE--AHALALFSLE- 235 P +GV++IF+ER GLP+T++ GD RD+VYV D+ + A+ + +LE Sbjct: 183 PSSPYSGVISIFSERAQKGLPITVF-----GDGEQTRDFVYVEDLVDLLVQAIEMPTLEV 237 Query: 236 GIYNVGTGEGHTTREVLEAVAEAAGKAPQVQPAPPRPGDLERSVLSPLKLM 286 G NVG + T +++L+A+ E G+ P + P R GD+ S + +L+ Sbjct: 238 GAVNVGWNQATTLKQMLQALEEVVGQLPPIAYGPARSGDIRHSRANNQRLL 288 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: 267 Number of extensions: 16 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 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