Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate GFF272 PS417_01385 NAD-dependent dehydratase
Query= BRENDA::F2NQX6 (314 letters) >FitnessBrowser__WCS417:GFF272 Length = 310 Score = 203 bits (517), Expect = 4e-57 Identities = 123/299 (41%), Positives = 171/299 (57%), Gaps = 14/299 (4%) Query: 2 RVLVTGGAGFIGSHLVHALHQKGIPVAVLDDLSTGKRAHIP---PDVPLYQTDIRDLNAV 58 R+LVTGGAGFIGSHLV AL KG + VLD+LSTGK A++P PD+ L D+ D V Sbjct: 5 RILVTGGAGFIGSHLVEALLGKGYKIRVLDNLSTGKVANLPVAHPDLELMIGDVADSAVV 64 Query: 59 LHAFQDFQPTHVAHQAAQASVKHSVQNPCKDAEINLLGGLNILEAMRATGTQKIVFASTG 118 A D V H AA ASV+ SV +P + N +G LN+ ++M G ++VFAS+ Sbjct: 65 EQAMADCSA--VVHLAAVASVQASVDDPVATHQANFVGTLNVCQSMLKAGVTRVVFASSA 122 Query: 119 GAIYGEVPEGRRAPETWPPKPKSPYAASKAAFEHYLEVYRQTHGLTYTTLRYANVYGPRQ 178 A YG EG E P P +PYA+ K A E+YL+ YR+ HGL R+ N++GPRQ Sbjct: 123 -ATYGNNGEGTAIAEDTPKSPLTPYASDKLASEYYLDFYRREHGLEPVIFRFFNIFGPRQ 181 Query: 179 DPHGE-AGVVAIFTNRLLHAQPVTLYARKEPGDPGCIRDYIHVEDVTRANLLALETNLEG 237 DP +GV++IFT R L +P+T++ GD RD+++V+D+ + A+ET Sbjct: 182 DPSSPYSGVISIFTERALAGKPITVF-----GDGEQTRDFVYVQDLVSILVQAVETREPA 236 Query: 238 TYNVSTGQGRTT--EDVLYTIARALGTTPRVTYAPPRDGDLEVSVLDPTQLQAHGWRPQ 294 ++ G R+T D++ + A GT VTY PR GD+ S + T+L PQ Sbjct: 237 PEAINVGLSRSTSLNDLIAELGNATGTALNVTYQAPRQGDIRHSRANNTRLLERFALPQ 295 Lambda K H 0.318 0.135 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: 261 Number of extensions: 14 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: 314 Length of database: 310 Length adjustment: 27 Effective length of query: 287 Effective length of database: 283 Effective search space: 81221 Effective search space used: 81221 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