Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate RR42_RS35005 RR42_RS35005 L-idonate 5-dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS35005 Length = 342 Score = 79.0 bits (193), Expect = 2e-19 Identities = 68/225 (30%), Positives = 98/225 (43%), Gaps = 24/225 (10%) Query: 47 EPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFSGVVVEAGP 106 EP P E+ +++ A GICGSD+H + G + P+T GHE +G+V G Sbjct: 19 EPAAPGPFEVEVRLGAAGICGSDLHYYFHGKVGAFVIRE----PLTPGHEAAGIVSRVGS 74 Query: 107 EAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGF-----NVDGAFAE 161 R G V CG C C G N C ++ LG +V G F E Sbjct: 75 AVT------RVAPGNKVAINPSHACGQCDYCRAGRDNLCRSMRFLGSASIYPHVQGMFRE 128 Query: 162 YVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVILGGG 221 + + R+L V + D + EP SVA + V G G V++ GGG Sbjct: 129 H------FLMHERQLTPV-DSDISLGELAFAEPLSVALHGV--NRAGELLGKTVLVTGGG 179 Query: 222 PIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTKE 266 IG AV + AGA+ +I + ++ +A +GAD VI +E Sbjct: 180 TIGSLAVMAARLAGAAHIIACDIADRPLEVALRVGADQVIRTDRE 224 Lambda K H 0.319 0.138 0.418 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: 307 Number of extensions: 17 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: 395 Length of database: 342 Length adjustment: 30 Effective length of query: 365 Effective length of database: 312 Effective search space: 113880 Effective search space used: 113880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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