Align Inositol 2-dehydrogenase; EC 1.1.1.18; Myo-inositol 2-dehydrogenase; MI 2-dehydrogenase (uncharacterized)
to candidate WP_086508598.1 BZY95_RS03490 gfo/Idh/MocA family oxidoreductase
Query= curated2:A6WFC5 (329 letters) >NCBI__GCF_002151265.1:WP_086508598.1 Length = 393 Score = 81.3 bits (199), Expect = 4e-20 Identities = 62/197 (31%), Positives = 92/197 (46%), Gaps = 11/197 (5%) Query: 6 LGVGMMGQDHARRLATLTK--GAQLVAVSDVDAARTDAVAAELGVRAVHDPAAAIADPEV 63 LGV +G+ L TL G +LVA +D A+ G R + A ADP+V Sbjct: 8 LGVAGLGRGFMLLLPTLAAHPGIRLVAAADPREEARRQFRADFGARTYAEVADLCADPDV 67 Query: 64 DAVVIATPGFTHEGLVLEAIAAGKPTLCEKPLTTSPETARAVVEAERALGRPLVQVGFMR 123 +A+ +ATP H V A A GK L EKP+ S E +A+++A R GR LV VG Sbjct: 68 EAIYVATPHQFHREHVELAAAHGKHALVEKPMALSLEDCQAMIDAMRRAGRWLV-VGHSH 126 Query: 124 RFDAEYEQLRALVASRELGRPLFLHCV-HRNATTPPNFNSEM-------LILDSVVHEVD 175 FDA Y + R ++ S+ G + + + + P E+ ++ H+VD Sbjct: 127 SFDAPYLRTREMIDSQGFGAVRMISALNYTDFLYRPRRPEELDTSQGGGVVFSQAAHQVD 186 Query: 176 IARFLLGEEITAITVLT 192 I R L G + ++ T Sbjct: 187 IVRLLGGGHVKSVRAAT 203 Lambda K H 0.320 0.135 0.392 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: 295 Number of extensions: 7 Number of successful extensions: 1 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: 329 Length of database: 393 Length adjustment: 29 Effective length of query: 300 Effective length of database: 364 Effective search space: 109200 Effective search space used: 109200 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 (21.8 bits) S2: 49 (23.5 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