Align Inositol 2-dehydrogenase 1; EC 1.1.1.18; Myo-inositol 2-dehydrogenase 1; MI 2-dehydrogenase 1 (uncharacterized)
to candidate GFF711 PGA1_c07260 putative inositol 2-dehydrogenase
Query= curated2:A4FDY3 (337 letters) >FitnessBrowser__Phaeo:GFF711 Length = 401 Score = 60.8 bits (146), Expect = 5e-14 Identities = 52/165 (31%), Positives = 72/165 (43%), Gaps = 36/165 (21%) Query: 3 VRVGVVGTGVMGADHVRTLTGGVAGARVVAVSDADQGRGRAVAAEAGDEVVFHADPVD-- 60 + +G++G G MG H VA A V AV D A E+V PV Sbjct: 38 IGIGILGGGYMGKAHA------VAMAAVGAVFDT--------ALRPRLEMVCATSPVSAE 83 Query: 61 -----------------LIGDAGVDAVVVASPDHTHEALATACVEAGKPVLCEKPLAATA 103 L+ D V+A+V+ASP TH +A A GKPV CEKPL A+ Sbjct: 84 RYRKAYGFQRATDDWQVLVNDPKVEAIVIASPQQTHRVVAEAAFALGKPVFCEKPLGASL 143 Query: 104 ADCLRIVAHEVAKG-RRLVQAGYMRRFDPSYVDMKRALDAGSIGD 147 AD +VA + G +V Y+R P+ ++ + G IG+ Sbjct: 144 ADSRAMVAAAQSSGCPNMVGFNYIR--TPASQYARQLIADGLIGE 186 Lambda K H 0.321 0.133 0.396 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: 242 Number of extensions: 14 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: 337 Length of database: 401 Length adjustment: 30 Effective length of query: 307 Effective length of database: 371 Effective search space: 113897 Effective search space used: 113897 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 (21.9 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