Align Inositol 2-dehydrogenase 2; EC 1.1.1.18; Myo-inositol 2-dehydrogenase 2; MI 2-dehydrogenase 2 (uncharacterized)
to candidate Ga0059261_0656 Ga0059261_0656 Predicted dehydrogenases and related proteins
Query= curated2:A4FID1 (339 letters) >FitnessBrowser__Korea:Ga0059261_0656 Length = 343 Score = 76.3 bits (186), Expect = 1e-18 Identities = 63/211 (29%), Positives = 93/211 (44%), Gaps = 13/211 (6%) Query: 3 MNIGVIGCGLMGADHIRTLTTAVSGARVAAVNDADEGRAAGAAAEAEGARVHSDPFGLID 62 + +G+IG GL G G + AV D + A+ G RV D GL+ Sbjct: 4 IGVGLIGYGLGGRAFHAPYVGNTPGMALRAVVSRDPAKVH---ADLPGMRVVPDVAGLLA 60 Query: 63 DAEVDAVVVASADETHEEFALACVRAGKPVLCEKPLATTSEACLRVVEAEMRGGRPLVQV 122 + +D V+V+S D+ H E ALA +RAGK VL +KP ATT A R + AE +V Sbjct: 61 EPGIDLVIVSSPDDLHAEHALAAIRAGKHVLIDKPFATTL-ADARAIAAEGEARGVIVTA 119 Query: 123 GFMRRFDPSYLEMKRVLDSGRIGRALMLHSVHRNAGYPPALPD-------SALITGTGVH 175 RR+D + ++ ++ +G G + + S R + P D + G H Sbjct: 120 FQNRRWDADFRTLQGLIAAGTFGEIVEVES--RFDRWRPVPADVWKEARPGGVWLDLGPH 177 Query: 176 DIDIARWLLGQEIVTATAHTPRRSGLARPDF 206 +D A L GQ + R G PD+ Sbjct: 178 LVDQALQLFGQPLGITADIATLREGAPAPDY 208 Lambda K H 0.319 0.135 0.399 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: 292 Number of extensions: 21 Number of successful extensions: 2 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: 339 Length of database: 343 Length adjustment: 29 Effective length of query: 310 Effective length of database: 314 Effective search space: 97340 Effective search space used: 97340 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 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