Align Inositol 2-dehydrogenase; EC 1.1.1.18; Myo-inositol 2-dehydrogenase; MI 2-dehydrogenase (uncharacterized)
to candidate GFF2753 PGA1_c27960 putative oxidoreductase
Query= curated2:A6WFC5 (329 letters) >FitnessBrowser__Phaeo:GFF2753 Length = 363 Score = 64.3 bits (155), Expect = 4e-15 Identities = 56/182 (30%), Positives = 86/182 (47%), Gaps = 13/182 (7%) Query: 2 RVAVLGVGMMGQDHARRLATLTKGAQLVAVSDVDAARTDAVAAELGVRAVHDPAAAIADP 61 RV + G+G MG HA + AQ+V + + A + V + D A+A Sbjct: 3 RVLIAGLGNMGFSHALAHHH-DETAQIVGLVNRSGAAARPPLQDYPVYS--DFHHALAQT 59 Query: 62 EVDAVVIATPGFTHEGLVLEAIAAGKPTLCEKPLTTSPETARAVVEAERALGRPLVQVGF 121 + D VVIAT +H + A+ AG EKPL T+ ARAV +A R LGR L+ VG+ Sbjct: 60 KPDLVVIATYSDSHAPYAIAAMEAGADVFVEKPLATTVADARAVTDAARRLGRKLM-VGY 118 Query: 122 MRRFDAEYEQLRALVASRELGRPLFLHCVHRNATTPPNFNSEML-------ILDSVVHEV 174 + R +++L + +R+LG P + P +++ I+D VH V Sbjct: 119 ILRHHPSWQRL--IAEARDLGPPYVFRMNLNQQSDGPTWDTHKALMQTTSPIVDCGVHYV 176 Query: 175 DI 176 D+ Sbjct: 177 DV 178 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: 255 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 329 Length of database: 363 Length adjustment: 29 Effective length of query: 300 Effective length of database: 334 Effective search space: 100200 Effective search space used: 100200 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