Align Inositol 2-dehydrogenase 4; EC 1.1.1.18; Myo-inositol 2-dehydrogenase 4; MI 2-dehydrogenase 4 (uncharacterized)
to candidate PfGW456L13_1420 Probable oxidoreductase
Query= curated2:A4FK61 (338 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1420 Length = 351 Score = 83.2 bits (204), Expect = 9e-21 Identities = 64/211 (30%), Positives = 99/211 (46%), Gaps = 13/211 (6%) Query: 3 NRELRVGLVGAGLMGSDHATRIHRRISGASLVAVGDPDLERAERAAAGIEGCQVETDPLK 62 N LR+ L+GAG MG H + + ++ A+L AV DP + A AA C D + Sbjct: 2 NSPLRIALIGAGNMGQQHYQHL-QSLTEATLCAVADPGPQAASLAAQWGVACFA--DHRQ 58 Query: 63 VIEASDVDAVVLATPGRTHEPLLLAAIERGIPVLCEKPLTPDSKSSLRVVEAEVAAGRRL 122 ++E + DAV++A P H L + G+PVL EKP+ + +V A A+G Sbjct: 59 MLEQAKPDAVIVANPNTLHVSTALDCLAAGVPVLLEKPVGVHLDEARELVTASKASGVP- 117 Query: 123 VQVGFMRRFDPEYAELKRTLHAGALGRPLLMHCAHRNASAPPGFTSQM-------MIFDS 175 V VG RR +P +H+GALGR + + F + M+ + Sbjct: 118 VLVGHHRRHNPLIVRAHELVHSGALGRLTTVTALWQLRKPDSYFETPWRREAGAGMLLTN 177 Query: 176 VVHEFDTTRWLLGE--EITAVSVRHPRSTAN 204 ++H+ D R L GE ++ A++ R AN Sbjct: 178 LIHDLDLLRHLCGEVRQVQAITSNAIRGFAN 208 Lambda K H 0.319 0.134 0.402 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: 298 Number of extensions: 18 Number of successful extensions: 3 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: 338 Length of database: 351 Length adjustment: 29 Effective length of query: 309 Effective length of database: 322 Effective search space: 99498 Effective search space used: 99498 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