Align Inositol 2-dehydrogenase 2; EC 1.1.1.18; Myo-inositol 2-dehydrogenase 2; MI 2-dehydrogenase 2 (uncharacterized)
to candidate PP_2602 PP_2602 putative 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= curated2:A4FID1 (339 letters) >FitnessBrowser__Putida:PP_2602 Length = 350 Score = 91.3 bits (225), Expect = 3e-23 Identities = 76/231 (32%), Positives = 115/231 (49%), Gaps = 24/231 (10%) Query: 3 MNIGVIGCGLMGADHIRTLTTAVSGARVAAVNDADEGRAAGAAAEAEGARVHSDPFGLID 62 + I +IG G+MG H + L V A++ AV AD G A A A G +D +++ Sbjct: 5 LRIALIGAGIMGRQHYQHLRN-VPQAQLCAV--ADPGPQAEAFAAECGVPCFADHRQMLE 61 Query: 63 DAEVDAVVVASADETHEEFALACVRAGKPVLCEKPLATTSEACLRVVEAEMRGGRPLVQV 122 +AV+VA+ + H AL CV AG PVL EKP+ + +VEA R G P V V Sbjct: 62 QVRPEAVIVANPNTLHVATALDCVEAGVPVLVEKPVGVNLDEVRALVEASRRRGVP-VLV 120 Query: 123 GFMRRFDPSYLEMKRVLDSGRIGRALMLHSVHRNAGYPPALPDSALIT------GTG--- 173 G RR +P + +V++ G++GR ++ A + PDS T G G Sbjct: 121 GHHRRHNPLIAKAHQVINEGKLGRL-----INVTALWQLQKPDSYFETPWRREPGAGFLL 175 Query: 174 ---VHDIDIARWLLGQEIVTATAHTPRRSGLARPDFQDTRFLVLETENGVL 221 +HD+D+ R+L G E+V A T R+ + +D+ ++L+ NG L Sbjct: 176 TNLIHDLDLLRYLCG-EVVQVQAFT--RNDVRGFANEDSAAVLLQFANGAL 223 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: 263 Number of extensions: 16 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: 339 Length of database: 350 Length adjustment: 29 Effective length of query: 310 Effective length of database: 321 Effective search space: 99510 Effective search space used: 99510 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