Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate 18292 b4267 L-idonate 5-dehydrogenase, NAD-binding (NCBI)
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Keio:18292 Length = 343 Score = 176 bits (447), Expect = 6e-49 Identities = 98/315 (31%), Positives = 168/315 (53%), Gaps = 14/315 (4%) Query: 29 DINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQFKV 88 D N++ L+++ GICGSDLHYY G++GN++++ P +LGHE G++ + S + Sbjct: 24 DWNNNGTLVQITRGGICGSDLHYYQEGKVGNFMIKAPMVLGHEVIGKV--IHSDSSELHE 81 Query: 89 GDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLAT----PPVDGAFVQYIKMRQDFVFLIP 144 G VA+ P CG C+ C E N C D++F + P VDG F +Y + P Sbjct: 82 GQTVAINPSKPCGHCKYCIEHNENQCTDMRFFGSAMYFPHVDGGFTRYKMVETSQCVPYP 141 Query: 145 DSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTD 204 + A EP +V IHAA + G + I G+GP+G + V+A K GA I+ D Sbjct: 142 AKADEKVMAFAEPLAVAIHAAHQAGELQGKRVFISGVGPIGCLIVSAVKTLGAAEIVCAD 201 Query: 205 LEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRG-VDVAWETAGNPAALQSALASVR 263 + P L K+MGA ++N + D ++ K ++G DV++E +G+P+++ + L R Sbjct: 202 VSPRSLSLGKEMGADVLVN-PQNDDMDHWKA---EKGYFDVSFEVSGHPSSVNTCLEVTR 257 Query: 264 RGGKLAIVGL-PSQNEIPLNVPFIADNEIDIYGIFRYANTYPKGIEFLASGIVDTKHLVT 322 G + VG+ + E P+ + EI + G FR+ + + + +LA+G+++ L++ Sbjct: 258 ARGVMVQVGMGGAMAEFPMMT--LIGKEISLRGSFRFTSEFNTAVSWLANGVINPLPLLS 315 Query: 323 DQYSLEQTQDAMERA 337 +Y ++A+ A Sbjct: 316 AEYPFTDLEEALRFA 330 Lambda K H 0.320 0.137 0.401 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: 246 Number of extensions: 9 Number of successful extensions: 5 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: 353 Length of database: 343 Length adjustment: 29 Effective length of query: 324 Effective length of database: 314 Effective search space: 101736 Effective search space used: 101736 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