Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_042615137.1 ABB28_RS02015 L-threonine 3-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_001431535.1:WP_042615137.1 Length = 344 Score = 176 bits (445), Expect = 1e-48 Identities = 97/268 (36%), Positives = 147/268 (54%), Gaps = 4/268 (1%) Query: 7 QNMKAAVMHNTRE-IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKP 65 Q MKA V + I +E +PVP +EVLIK+ ICG+DLH Y + Sbjct: 3 QTMKALVKREAAKGIWLEEVPVPVPGPNEVLIKLEKTAICGTDLHIYLWDEWSQRTITPG 62 Query: 66 FILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPV 125 +GHE G +AA+GS+V ++VG RV+ E + CG C C+ GR +LCP+ + V Sbjct: 63 LTIGHEFVGRVAALGSAVTGYEVGQRVSAEGHIVCGHCRNCRGGRQHLCPNTVGIGV-NV 121 Query: 126 DGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVG 185 +GAF +Y+ M ++ IPD + E AA +P+ H A + G + I G GP+G Sbjct: 122 NGAFAEYMVMPATNLWPIPDQIPSELAAFFDPYGNAAHCALEFNV-IGEDVLITGAGPIG 180 Query: 186 LMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVA 245 ++A K GA ++VTD+ RL+ A MGAT ++N+ Q +L+++ + G DV Sbjct: 181 IIAAGICKHIGARNVVVTDVNDFRLKLAADMGATRVVNVANQ-SLKDVMKELHMEGFDVG 239 Query: 246 WETAGNPAALQSALASVRRGGKLAIVGL 273 E +GNP A L + GGK+A++G+ Sbjct: 240 LEMSGNPRAFNDMLDCMYHGGKIAMLGI 267 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: 285 Number of extensions: 12 Number of successful extensions: 4 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: 344 Length adjustment: 29 Effective length of query: 324 Effective length of database: 315 Effective search space: 102060 Effective search space used: 102060 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 24 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