Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate 6935882 Sama_0097 L-threonine 3-dehydrogenase (RefSeq)
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__SB2B:6935882 Length = 341 Score = 193 bits (490), Expect = 6e-54 Identities = 103/312 (33%), Positives = 171/312 (54%), Gaps = 6/312 (1%) Query: 26 PVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQ 85 P P++ H+++LIK+ ICG+D+H Y + P ++GHE GE+ +G V Sbjct: 19 PKPEMGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVRG 78 Query: 86 FKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPD 145 FK+GDRV+ E +TCG C C+ GR +LC + + +G+F +Y+ + F IPD Sbjct: 79 FKIGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNR-EGSFAEYLVIPAFNAFKIPD 137 Query: 146 SLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDL 205 +S + AA+ +PF +H A L G + I G GP+G+MA A + GA +++TD+ Sbjct: 138 DISDDLAAIFDPFGNAVHTALSFDL-VGEDVLITGAGPIGIMAAAVCRHVGARHVVITDV 196 Query: 206 EPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRG 265 RLE A+KMGAT +N+ +++ + +K + G DV E +G PAA + L ++ G Sbjct: 197 NEYRLELARKMGATRAVNVAKENLKDVMKDLGMTEGFDVGLEMSGVPAAFHAMLDTMNHG 256 Query: 266 GKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF--RYANTYPKGIEFLASGIVDTKHLVTD 323 GK+A++G+P E+ ++ + + I GI+ T+ K L SG+ D +VT Sbjct: 257 GKIAMLGIPG-GEMAIDWSKVIFKGLIIKGIYGREMFETWYKMASLLQSGL-DLSPIVTH 314 Query: 324 QYSLEQTQDAME 335 + ++ Q + Sbjct: 315 HFKVDDFQQGFD 326 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: 278 Number of extensions: 15 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: 353 Length of database: 341 Length adjustment: 29 Effective length of query: 324 Effective length of database: 312 Effective search space: 101088 Effective search space used: 101088 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