Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate BWI76_RS27250 BWI76_RS27250 L-threonine 3-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Koxy:BWI76_RS27250 Length = 341 Score = 186 bits (472), Expect = 8e-52 Identities = 96/313 (30%), Positives = 172/313 (54%), Gaps = 6/313 (1%) Query: 25 LPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVD 84 +P P++ H+++LIK+ ICG+D+H Y + P ++GHE GE+ +G V Sbjct: 18 VPEPEVGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVR 77 Query: 85 QFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIP 144 FK+GDRV+ E +TCG C C+ GR +LC + + G F +Y+ + F IP Sbjct: 78 GFKLGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNR-PGCFAEYLVIPAFNAFKIP 136 Query: 145 DSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTD 204 D++S + A++ +PF +H A L G + + G GP+G+MA A AK GA +++TD Sbjct: 137 DNISDDLASIFDPFGNAVHTALSFDL-VGEDVLVSGAGPIGVMAAAVAKHVGARNVVITD 195 Query: 205 LEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRR 264 + RLE A+KMG T +N+ +++ + + + G DV E +G P A ++ L ++ Sbjct: 196 VNEYRLELARKMGVTRAVNVSKENLNDVMAELGMTEGFDVGLEMSGAPPAFRTMLDTINH 255 Query: 265 GGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF--RYANTYPKGIEFLASGIVDTKHLVT 322 GG++A++G+P +++ ++ + + I GI+ T+ K + SG+ D ++T Sbjct: 256 GGRIAMLGIP-PSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAALIQSGL-DLSPIIT 313 Query: 323 DQYSLEQTQDAME 335 ++ ++ Q + Sbjct: 314 HRFGIDDFQQGFD 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: 14 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