Align Sorbitol dehydrogenase; SDH; (R,R)-butanediol dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Ribitol dehydrogenase; RDH; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.4; EC 1.1.1.14; EC 1.1.1.56; EC 1.1.1.9 (characterized)
to candidate GFF3379 PGA1_c34320 L-threonine 3-dehydrogenase Tdh
Query= SwissProt::Q00796 (357 letters) >FitnessBrowser__Phaeo:GFF3379 Length = 342 Score = 167 bits (422), Expect = 5e-46 Identities = 101/329 (30%), Positives = 176/329 (53%), Gaps = 12/329 (3%) Query: 26 PIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLGHEASGTVEKVGSSVKH 85 P+PE GP+EVL+++ + GICG+D+H W + + V PM+ GHE +G + ++G +V Sbjct: 19 PVPEIGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPMITGHEFAGEIVEIGRNVTD 78 Query: 86 LKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCATPPDDGNLCRFYKHNAAFCYKLPD 145 L G R + E + + + G+++L P + G ++ K A LP+ Sbjct: 79 LAVGQRCSGEGHLIQTDSRQSRAGKFHLDPGTRGIGV-NEQGAFAQYLKLPAFNVVPLPE 137 Query: 146 NVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIGMVTLLVAKAMGAAQVVVTDL 205 ++ E GA+++PL +H + LG VL+ GAGPIG++ VA+ GA VV+TD+ Sbjct: 138 DIPDEIGAILDPLGNAVHTALSFDL-LGEDVLITGAGPIGVMAAAVARHAGARHVVITDI 196 Query: 206 SATRLSKAKE-IGADLVLQISKESPQEIARKVEGQLGCKP--EVTIECTGAEASIQAGIY 262 + RL+ A+ + A + +++E Q++ R +LG K +V +E +G++A++ + Sbjct: 197 NPDRLALAEHVVPAVRAVNVAEEDLQDVVR----ELGLKQGFDVGLEMSGSQAALDQMVE 252 Query: 263 ATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVF--RYCNTWPVAISMLASKSVNVKP 320 A GG + L+G+ + V + + IKGV+ TW I+ML ++V Sbjct: 253 ALVMGGKIALLGIPPGKSPVDWSRIVFKAITIKGVYGREMFETWYKMIAML-QNGLDVSR 311 Query: 321 LVTHRFPLEKALEAFETFKKGLGLKIMLK 349 ++THRF +E E F K G K++L+ Sbjct: 312 VITHRFDVEDFAEGFAAMKSGRSGKVVLR 340 Lambda K H 0.319 0.137 0.415 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: 289 Number of extensions: 11 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: 357 Length of database: 342 Length adjustment: 29 Effective length of query: 328 Effective length of database: 313 Effective search space: 102664 Effective search space used: 102664 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 (21.7 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