Align Sorbitol dehydrogenase; SDH; SORD; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 (characterized)
to candidate WP_009564818.1 RSPH17029_RS05295 L-threonine 3-dehydrogenase
Query= SwissProt::Q64442 (357 letters) >NCBI__GCF_000015985.1:WP_009564818.1 Length = 341 Score = 159 bits (403), Expect = 8e-44 Identities = 101/330 (30%), Positives = 169/330 (51%), Gaps = 9/330 (2%) Query: 22 LENYPIPELGPNDVLLKMHSVGICGSDVHYWEHGRIGDFVVKKPMVLGHEAAGTVTKVGE 81 +E P+PE+GP++VL+++ GICG+DVH W V P+V GHE AG + +VG Sbjct: 15 MEERPVPEIGPDEVLIRVRKTGICGTDVHIWNWDDWAAKTVPVPLVTGHEFAGEIVEVGR 74 Query: 82 LVKHLKPGDRVAIEPGVPREVDEYCKIGRYNLTP-TIFFCATPPDDGNLCRFYKHNADFC 140 V+ L PG R + E + + GR++L P T P G + + A Sbjct: 75 DVRDLSPGQRCSGEGHLIGHHSRQVRAGRFHLDPETRGIGVNVP--GAFADYLRLPAFNV 132 Query: 141 YKLPDSVTFEEGALIEPLSVGIYACRRGSVSLGNKVLVCGAGPVGMVTLLVAKAMGAAQV 200 LPD++ E GA+++PL ++ + +G VLV GAGP+G++ VA+ +GA V Sbjct: 133 VPLPDAIDDEVGAILDPLGNAVHTALSFDL-VGEDVLVTGAGPIGIMAAAVARHVGARHV 191 Query: 201 VVTDLSASRLTKAKEVGADFTIQVGKETPQEIASKVESLLGSKPEVTIECTGAESSVQTG 260 V+TD++A RL + EV + V E + + +++ + G +V +E +GA + Sbjct: 192 VITDVNADRLRLSTEVADVVPVNVATEDLRSVMGRLKIVQGF--DVGMEMSGAPAGFDQM 249 Query: 261 IYATHSGGTLVIVGMGAEMVNLPLVHAAIREVDIKGVF--RYCNTWPMAISMLASKTLNV 318 + A GG + ++G+ + + + IKGV+ TW I+ML L++ Sbjct: 250 VEAMVMGGRIAMLGIPPGRSPVDWSRIVFKALTIKGVYGREIFETWYKMIAML-ENGLDI 308 Query: 319 KPLVTHRFPLEKAVEAFETAKKGVGLKVMI 348 + ++THRFP+ E F + G KV++ Sbjct: 309 RRVITHRFPVADFAEGFAAMRSGASGKVVL 338 Lambda K H 0.318 0.137 0.412 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: 328 Number of extensions: 20 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: 357 Length of database: 341 Length adjustment: 29 Effective length of query: 328 Effective length of database: 312 Effective search space: 102336 Effective search space used: 102336 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 Apr 10 2024. 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