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 WP_043828506.1 RSPH17029_RS18305 L-idonate 5-dehydrogenase
Query= SwissProt::Q00796 (357 letters) >NCBI__GCF_000015985.1:WP_043828506.1 Length = 348 Score = 206 bits (525), Expect = 6e-58 Identities = 126/352 (35%), Positives = 194/352 (55%), Gaps = 18/352 (5%) Query: 11 SLVVHGPGDLRLENYPIP-EPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLG 69 +LV+H P DLRL+ +PGP EV + + GICGSD+HY+ +G G +++PM LG Sbjct: 4 ALVLHAPHDLRLDEIAAAADPGPGEVRVAVSHGGICGSDLHYYHHGGFGTVRLREPMALG 63 Query: 70 HEASGTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMG--------RYNLSPSIFFCA 121 HE SG V +G+ V L+ GDRVA+ P P ++C+ G R+N S F Sbjct: 64 HEVSGIVTALGAGVTDLREGDRVAVNPSRPCGRCDYCRRGLAHHCLDMRFNGSAMRF--- 120 Query: 122 TPPDDGNLCRFYKHNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGA 181 P + G AA +LP A+ EPL+V +HA G +G +VLV G Sbjct: 121 -PHEQGLFRAAVTLPAAQAVRLPAETDLALAAMSEPLAVCLHAVAGAGSLIGKRVLVSGC 179 Query: 182 GPIGMVTLLVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESPQEIARKVEGQLG 241 GPIG +T+L A+A GA ++V +D++A L+ A+ +GAD VL ++ ES + + EG+ Sbjct: 180 GPIGCLTILAARAAGAEEIVASDIAAPALAAARAVGADRVLDLAAES-EALEPFAEGK-- 236 Query: 242 CKPEVTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYC 301 + +V +EC+GA ++ A + R G LV VGLG E+ +P+ RE+ ++G FR+ Sbjct: 237 GRIDVVLECSGAPPALLAALRVLRPQGLLVAVGLGPEV-ALPVTALVAREIRLQGSFRFD 295 Query: 302 NTWPVAISMLASKSVNVKPLVTHRFPLEKALEAFE-TFKKGLGLKIMLKCDP 352 + A +AS ++V PL+T P+ +A +AF K +K+ + P Sbjct: 296 AEFATAARAIASGRIDVSPLLTRVLPVTEAADAFALASDKSRAMKVQIAFPP 347 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: 343 Number of extensions: 18 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: 348 Length adjustment: 29 Effective length of query: 328 Effective length of database: 319 Effective search space: 104632 Effective search space used: 104632 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