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 RR42_RS35005 RR42_RS35005 L-idonate 5-dehydrogenase
Query= SwissProt::Q00796 (357 letters) >FitnessBrowser__Cup4G11:RR42_RS35005 Length = 342 Score = 190 bits (482), Expect = 5e-53 Identities = 110/333 (33%), Positives = 180/333 (54%), Gaps = 15/333 (4%) Query: 10 LSLV--VHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMV 67 +SLV +H DLR PGP EV +R+ + GICGSD+HY+ +G++G F++++P+ Sbjct: 1 MSLVCHIHASEDLRFTQVEPAAPGPFEVEVRLGAAGICGSDLHYYFHGKVGAFVIREPLT 60 Query: 68 LGHEASGTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCAT----P 123 GHEA+G V +VGS+V + PG++VAI P ++C+ GR NL S+ F + P Sbjct: 61 PGHEAAGIVSRVGSAVTRVAPGNKVAINPSHACGQCDYCRAGRDNLCRSMRFLGSASIYP 120 Query: 124 PDDGNLCRFYKHNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGP 183 G + + + +++ E A EPLSV +H R G LG VLV G G Sbjct: 121 HVQGMFREHFLMHERQLTPVDSDISLGELAFAEPLSVALHGVNRAGELLGKTVLVTGGGT 180 Query: 184 IGMVTLLVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESPQEIARKVEGQLGCK 243 IG + ++ A+ GAA ++ D++ L A +GAD V++ +E P+ + Sbjct: 181 IGSLAVMAARLAGAAHIIACDIADRPLEVALRVGADQVIRTDREPPRALQDLA------- 233 Query: 244 PEVTIECTGAEASIQAGIYATRSGGNLVLVG-LGSEMTTVPLLHAAIREVDIKGVFRYCN 302 +V +E G+ A++ + A R G +V +G L +E P + RE++ G FR+ Sbjct: 234 -DVCLEAAGSGAALDTCLLAARRGARIVQIGTLPAEGLHFPANNIMARELEYVGAFRFGR 292 Query: 303 TWPVAISMLASKSVNVKPLVTHRFPLEKALEAF 335 + A+ L ++V+PL++ + PL +A+EAF Sbjct: 293 EFDWAVRYLTQGRLDVRPLLSAQLPLAQAVEAF 325 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: 331 Number of extensions: 16 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: 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