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_012385190.1 BIND_RS11215 zinc-binding dehydrogenase
Query= SwissProt::Q00796 (357 letters) >NCBI__GCF_000019845.1:WP_012385190.1 Length = 357 Score = 209 bits (531), Expect = 1e-58 Identities = 133/357 (37%), Positives = 195/357 (54%), Gaps = 20/357 (5%) Query: 11 SLVVHGPGDLRLENYPIPEP--GPNEVLLRMHSVGICGSDVHYWEYGRIGNFI------- 61 +L H DLR+E+ P P P GP EVL++ GICG+D+H + G I FI Sbjct: 3 ALRFHAAKDLRIEDIPAPPPTPGPGEVLVKNRFCGICGTDLHEYVSGPI--FIPVEPHPF 60 Query: 62 --VKKPMVLGHEASGTVEKVGSSVKHLKPGDRVAIEPGA-PRENDEFCKMGRYNLSPSIF 118 V P +LGHE G V VG V KPGDRV+I+P PR D F G ++LSP + Sbjct: 61 TKVSGPQILGHEFGGEVVAVGPGVTSAKPGDRVSIQPLLMPRSGDYFSDRGLFHLSPVLA 120 Query: 119 FCATPPDDGNLCRFYKHNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLV 178 G + + N + +P+ +T EE AL+EP +V ++AC RGGVT G VLV Sbjct: 121 LVGLSWQWGGMAEYALVNDYNIHVIPNEMTDEEAALVEPTAVAVYACDRGGVTAGSSVLV 180 Query: 179 CGAGPIGMVTLLVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKES--PQEIARKV 236 GAGPIGM+TLL A+A GA Q+ ++DL+ TRL AK I D++ K+ + + Sbjct: 181 TGAGPIGMLTLLAARAAGATQLFLSDLNETRLQIAKFILPDVITLNPKKDNVGDRVREES 240 Query: 237 EGQLGCKPEVTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKG 296 EG++GC +V IEC G E +++A A R G +V GL + + +++DI+G Sbjct: 241 EGKVGC--DVAIECVGNEHALKACADAVRKQGVVVQTGLHPGENPLNWFNVTFKDIDIRG 298 Query: 297 VFRY-CNTWPVAISMLASKSVNVKPLVTHRFPLEKAL-EAFETFKKGLGLKIMLKCD 351 + Y + WP ++ASK + + +VT R L++A+ E F+ G ++ + D Sbjct: 299 SWAYPTHYWPRVSRLIASKQLPAQKVVTKRIKLDQAVKEGFDALLDPAGQQLKILID 355 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: 366 Number of extensions: 21 Number of successful extensions: 6 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: 357 Length adjustment: 29 Effective length of query: 328 Effective length of database: 328 Effective search space: 107584 Effective search space used: 107584 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 24 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