Align Sorbitol dehydrogenase; SDH; EC 1.1.1.-; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; EC 1.1.1.14; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.9 (uncharacterized)
to candidate AZOBR_RS16135 AZOBR_RS16135 sorbitol dehydrogenase
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__azobra:AZOBR_RS16135 Length = 334 Score = 162 bits (409), Expect = 1e-44 Identities = 104/328 (31%), Positives = 162/328 (49%), Gaps = 7/328 (2%) Query: 15 AVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYP-VAAPVTLGHEFSGEIVELGEGV 73 A+ E EPTPG +V + +++ +CGSD+ T++G P V+ P GHE GEI +GEGV Sbjct: 9 AIHEVAEPTPGPGEVLLAIRHVALCGSDLSTFKGLNPLVSLPRIPGHEIGGEIAAVGEGV 68 Query: 74 TGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSFAKYVIARQESLHHL 133 R Y+ CG C C G N C + LG QQ+G A+ ++ L L Sbjct: 69 PAEYTVGRRAIVIPYTACGTCPSCRKGRVNACRSNRTLGVQQNGGLAERIVLPYGKL-IL 127 Query: 134 PAGVDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIGLLAAQVAKSHGGTVIITG 193 + R A+ EPL+ HA A+ + D V+V G G IG+ A + G TVI Sbjct: 128 NDTLAPRHLALVEPLSVGFHAAARGRVEAADTVLVLGCGMIGMGAIAGSVHRGATVIAVD 187 Query: 194 LSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLECSGAVPAAKQGIDLL 253 + + L A+ G + ID + D+ ++ELT+G GADVV+E G Q IDL+ Sbjct: 188 IGEAKTGL--ARRYGAAHTIDAGKEDVAARIAELTNGDGADVVIEAVGLPATFTQAIDLV 245 Query: 254 RKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPALSLLNEKKVNAKTLV 313 G+ +G +A+ + + + KE+ ++GSR+ D++ + L L+ Sbjct: 246 SFAGRVVYIG-YAKEPVSYKTQFFNLKELDIMGSRNATSEDFQAVIHYLETLDHAPDDLI 304 Query: 314 THEYTISEWDKA--YHAIKSGEAIKVLL 339 + + E DKA Y A + +KV++ Sbjct: 305 SKVFPFEEADKALPYWAKERDTTVKVMI 332 Lambda K H 0.315 0.133 0.388 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: 323 Number of extensions: 23 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: 343 Length of database: 334 Length adjustment: 28 Effective length of query: 315 Effective length of database: 306 Effective search space: 96390 Effective search space used: 96390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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