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 353143 BT3617 sorbitol dehydrogenase (NCBI ptt file)
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__Btheta:353143 Length = 338 Score = 179 bits (454), Expect = 9e-50 Identities = 109/322 (33%), Positives = 177/322 (54%), Gaps = 12/322 (3%) Query: 16 VQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYP-VAAPVTLGHEFSGEIVELGEGV- 73 V E +PT G +V +++KY G CGSD++T+ G P V PV GHE I E+G V Sbjct: 14 VVELEKPTVGAGEVLVRIKYVGFCGSDLNTFLGRNPMVKLPVIPGHEVGAVIEEIGPDVP 73 Query: 74 TGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSFAKYVIARQESLHHL 133 GF G VT Y+ CGKC+ C +G N C H + LG Q++G +Y + + + Sbjct: 74 AGFEKGMNVTLNP-YTNCGKCASCRNGRVNACEHNETLGVQRNGVMCEYAVLPWTKI--I 130 Query: 134 PAG-VDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIGLLAAQVAKSHGGTVIIT 192 PAG + R A+ EP++ HA+++ + + V+V G G IG+ A A G TVI Sbjct: 131 PAGNISSRDCALIEPMSVGFHAVSRAQVIDNEYVMVIGCGMIGIGAIVRAALRGATVIAV 190 Query: 193 GLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLECSGAVPAAKQGIDL 252 L ++++ L AK VG YA++++ ++ E + E+T G+GADVV+E G+ +D Sbjct: 191 DLDDEKLVL--AKRVGASYAVNSKTENVHERIQEITAGFGADVVIEAVGSPVTYVMAVDE 248 Query: 253 LRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPALSLLNEKKVNAKTL 312 + G+ +G +A+ E+ F + +QKE+ + GSR+ PAD+ ++ + E K + L Sbjct: 249 VGFTGRVVCIG-YAKKEVAFQTKYFVQKELDIRGSRNALPADFRAVINYMKEGKCPVEEL 307 Query: 313 VTHEYTISEWDKAYHAIKSGEA 334 ++ I++ + A A+K A Sbjct: 308 IS---KIAKPEDALEAMKEWAA 326 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: 313 Number of extensions: 22 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: 343 Length of database: 338 Length adjustment: 28 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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