Align Sorbitol dehydrogenase; SDH; L-iditol 2-dehydrogenase; Polyol dehydrogenase; Xylitol dehydrogenase; XDH; EC 1.1.1.-; EC 1.1.1.14; EC 1.1.1.9 (characterized)
to candidate SMa0512 SMa0512 IdnD L-idonate 5-dehydrogenase
Query= SwissProt::Q58D31 (356 letters) >FitnessBrowser__Smeli:SMa0512 Length = 343 Score = 223 bits (567), Expect = 8e-63 Identities = 131/344 (38%), Positives = 198/344 (57%), Gaps = 12/344 (3%) Query: 10 SLVVHGPGDLRLENYPIPEPGPNEVLLKMHSVGICGSDVHYWQHGRIGDFVVKKPMVLGH 69 ++V+H DLR+E + +PGP EV +++ + GICGSD+HY+ HG G +K+PM+LGH Sbjct: 3 AIVIHTAKDLRVEECAVEKPGPGEVEIRLAAGGICGSDLHYYNHGGFGTVRLKEPMILGH 62 Query: 70 EASGTVVKVGSLVRHLQPGDRVAIEPGAPRETDEFCKIGRYNLSPTIFFCAT----PPDD 125 E SG V +G V L GD VA+ P P ++C G N + F + P Sbjct: 63 EVSGHVAALGEGVSDLAIGDLVAVSPSRPCGACDYCLKGLPNHCFHMRFYGSAMPFPHIQ 122 Query: 126 GNLCRFYKHNANFCYKLPDNVTFEEGALIEPLSVGIHACRRAGVTLGNKVLVCGAGPIGL 185 G A+ C K + ++ E A+ EPLSV +HA RRAG LG +VLV G GPIG Sbjct: 123 GAFRERLVAKASQCVK-AEGLSAGEAAMAEPLSVTLHATRRAGEMLGKRVLVTGCGPIGT 181 Query: 186 VSLLAAKAMGAAQVVVTDLSASRLSKAKEVGADFILQISNESPQEIA-KKVEGLLGSKPE 244 +S+LAA+ GAA++V DLS L A+ VGAD + +S + + + +G + Sbjct: 182 LSILAARRAGAAEIVAADLSERALGFARAVGADRTVNLSEDRDGLVPFSENKGTF----D 237 Query: 245 VTIECTGVETSIQAGIYATHSGGTLVLVGLGSEMTSVPLVHAATREVDIKGVFRYCNTWP 304 V EC+G + ++ AGI A G +V +GLG +M ++P++ +E+D++G FR+ + Sbjct: 238 VLYECSGAQPALVAGIQALRPRGVIVQLGLGGDM-ALPMMAITAKELDLRGSFRFHEEFA 296 Query: 305 MAISMLASKSVNVKPLVTHRFPLEKALEAFE-TSKKGLGLKVMI 347 A+ ++ ++VKPL+TH PL +AL+AFE S KG +K I Sbjct: 297 TAVKLMQGGLIDVKPLITHTLPLGEALKAFEIASDKGQSMKTQI 340 Lambda K H 0.318 0.136 0.410 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: 317 Number of extensions: 19 Number of successful extensions: 4 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: 356 Length of database: 343 Length adjustment: 29 Effective length of query: 327 Effective length of database: 314 Effective search space: 102678 Effective search space used: 102678 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: 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