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_037449134.1 N825_RS07515 L-idonate 5-dehydrogenase
Query= SwissProt::Q00796 (357 letters) >NCBI__GCF_000576635.1:WP_037449134.1 Length = 343 Score = 222 bits (566), Expect = 1e-62 Identities = 122/331 (36%), Positives = 195/331 (58%), Gaps = 8/331 (2%) Query: 10 LSLVVHGPGDLRLENYPIPEPGPNEVLLRMHSVGICGSDVHYWEYGRIGNFIVKKPMVLG 69 L +V+H P DLR+E P GP +V +R+ S GICGSD+HY+ +G G +++PM LG Sbjct: 2 LGVVIHAPKDLRVEEIPATPLGPRDVQVRIASGGICGSDLHYYHHGGFGVVRIREPMALG 61 Query: 70 HEASGTVEKVGSSVKHLKPGDRVAIEPGAPRENDEFCKMGRYNLSPSIFFCAT----PPD 125 HE +GTVEKVG+ V + G RVA+ P P ++ +C+ G+ N + F + P Sbjct: 62 HEIAGTVEKVGAEVSRVTVGQRVAVNPSRPCDDCRYCRAGQRNQCLDMRFIGSAMRFPHV 121 Query: 126 DGNLCRFYKHNAAFCYKLPDNVTFEEGALIEPLSVGIHACRRGGVTLGHKVLVCGAGPIG 185 G + + + +T E A+ EPL+V +HA R G +G +VLV G GPIG Sbjct: 122 QGGFRQALAVDERQAIPIAPGMTMAEAAMAEPLAVCLHAASRAGSLMGARVLVTGCGPIG 181 Query: 186 MVTLLVAKAMGAAQVVVTDLSATRLSKAKEIGADLVLQISKESPQEIARKVEGQLGCKPE 245 + ++ A+ GAA++VVTD+SA LS A+ +GA + I+ E P+ +A + + G + Sbjct: 182 ALAVVAARFGGAAEIVVTDVSAYPLSLARSVGATHAINIA-EDPKALAPYGQDKGGF--D 238 Query: 246 VTIECTGAEASIQAGIYATRSGGNLVLVGLGSEMTTVPLLHAAIREVDIKGVFRYCNTWP 305 V E +G EA++ + A R GG +V +GLG +M +P+ +E+ ++G FR+ + Sbjct: 239 VLFEASGNEAALLGALEAVRPGGIVVQLGLGGDM-KLPINLIVAKEIQLRGTFRFDGEFQ 297 Query: 306 VAISMLASKSVNVKPLVTHRFPLEKALEAFE 336 +A+ ++ S ++VKPLV+ P ++A+EAFE Sbjct: 298 LAVDLMGSGLIDVKPLVSQTIPFQRAVEAFE 328 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: 330 Number of extensions: 19 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: 343 Length adjustment: 29 Effective length of query: 328 Effective length of database: 314 Effective search space: 102992 Effective search space used: 102992 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