Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate N515DRAFT_0211 N515DRAFT_0211 Threonine dehydrogenase
Query= BRENDA::P35497 (357 letters) >FitnessBrowser__Dyella79:N515DRAFT_0211 Length = 338 Score = 94.0 bits (232), Expect = 5e-24 Identities = 85/276 (30%), Positives = 119/276 (43%), Gaps = 25/276 (9%) Query: 10 VLEKVGDIAIEQRPIPTIKDPHYVKLAIKATGICGSDIHYYRSGGIGKYILKAPMVLGHE 69 VL DI E+ P P I+ P + I T +CGSD+ YR G P +GHE Sbjct: 5 VLHGPNDIRFEEVPEPKIEKPTDAIIRIAVTCVCGSDLWPYRGISPGS----GPTRMGHE 60 Query: 70 SSGQVVEVGDAVTRVKVGDRVAIEPGVPSRYSDETKEGRYNLCPHMAF---AATPPI--- 123 G V EVG AV +K G V G + C F A +P + Sbjct: 61 YCGYVEEVGSAVMAIKKGQFVVGSFATSDNTCPTCNIGYQSSCVQREFVSQAQSPYLRVA 120 Query: 124 --DGTLVKYYLSPEDFLVKLPEGVSYEEGACVEPLSVGVHSNKLAGVRFGTKVVVFGAGP 181 DGTLV +P+ +V G+ A + L G ++ A VR G VV G G Sbjct: 121 HADGTLVATREAPDASMVP---GLL----ASSDVLGTGWYAADAARVRPGVTAVVVGDGA 173 Query: 182 VGLLTGAVARAFGATDVIFVDVFDNKLQRAKDFGATNTFNSSQFSTDKAQDLADGVQKLL 241 VGLL A+ GA +I + + + A DFGAT+ ++ ++ + +L Sbjct: 174 VGLLAVLSAKQMGAERIIVMSRHPARQKLALDFGATD------IVAERGEEGVARIMELT 227 Query: 242 GGNHADVVFECSGADVCIDAAVKTTKVGGTMVQVGM 277 G AD V EC G + A++ T+ GG M VG+ Sbjct: 228 RGLGADSVLECVGTGESMQQAMRVTRKGGHMSFVGV 263 Lambda K H 0.318 0.137 0.403 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: 292 Number of extensions: 16 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: 357 Length of database: 338 Length adjustment: 29 Effective length of query: 328 Effective length of database: 309 Effective search space: 101352 Effective search space used: 101352 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