Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Dyella79:N515DRAFT_0039 Length = 344 Score = 183 bits (465), Expect = 5e-51 Identities = 113/347 (32%), Positives = 179/347 (51%), Gaps = 10/347 (2%) Query: 5 VPQNMKAAVMHNTRE-IKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVE 63 +PQ MKA V + I +E +PVP++ +EVLIK+ ICG+DLH Y ++ Sbjct: 1 MPQTMKALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIK 60 Query: 64 KPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATP 123 +GHE G I +G V +KVGDRV+ E + CG C C+ GR +LCP+ + Sbjct: 61 PGLTIGHEFVGRIVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVN 120 Query: 124 PVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGP 183 +GAF +Y+ M ++ IPD + E AA +P+ H A L G + I G GP Sbjct: 121 R-NGAFAEYMTMPASNLWPIPDQIPSELAAFFDPYGNAAHCALEFDL-IGEDVLITGAGP 178 Query: 184 VGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVD 243 +G++A AK GA ++VTD+ RL+ A MGAT ++N+ Q + +K + + G D Sbjct: 179 IGIIAAGIAKHVGARNVVVTDVNDYRLKLAADMGATRVVNVANQSLRDVVKDL-HIEGFD 237 Query: 244 VAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF--RYAN 301 V E +GNP A L + GGK+A++G+ + ++ + + + GI+ R Sbjct: 238 VGLEMSGNPRAFNDMLDCMYHGGKIALLGIMPRG-AGIDWDKVIFKGLTLQGIYGRRMYE 296 Query: 302 TYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVM 348 T+ K + + SG + ++T Q ++ Q + L C KV+ Sbjct: 297 TWYKMTQMVLSGF-PLQKVLTHQIHIDDFQKGFD--LMDAGHCGKVV 340 Lambda K H 0.320 0.137 0.401 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: 286 Number of extensions: 15 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: 353 Length of database: 344 Length adjustment: 29 Effective length of query: 324 Effective length of database: 315 Effective search space: 102060 Effective search space used: 102060 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 (21.8 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