Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_042615137.1 ABB28_RS02015 L-threonine 3-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_001431535.1:WP_042615137.1 Length = 344 Score = 290 bits (741), Expect = 5e-83 Identities = 153/344 (44%), Positives = 211/344 (61%), Gaps = 4/344 (1%) Query: 1 MSEKMVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIR 60 M++ M A++K + G L EV VP PGP EVLIK+ T+ICGTDLHIY W+EW+Q I Sbjct: 1 MAQTMKALVKREAAKGIWLEEVPVPVPGPNEVLIKLEKTAICGTDLHIYLWDEWSQRTIT 60 Query: 61 PPQIMGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVD 120 P +GHE G V +G V G EVG VS E HIVCG C C+ G+ H+C NT GV+ Sbjct: 61 PGLTIGHEFVGRVAALGSAVTGYEVGQRVSAEGHIVCGHCRNCRGGRQHLCPNTVGIGVN 120 Query: 121 TDGVFAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLG 180 +G FAEY V+PA N+W P IP E A +P GNA L + G+ VLITGAGP+G Sbjct: 121 VNGAFAEYMVMPATNLWPIPDQIPSELAAFFDPYGNAAHCALEFNVIGEDVLITGAGPIG 180 Query: 181 LLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVF 240 ++ + K GA V+V++ ++FR LA +GA V+N + +K+VM G DV Sbjct: 181 IIAAGICKHIGARNVVVTDVNDFRLKLAADMGATRVVNVANQS-LKDVMKELHMEGFDVG 239 Query: 241 LEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETW 300 LE SG P+A L + G++++LG+ P D++ IIFK LTV GI GR ++ETW Sbjct: 240 LEMSGNPRAFNDMLDCMYHGGKIAMLGIMPRGAGCDWDK-IIFKGLTVQGIYGRKMYETW 298 Query: 301 YTVSRLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 Y +++L+ SG + ++TH+ D +++ F+LM GK GKVV Sbjct: 299 YKMTQLVLSG-FPLGKVMTHQLP-IDDFQKGFDLMEEGKAGKVV 340 Lambda K H 0.318 0.138 0.417 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: 359 Number of extensions: 18 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: 348 Length of database: 344 Length adjustment: 29 Effective length of query: 319 Effective length of database: 315 Effective search space: 100485 Effective search space used: 100485 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 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