Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_004309492.1 C665_RS11135 L-threonine 3-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_000310185.1:WP_004309492.1 Length = 345 Score = 289 bits (740), Expect = 6e-83 Identities = 145/340 (42%), Positives = 215/340 (63%), Gaps = 3/340 (0%) Query: 5 MVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQI 64 M A+ K P G L V+ P+ GP +VLIKI T+ICGTD+HI++W+EWAQ I P Sbjct: 1 MKALAKLTPSVGLTLTSVEKPEVGPNDVLIKIKKTAICGTDIHIWKWDEWAQKTIPVPMH 60 Query: 65 MGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGV 124 +GHE G + E+G V G ++GD VS E HI CG C C+ G+ H+C+NT GV+ G Sbjct: 61 VGHEYVGVIAEMGQEVRGFKIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNRAGA 120 Query: 125 FAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLGLLGI 184 FAEY +PA N +K P +I + A + +P GNA T L+ + G+ VLITGAGP+G++ + Sbjct: 121 FAEYLAIPAVNAFKIPDDISDDLAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAV 180 Query: 185 AVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFS 244 A+A+ GA V++++ ++ R LA+K+GA +N E++ ++ G DV LE S Sbjct: 181 AIARHVGARHVVITDVNDHRLELARKMGATRAVNVSRENLADVKTELHMVEGFDVGLEMS 240 Query: 245 GAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYTVS 304 G P A L+ + G+++LLG+ P +ID+N +IFK L + GI GR ++ETWY + Sbjct: 241 GVPSAFTSMLEHMNHGGKIALLGIPPSNTAIDWNQ-VIFKGLEIKGIYGREMFETWYKMV 299 Query: 305 RLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 +LQSG L++ PIITH Y ++++ FE M +G +GKV+ Sbjct: 300 AMLQSG-LDLSPIITHHYP-VEEFKTGFETMLSGNSGKVI 337 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: 328 Number of extensions: 9 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: 345 Length adjustment: 29 Effective length of query: 319 Effective length of database: 316 Effective search space: 100804 Effective search space used: 100804 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