Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_099019607.1 CCS90_RS11000 L-threonine 3-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_002591915.1:WP_099019607.1 Length = 340 Score = 286 bits (733), Expect = 4e-82 Identities = 146/342 (42%), Positives = 220/342 (64%), Gaps = 8/342 (2%) Query: 5 MVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQI 64 M A++K KPE G + +V +P+ G +VLIKI T+ICGTDLHIY+W+EW+ I+PP + Sbjct: 1 MKALVKKKPELGIWMEDVPMPEMGHNDVLIKIEKTAICGTDLHIYKWDEWSAKAIKPPLV 60 Query: 65 MGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGV 124 +GHE G +V++G V+G EVG VS E HIVCG C C+ G H+C NT+ GV+ +G Sbjct: 61 IGHEFVGHIVDMGSEVKGYEVGQRVSAEGHIVCGVCRNCRAGTPHLCPNTQGIGVNRNGA 120 Query: 125 FAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLGLLGI 184 FAE+ +P QN+W P IP A +P GNA L + G+ VLITGAGP+G++ Sbjct: 121 FAEFISMPVQNLWPVPDKIPSNLAAFFDPFGNAAHCALEYDMVGEDVLITGAGPIGIIAT 180 Query: 185 AVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDV--VKEVMDITDGNGVDVFLE 242 + K GA V++++ +++R +LAK +GA +N +E + V + M+IT G D+ +E Sbjct: 181 GICKHVGARNVVITDVNDYRLSLAKDMGATRCVNVTKEKLPAVMKEMNIT---GFDLGME 237 Query: 243 FSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYT 302 SG P A L ++ G+++LLG+ P I+++N IIFK L++ GITGR ++ETWY Sbjct: 238 MSGNPMAFNDMLNSMYNGGKITLLGMLPDHTQINWDN-IIFKGLSIRGITGRKMYETWYK 296 Query: 303 VSRLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 +++LL SG ++ +TH+ D ++ F+LM +G+ GKVV Sbjct: 297 MTQLLLSG-FPLEKALTHEIH-IDDFQTGFDLMNSGQCGKVV 336 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: 338 Number of extensions: 20 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: 340 Length adjustment: 29 Effective length of query: 319 Effective length of database: 311 Effective search space: 99209 Effective search space used: 99209 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