Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_009564818.1 RSPH17029_RS05295 L-threonine 3-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_000015985.1:WP_009564818.1 Length = 341 Score = 250 bits (639), Expect = 3e-71 Identities = 134/340 (39%), Positives = 208/340 (61%), Gaps = 3/340 (0%) Query: 5 MVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQI 64 M A++K K E G + E VP+ GP EVLI++ T ICGTD+HI+ W++WA + P + Sbjct: 1 MRALVKAKAEPGLWMEERPVPEIGPDEVLIRVRKTGICGTDVHIWNWDDWAAKTVPVPLV 60 Query: 65 MGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGV 124 GHE AGE+VEVG V + G S E H++ + G++H+ T+ GV+ G Sbjct: 61 TGHEFAGEIVEVGRDVRDLSPGQRCSGEGHLIGHHSRQVRAGRFHLDPETRGIGVNVPGA 120 Query: 125 FAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLGLLGI 184 FA+Y +PA NV P I E + +PLGNAV T L+ + G+ VL+TGAGP+G++ Sbjct: 121 FADYLRLPAFNVVPLPDAIDDEVGAILDPLGNAVHTALSFDLVGEDVLVTGAGPIGIMAA 180 Query: 185 AVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFS 244 AVA+ GA V++++ + R L+ +V +N ED+ + + G DV +E S Sbjct: 181 AVARHVGARHVVITDVNADRLRLSTEVADVVPVNVATEDLRSVMGRLKIVQGFDVGMEMS 240 Query: 245 GAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYTVS 304 GAP +Q ++A+ GR+++LG+ PG+ +D++ I+FKALT+ G+ GR ++ETWY + Sbjct: 241 GAPAGFDQMVEAMVMGGRIAMLGIPPGRSPVDWSR-IVFKALTIKGVYGREIFETWYKMI 299 Query: 305 RLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 +L++G L+I +ITH++ D + E F MR+G +GKVV Sbjct: 300 AMLENG-LDIRRVITHRFPVAD-FAEGFAAMRSGASGKVV 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: 335 Number of extensions: 9 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 319 Effective length of database: 312 Effective search space: 99528 Effective search space used: 99528 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 Apr 10 2024. 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