Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate GFF3379 PGA1_c34320 L-threonine 3-dehydrogenase Tdh
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__Phaeo:GFF3379 Length = 342 Score = 267 bits (683), Expect = 3e-76 Identities = 142/341 (41%), Positives = 218/341 (63%), Gaps = 4/341 (1%) Query: 5 MVAIMKTKPEYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQI 64 M A+ K+ P G +V+ VP+ GP EVLIKI T ICGTD+HI+ W+EWA + P I Sbjct: 1 MKALEKSHPREGLWMVQAPVPEIGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPMI 60 Query: 65 MGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGV 124 GHE AGE+VE+G V + VG S E H++ + G++H+ T+ GV+ G Sbjct: 61 TGHEFAGEIVEIGRNVTDLAVGQRCSGEGHLIQTDSRQSRAGKFHLDPGTRGIGVNEQGA 120 Query: 125 FAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAGKSVLITGAGPLGLLGI 184 FA+Y +PA NV P++IP E + +PLGNAV T L+ + G+ VLITGAGP+G++ Sbjct: 121 FAQYLKLPAFNVVPLPEDIPDEIGAILDPLGNAVHTALSFDLLGEDVLITGAGPIGVMAA 180 Query: 185 AVAKASGAYPVIVSEPSEFRRNLAKK-VGADYVINPFEEDVVKEVMDITDGNGVDVFLEF 243 AVA+ +GA V++++ + R LA+ V A +N EED+ V ++ G DV LE Sbjct: 181 AVARHAGARHVVITDINPDRLALAEHVVPAVRAVNVAEEDLQDVVRELGLKQGFDVGLEM 240 Query: 244 SGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYTV 303 SG+ AL+Q ++A+ G+++LLG+ PGK +D++ I+FKA+T+ G+ GR ++ETWY + Sbjct: 241 SGSQAALDQMVEALVMGGKIALLGIPPGKSPVDWSR-IVFKAITIKGVYGREMFETWYKM 299 Query: 304 SRLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 +LQ+G L++ +ITH++ + + E F M++G++GKVV Sbjct: 300 IAMLQNG-LDVSRVITHRF-DVEDFAEGFAAMKSGRSGKVV 338 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: 12 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: 342 Length adjustment: 29 Effective length of query: 319 Effective length of database: 313 Effective search space: 99847 Effective search space used: 99847 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 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