Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 133 bits (334), Expect = 8e-36 Identities = 97/291 (33%), Positives = 143/291 (49%), Gaps = 29/291 (9%) Query: 14 EYGAELV--EVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAG 71 E+G L +V VP P PG++L+K A+ +C TDLH +W + PP I GHE G Sbjct: 12 EFGKPLSIEQVPVPTPAPGQILVKFEASGVCHTDLHAAH-GDW-PVKPTPPFIPGHEGTG 69 Query: 72 EVVEVGPGVEGIEVGDYVSVE-THIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAV 130 V VG GV+ ++ GD V V H CG C C+ G +C + G +G FAEY + Sbjct: 70 YVAAVGAGVKHVKEGDRVGVPWLHTACGCCSPCRTGWETLCAEQQNTGYSVNGSFAEYGL 129 Query: 131 VPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIA-----------GKSVLITGAGPL 179 + V P N+ G A + AG G+ V+I+G G L Sbjct: 130 ADPKFVGHLPDNL---------DFGPAAPVLCAGVTVYKGLKETEVRPGEWVVISGIGGL 180 Query: 180 GLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDV 239 G + + AKA G + V+ ++ E + LAKK+GAD ++ + V EV I G Sbjct: 181 GHMAVQYAKAMGMH-VVAADIHEDKLALAKKLGADLTVDGRNHNAVAEVQRII--GGAHG 237 Query: 240 FLEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYG 290 L + +PKA+EQ + G ++L+GL PG +S+ N ++ K +TV G Sbjct: 238 ALVTAVSPKAMEQAFGFLRARGTMALVGLPPGDISLPVFNTVL-KRITVRG 287 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: 278 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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 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