Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate PfGW456L13_1122 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1122 Length = 399 Score = 102 bits (255), Expect = 1e-26 Identities = 68/202 (33%), Positives = 103/202 (50%), Gaps = 28/202 (13%) Query: 28 LLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVKGFKIGDRVSG 87 +++++ T ICG+D H+ + T +V+GHE GEV+ G +V+ +IGD VS Sbjct: 37 VILRVVSTNICGSDQHMVR----GRTTAQTGLVLGHEITGEVIEKGSDVENLQIGDLVSV 92 Query: 88 EGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGCF-------------AEYLVIP--AFNA 132 ++ CG CR+C+ T +C + V RPG AEY ++P FN Sbjct: 93 PFNVACGRCRSCKEMHTGVC---LSVNPARPGGAYGYVDMGDWTGGQAEYAMVPYADFNL 149 Query: 133 FKIPDNIS-----DDLAAIFDPFGNAVHTALSFDL-VGEDVLVSGAGPIGIMAAAVAKHV 186 K+PD DL + D H A++ + G V ++GAGP+G+ AAA A+ + Sbjct: 150 LKLPDRDRAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYIAGAGPVGLAAAASARLL 209 Query: 187 GARNVVITDVNEYRLELARKMG 208 GA V+I DVN RL A+ G Sbjct: 210 GAAVVIIGDVNTVRLAHAKAQG 231 Lambda K H 0.322 0.140 0.433 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: 340 Number of extensions: 23 Number of successful extensions: 4 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: 341 Length of database: 399 Length adjustment: 30 Effective length of query: 311 Effective length of database: 369 Effective search space: 114759 Effective search space used: 114759 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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