Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_086509112.1 BZY95_RS06260 formaldehyde dehydrogenase, glutathione-independent
Query= BRENDA::P07913 (341 letters) >NCBI__GCF_002151265.1:WP_086509112.1 Length = 397 Score = 113 bits (283), Expect = 7e-30 Identities = 77/218 (35%), Positives = 111/218 (50%), Gaps = 34/218 (15%) Query: 18 VPVPELG------HNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVG 71 +P PEL + +++K+ T ICG+D H+ + T P +V+GHE G VV Sbjct: 21 IPYPELALGNRKCDHGVILKVVTTNICGSDQHMVR----GRTTAPAGLVLGHEITGLVVE 76 Query: 72 IGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGCF---------- 121 G++V+ K GD VS +I CG CRNC+ GRT +C N V RPG Sbjct: 77 CGRDVEFIKPGDLVSVPFNIACGRCRNCKEGRTGICLN---VNPARPGAAYGYVDMGGWV 133 Query: 122 ---AEYLVIP--AFNAFKIPDNIS-----DDLAAIFDPFGNAVHTALSFDL-VGEDVLVS 170 EY+++P FN K PD+ DL + D F H ++ + G V ++ Sbjct: 134 GGQTEYVMVPYADFNLLKFPDSDQAMEKIRDLTLLSDIFPTGFHGCVTAGVGPGSTVYIA 193 Query: 171 GAGPIGIMAAAVAKHVGARNVVITDVNEYRLELARKMG 208 GAGP+G+ AAA A+ +GA V++ D+ E RL AR G Sbjct: 194 GAGPVGLAAAASAQLLGAACVIVGDMIEERLAQARSFG 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: 324 Number of extensions: 23 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: 341 Length of database: 397 Length adjustment: 30 Effective length of query: 311 Effective length of database: 367 Effective search space: 114137 Effective search space used: 114137 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 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