Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate WP_043527898.1 JH15_RS05915 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= curated2:Q65JE7 (346 letters) >NCBI__GCF_000759345.1:WP_043527898.1 Length = 369 Score = 127 bits (318), Expect = 6e-34 Identities = 110/370 (29%), Positives = 165/370 (44%), Gaps = 51/370 (13%) Query: 14 EPGASFELVPI----PKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFGHEF 69 E G EL I PK EVL+++KA S+C TD + A P V GHE Sbjct: 10 EAGKPLELTEIEVDGPKAG--EVLVQIKATSVCHTDAFTLSG---ADPEGLFPSVLGHEG 64 Query: 70 SGEVVQVGENVTTVKEGEYVSAETHIVCGKCLPCLTGKEHVC---KKTLILGVDTDG--- 123 +G V +VGE VT++K G++V CGKC CL+GK ++C + T GV DG Sbjct: 65 AGIVQEVGEGVTSLKPGDHVIPLYTAECGKCKFCLSGKTNLCSAVRATQGRGVMPDGTSR 124 Query: 124 ---------------CFAEYVKMPAANIWKNPAGMPEDL-----ASIQEPLGNAVHTVLT 163 F+EY +P ++ K P D + +G ++T Sbjct: 125 FSLNGQTLHHYMGCSTFSEYTVLPEVSLAKVSPEAPLDKICLLGCGVTTGIGAVMNT--A 182 Query: 164 GMTAGVKVAVVGCGPIGLMAVAVAKASGAAQVIAIDKNEYRLDLALQMGATDIIS-VEKE 222 + G VAV G G IGL + A+ GA+++IAID N + +LA Q GATD ++ + Sbjct: 183 KVEPGSTVAVFGLGAIGLAVIQGAQMVGASRIIAIDINADKFELARQFGATDFVNPKDHA 242 Query: 223 DPLKNVSALTNGEGADLVCEMSGHPTAIRQSLKMAANGGRVHVL--------SLPEHPVC 274 DP++ V G D E G+ +RQ+L+ G V+ + P Sbjct: 243 DPIQQVIVDMTDGGVDYSFECIGNVNVMRQALECCHKGWGESVIIGVAGAGEEISTRP-- 300 Query: 275 IDMTNDIVFKGLTVQGITGRKMFETWRQVSGLLQSGTIQIKPVITHRFPMEEFEKGFELM 334 + V++G G+ GR + + G I+I +TH P E+ + FEL+ Sbjct: 301 FQLVTGRVWRGSAFGGVKGRTELPGYVE---RYMKGEIKIDEFVTHDMPFEQINEAFELL 357 Query: 335 RKGQCGKVVL 344 G+ + VL Sbjct: 358 HAGKSIRSVL 367 Lambda K H 0.318 0.136 0.410 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: 359 Number of extensions: 24 Number of successful extensions: 5 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: 346 Length of database: 369 Length adjustment: 29 Effective length of query: 317 Effective length of database: 340 Effective search space: 107780 Effective search space used: 107780 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 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