Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate 5209062 Shew_1540 alcohol dehydrogenase (RefSeq)
Query= curated2:Q65JE7 (346 letters) >FitnessBrowser__PV4:5209062 Length = 376 Score = 123 bits (308), Expect = 9e-33 Identities = 104/360 (28%), Positives = 162/360 (45%), Gaps = 42/360 (11%) Query: 12 PGEPGASFELVPIPKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFGHEFSG 71 PG+P S E V + EVL+K+ A +C TD + D+ P + GHE G Sbjct: 16 PGQP-LSVEEVDVMYPKAGEVLVKIVATGVCHTDAFTLSGDD---PEGVFPAILGHEGGG 71 Query: 72 EVVQVGENVTTVKEGEYVSAETHIVCGKCLPCLTGKEHVCKK---TLILGVDTDGC---- 124 V VGE VT+V G++V CG+C C +GK ++C+K T G+ DG Sbjct: 72 IVEAVGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQKIRETQGKGLMPDGTTRFF 131 Query: 125 --------------FAEYVKMPAANIWK-NPAGMPEDLASIQEPLGNAVHTVLTG--MTA 167 F+EY +P ++ K NP E++ + + + VL + Sbjct: 132 KDGQPIFHYMGCSTFSEYTVLPEISLAKVNPEAPLEEVCLLGCGVTTGMGAVLNTAKVEP 191 Query: 168 GVKVAVVGCGPIGLMAVAVAKASGAAQVIAIDKNEYRLDLALQMGATDIISVEKED-PLK 226 G VA+ G G IGL A+ A +GA+++IAID NE + +LA Q+GATD I+ + D P++ Sbjct: 192 GASVAIFGIGGIGLSAIIGATMAGASRIIAIDINESKFELARQLGATDCINPKNYDKPIQ 251 Query: 227 NVSALTNGEGADLVCEMSGHPTAIRQSLKMAANGGRVHVL--------SLPEHPVCIDMT 278 V G D E G+ +R +L+ G V+ + P + Sbjct: 252 EVIVELTDGGVDYSFECIGNVDVMRSALECCHKGWGESVIIGVAGAGQEISTRP--FQLV 309 Query: 279 NDIVFKGLTVQGITGRKMFETWRQVSGLLQSGTIQIKPVITHRFPMEEFEKGFELMRKGQ 338 V++G G+ GR ++ G ++ ITH +EE F+LM +G+ Sbjct: 310 TGRVWRGSAFGGVKGRSELP---EIVEKYLRGEFKLSDFITHTMALEEINTAFDLMHEGK 366 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: 351 Number of extensions: 19 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: 346 Length of database: 376 Length adjustment: 29 Effective length of query: 317 Effective length of database: 347 Effective search space: 109999 Effective search space used: 109999 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