Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate 7023067 Shewana3_0305 alcohol dehydrogenase (RefSeq)
Query= curated2:Q8R7K0 (347 letters) >FitnessBrowser__ANA3:7023067 Length = 358 Score = 97.4 bits (241), Expect = 5e-25 Identities = 70/229 (30%), Positives = 115/229 (50%), Gaps = 30/229 (13%) Query: 23 EIPKIGPDEVLIKVKATSICGTDVHIY-----VWNEWAKSRIKP-------PKTMGHEFV 70 ++PK +VL++ A ICG+D+HI V++ + K + P P +GHEF Sbjct: 25 DLPKPQVGQVLVRSLACGICGSDIHITRHYSEVFSFYRKLGVMPEGVDDHVPVMLGHEFC 84 Query: 71 GEVVEIG-ENVTSVKVGDLVSAETHIVCGKCRACRTGNAHICENTLILGVD--TDGAFAE 127 EVVE G + ++ VG V++ ++ +N +GV +GA++E Sbjct: 85 AEVVEFGPQTQQTLAVGTRVTSVPILMS--------------QNGAGVGVTPGVNGAYSE 130 Query: 128 YIKVPESNVWINDKNIPLEILSIQEPLGNAVHTVFSGDV-VGKSVAVIGCGPIGMMAIPL 186 Y + E+ + +++P E +++ EPL +H V GDV V + V+GCGPIG+ AI Sbjct: 131 YFILDEALLMPVPEHLPPEAVALTEPLAVGLHAVNRGDVGVEDTALVVGCGPIGLAAISA 190 Query: 187 LKRTGAAAIFAIEPADYRRELAHKLGATRVINPLREDVVSIIKSETEGY 235 L G I A + + +LA + GAT +NP +D V+ EG+ Sbjct: 191 LHLRGVRNIIAADLQGEKLQLAREFGATHTVNPGEQDEVAYAAEVAEGH 239 Lambda K H 0.319 0.139 0.414 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: 322 Number of extensions: 27 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: 347 Length of database: 358 Length adjustment: 29 Effective length of query: 318 Effective length of database: 329 Effective search space: 104622 Effective search space used: 104622 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 (21.7 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