Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate PfGW456L13_4682 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= curated2:Q8R7K0 (347 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4682 Length = 370 Score = 106 bits (264), Expect = 1e-27 Identities = 105/368 (28%), Positives = 163/368 (44%), Gaps = 46/368 (12%) Query: 14 KEGADIVKKEIPKIGPDEVLIKVKATSICGTDVHIYVWNEWAKSRIKPPKTMGHEFVGEV 73 K+ +IV+ ++ EVL++V A+ +C TD + A P +GHE V Sbjct: 13 KKPLEIVEVDVAMPKAGEVLLRVVASGVCHTDAYTL---SGADPEGIFPSILGHEGGAIV 69 Query: 74 VEIGENVTSVKVGDLVSAETHIVCGKCRACRTGNAHICE---NTLILGVDTDG------- 123 IGE VTSV VGD V C +C+ C +G ++C+ T G+ DG Sbjct: 70 EAIGEGVTSVAVGDHVIPLYTPECRQCKFCLSGKTNLCQAIRATQGKGLMPDGTSRFSYK 129 Query: 124 -----------AFAEYIKVPESNVWINDKNIPLEILSIQEPLGNAVHTVFSGDV------ 166 F+EY +PE +V K PLE + + LG V T + Sbjct: 130 GETIFHYMGTSTFSEYTVLPEISVAKIAKEAPLEKVCL---LGCGVTTGIGAVLNTAKVK 186 Query: 167 VGKSVAVIGCGPIGMMAIPLLKRTGAAAIFAIEPADYRRELAHKLGATRVINPLRED--V 224 G +VA+ G G IG+ A+ + AA I AI+ + E+A +LGAT +NP D + Sbjct: 187 PGDTVAIFGLGGIGLSAVIGAVKAKAARIIAIDINPAKFEIAKQLGATDCVNPKDFDRPI 246 Query: 225 VSIIKSETEGYGADVVLDFSGNPTAIRQGLEYIAKGGRMSIL------GLPDNEVPIDIT 278 +I T+G G D + GN +R LE KG S++ G + P + Sbjct: 247 QEVIVDMTDG-GVDFSFECIGNVQLMRAALECCHKGWGESVIIGVAGAGQEISTRPFQLV 305 Query: 279 NNVVFKGITIQGITGRRMYDTWYTVKGLLKSGLAEDLKPIITHTFPLTEYQKGMELMIKG 338 V++G G+ GR ++ + ++G L ITHT L + K +LM +G Sbjct: 306 TGRVWRGSAFGGVRGRTELPSYVE---MAETG-EIPLDTFITHTMGLEDINKAFDLMHEG 361 Query: 339 QCGKVVLY 346 + + V++ Sbjct: 362 KSIRSVIH 369 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: 339 Number of extensions: 18 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: 347 Length of database: 370 Length adjustment: 29 Effective length of query: 318 Effective length of database: 341 Effective search space: 108438 Effective search space used: 108438 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