Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate PfGW456L13_3630 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= curated2:Q8R7K0 (347 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3630 Length = 372 Score = 115 bits (288), Expect = 2e-30 Identities = 107/366 (29%), Positives = 163/366 (44%), Gaps = 52/366 (14%) Query: 19 IVKKEIPKIGPDEVLIKVKATSICGTDVHIYVWNEWAKSRIKP----PKTMGHEFVGEVV 74 IV+ ++ EVL+++ AT +C TD + S P P +GHE G V Sbjct: 18 IVEVDVAPPQAGEVLVRIVATGVCHTDA-------FTLSGADPEGIFPVILGHEGGGIVE 70 Query: 75 EIGENVTSVKVGDLVSAETHIVCGKCRACRTGNAHICEN---TLILGVDTDG-------- 123 +GE VTS+ VGD V CG+C+ C +G ++C+ T G+ DG Sbjct: 71 AVGEGVTSLAVGDHVIPLYTPECGECKFCTSGKTNLCQKIRATQGKGLMPDGTSRFSYEG 130 Query: 124 ----------AFAEYIKVPESNVWINDKNIPLEIL-----SIQEPLGNAVHTVFSGDVVG 168 F+EY +PE ++ K+ PLE + + +G ++T + G Sbjct: 131 QPVFHYMGTSTFSEYTVLPEISLAKIPKDAPLEKVCLLGCGVTTGIGAVINTAKVEE--G 188 Query: 169 KSVAVIGCGPIGMMAIPLLKRTGAAAIFAIEPADYRRELAHKLGATRVINPLRED--VVS 226 SVA+ G G IG+ AI A I AI+ + E+A +LGAT INP D + Sbjct: 189 ASVAIFGLGGIGLAAIIGATMAKAGRIIAIDINPAKFEIARQLGATDFINPKDYDRPIQD 248 Query: 227 IIKSETEGYGADVVLDFSGNPTAIRQGLEYIAKGGRMSIL------GLPDNEVPIDITNN 280 +I TEG G D + GN +R LE KG S++ G + P + Sbjct: 249 VIIEMTEG-GVDYSFECIGNVHLMRAALECCHKGWGESVIIGVAGAGQEISTRPFQLVTG 307 Query: 281 VVFKGITIQGITGRRMYDTWYTVKGLLKSGLAEDLKPIITHTFPLTEYQKGMELMIKGQC 340 V++G G+ GR ++ V+ K + L ITHT L E + +LM KG+ Sbjct: 308 RVWRGSAFGGVKGRSELPSY--VENAQKGDI--PLDSFITHTMGLEEINRAFDLMHKGES 363 Query: 341 GKVVLY 346 + V++ Sbjct: 364 IRTVIH 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: 360 Number of extensions: 21 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: 372 Length adjustment: 29 Effective length of query: 318 Effective length of database: 343 Effective search space: 109074 Effective search space used: 109074 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