Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate N515DRAFT_3331 N515DRAFT_3331 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase
Query= curated2:Q72L62 (343 letters) >FitnessBrowser__Dyella79:N515DRAFT_3331 Length = 369 Score = 122 bits (307), Expect = 1e-32 Identities = 118/372 (31%), Positives = 162/372 (43%), Gaps = 42/372 (11%) Query: 2 RALAKLAPEEGLTLVDRPVPEPGPGEILVRVEAASICGTDLHIWKWDAWARGRIRPPLVT 61 RA P + L +V+ V P GE+LVR+ +C TD D G P V Sbjct: 4 RAAVAFGPGKPLEIVEIDVAPPRKGEVLVRITHTGVCHTDAFTLSGDD-PEGIF--PAVL 60 Query: 62 GHEFSGVVEAVGPGVKRPQVGDHVSLESHVVCHACPACRTGNYHVC---LNTKILGVDRD 118 GHE G+V VG GV + GDHV C C C +G ++C T+ G+ D Sbjct: 61 GHEGGGIVVEVGEGVSSVKPGDHVIPLYTAECRQCKFCLSGKTNLCQAVRATQGKGLMPD 120 Query: 119 GG------------------FAEYVVVPAEN-AWVNPKDLPFEVAAILE-PFGNAVHTVY 158 G F+EY VVP + A VNP+ P E +L + V+ Sbjct: 121 GSTRFSYNGEPVYHYMGTSTFSEYTVVPEISLAVVNPQ-APLEKVCLLGCGVTTGIGAVH 179 Query: 159 AGSGVS-GKSVLITGAGPIGLMAAMVARASGAGPILVSDPNPYRLAFARPY-ADRLVNPL 216 + V G +V + G G IGL A + AG I+ D NP + A AR A VNP Sbjct: 180 NTAKVKPGDTVAVFGLGGIGLAVIQGAVQAKAGRIIGVDTNPGKFALAREMGATDCVNPR 239 Query: 217 E--EDLLEVVRRVTGSGVEVLLEFSGNEAAIHQGLMALIPG-GEARILGI--PSDPIR-- 269 + + EV+ +T GV+ E GN + L G GE+ I+G+ IR Sbjct: 240 DHARPIQEVIVEMTDGGVDFSFECIGNVEVMRAALECCHKGWGESVIIGVAGAGQEIRTR 299 Query: 270 -FDLAGELVMRGITAFGIAGRRLWQTWMQG-TALVYSGRVDLSPLITHRLPLSRYREAFG 327 F L V RG G+ GR T + G G + L P ITH LPL R EAF Sbjct: 300 PFQLVTGRVWRGSAFGGVKGR----TQLPGMVEQAMQGEIRLDPFITHNLPLERINEAFE 355 Query: 328 LLASGQAVKVIL 339 L+ G++++ ++ Sbjct: 356 LMHEGKSIRTVI 367 Lambda K H 0.321 0.140 0.432 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: 442 Number of extensions: 33 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: 343 Length of database: 369 Length adjustment: 29 Effective length of query: 314 Effective length of database: 340 Effective search space: 106760 Effective search space used: 106760 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 (21.8 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