Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Pf1N1B4_3108 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= BRENDA::O58389 (348 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3108 Length = 370 Score = 124 bits (312), Expect = 3e-33 Identities = 113/374 (30%), Positives = 173/374 (46%), Gaps = 49/374 (13%) Query: 2 SEKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKP 61 S VA KP E+VEVDV P GEVL++V+A+ +C TD + A Sbjct: 4 SRAAVAFEAKKP---LEIVEVDVAMPKAGEVLLRVVASGVCHTDAYTL---SGADPEGIF 57 Query: 62 PQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQ---NTKIFG 118 P I+GHE V IG GV + VGD+V CGKC C G+ ++CQ T+ G Sbjct: 58 PSILGHEGGAVVEAIGEGVTSVAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKG 117 Query: 119 VDTDG------------------VFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDT 160 + DG F+EY V+P ++ K PK P E L LG V T Sbjct: 118 LMPDGTSRFSYKGETIFHYMGTSTFSEYTVLPEISVAKIPKEAPLEKVCL---LGCGVTT 174 Query: 161 VLAGPIS------GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGAD 214 + I+ G +V I G G +GL + A + A +I + + + E+AK++GA Sbjct: 175 GIGAVINTAKVKPGDTVAIFGLGGIGLSAVIGAVKAKAGRIIAIDINPAKFEIAKQLGAT 234 Query: 215 YVINP--FEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPG 271 +NP F+ + + ++D+TDG GVD E G + + L+ G ++G+ Sbjct: 235 DCVNPKDFDRPIQEVIVDMTDG-GVDFSFECIGNVQLMRAALECCHKGWGESVIIGVAGA 293 Query: 272 KVTIDFN--NLI---IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFD 326 I L+ +++ G+ GR ++ + Q+G++ LD ITH G + Sbjct: 294 GQEISTRPFQLVTGRVWRGSAFGGVRGRTELPSYV---EMAQTGEIPLDTFITHT-MGLE 349 Query: 327 KYEEAFELMRAGKT 340 +AF+LM GK+ Sbjct: 350 DINKAFDLMHEGKS 363 Lambda K H 0.318 0.139 0.418 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: 359 Number of extensions: 24 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: 348 Length of database: 370 Length adjustment: 29 Effective length of query: 319 Effective length of database: 341 Effective search space: 108779 Effective search space used: 108779 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