Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate PP_1616 PP_1616 formaldehyde dehydrogenase, glutathione-dependent
Query= BRENDA::O58389 (348 letters) >FitnessBrowser__Putida:PP_1616 Length = 371 Score = 118 bits (295), Expect = 3e-31 Identities = 108/374 (28%), Positives = 172/374 (45%), Gaps = 49/374 (13%) Query: 2 SEKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKP 61 S VA KP E+VEVDV P GEVL++V+A+ +C TD + A Sbjct: 5 SRAAVAFEAKKP---LEIVEVDVAMPKAGEVLLRVVASGVCHTDAYTL---SGADPEGIF 58 Query: 62 PQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVCQ---NTKIFG 118 P I+GHE V +G GV + VGD+V CGKC C G+ ++CQ T+ G Sbjct: 59 PSILGHEGGAIVEAVGEGVTSLAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKG 118 Query: 119 VDTDG------------------VFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDT 160 + DG F+EY V+P ++ K K P E L LG V T Sbjct: 119 LMPDGTTRFSYKGQQLFHYMGTSTFSEYTVLPEISVAKIQKEAPLEKVCL---LGCGVTT 175 Query: 161 VLAGPIS------GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGAD 214 + ++ G +V I G G +GL + A + A +I + + + E+A+++GA Sbjct: 176 GIGAVLNTAKVKPGDTVAIFGLGGIGLSAVIGAVKAKASRIIAIDINPAKFEIARQLGAT 235 Query: 215 YVINP--FEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPG 271 +NP ++ + + ++D+TDG GVD E G + + L+ G ++G+ Sbjct: 236 DCVNPKDYDRPIQEVIVDLTDG-GVDFSFECIGNVQLMRAALECCHKGWGESVIIGVAGA 294 Query: 272 KVTIDFN--NLI---IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFD 326 I L+ +++ G+ GR ++ +S + G++ LD ITH G + Sbjct: 295 GQEISTRPFQLVTGRVWRGSAFGGVRGRSELPSYVEMS---EKGEIPLDTFITHT-MGLE 350 Query: 327 KYEEAFELMRAGKT 340 +AF+LM GK+ Sbjct: 351 DINKAFDLMHEGKS 364 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: 334 Number of extensions: 21 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: 371 Length adjustment: 29 Effective length of query: 319 Effective length of database: 342 Effective search space: 109098 Effective search space used: 109098 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