Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF4077 HP15_4017 formaldehyde dehydrogenase (glutathione-dependent)
Query= BRENDA::O58389 (348 letters) >FitnessBrowser__Marino:GFF4077 Length = 370 Score = 130 bits (326), Expect = 7e-35 Identities = 113/378 (29%), Positives = 181/378 (47%), Gaps = 49/378 (12%) Query: 2 SEKMVAIMKTKPGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKP 61 S VA KP E+VEVDV P GEVL++++AT +C TD + A Sbjct: 4 SRAAVAFEANKP---LEIVEVDVAPPQEGEVLVRIVATGVCHTDAYTLSG---ADPEGLF 57 Query: 62 PQIMGHEVAGEVVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVC---QNTKIFG 118 P I+GHE G V +GPGV+ +EVGD+V CG+C C G+ ++C + T+ G Sbjct: 58 PTILGHEGGGIVEAVGPGVKNLEVGDHVIPLYTAECGECKFCTSGKTNLCGAVRATQGKG 117 Query: 119 VDTDG------------------VFAEYAVVPAQNIWKNPKSIPPEYATLQEPLGNAVDT 160 V DG F+EY V+P ++ K PK P + L LG V T Sbjct: 118 VMPDGTSRFSYNGQPLYHYMGCSTFSEYTVLPEISLAKIPKDAPLDKVCL---LGCGVTT 174 Query: 161 VLAGPIS------GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGAD 214 + ++ G +V I G G +GL I AK + A +I + + + ++AK++GA Sbjct: 175 GIGAVLNTAKVEEGATVAIFGLGGIGLAAIIGAKMAKAGRIIGVDINPGKFDIAKQLGAT 234 Query: 215 YVINP--FEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPG 271 V+NP +++ + + ++D+TDG G D E G K + L+A G +++G+ Sbjct: 235 DVVNPNDYDKPIQEVIVDMTDG-GADYTFECVGNVKLMRAALEACHKGWGESTIIGVAGA 293 Query: 272 KVTIDFN--NLI---IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFD 326 I L+ +++ G+ GR + + + G++ LD ITH+ + Sbjct: 294 GEEISTRPFQLVTGRVWRGSAFGGVKGRTELPGYVEKA---EKGEIPLDVFITHEMP-LE 349 Query: 327 KYEEAFELMRAGKTGKVV 344 +AF+LM GK+ + V Sbjct: 350 DINKAFDLMHEGKSIRTV 367 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: 358 Number of extensions: 23 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: 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