Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 6935786 Sama_0004 alcohol dehydrogenase, zinc-binding (RefSeq)
Query= BRENDA::O58389 (348 letters) >FitnessBrowser__SB2B:6935786 Length = 377 Score = 117 bits (293), Expect = 5e-31 Identities = 109/360 (30%), Positives = 167/360 (46%), Gaps = 40/360 (11%) Query: 13 PGYGAELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGE 72 PG + EVDV P GEVL++++AT +C TD ++ P I+GHE G Sbjct: 16 PGQPLSVEEVDVMLPKAGEVLVRIVATGVCHTDAFTLSGDD---PEGVFPAILGHEGGGI 72 Query: 73 VVEIGPGVEGIEVGDYVSVETHIVCGKCYACRRGQYHVC---QNTKIFGVDTDG------ 123 V +G GV + VGD+V CGKC C G+ ++C + T+ G+ DG Sbjct: 73 VEMVGEGVTSVAVGDHVIPLYTAECGKCKFCTSGKTNLCSAVRATQGKGLMPDGTTRFYK 132 Query: 124 ------------VFAEYAVVPAQNIWK-NPKSIPPEYATLQEPLGNAVDTVL--AGPISG 168 F+EY V+P ++ K NP++ E L + + VL A G Sbjct: 133 DGEPIYHYMGCSTFSEYTVLPEISLAKVNPEAPLEEVCLLGCGVTTGMGAVLKTAKVKKG 192 Query: 169 KSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSDFRRELAKKVGADYVINP--FEEDVVK 226 +V I G G +GL + A +GA +I + +D + ELAKK+GA INP +++ + Sbjct: 193 DTVAIFGLGGIGLSAVIGATMAGASRIIGIDINDSKFELAKKLGATDCINPKDYDKPIQD 252 Query: 227 EVMDITDGNGVDVFLEFSGAPKALEQGLQAVTPA-GRVSLLGLYPGKVTIDFN--NLI-- 281 ++++TDG GVD E G + L+ G ++G+ I L+ Sbjct: 253 VIVEMTDG-GVDFSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTRPFQLVTG 311 Query: 282 -IFKALTIYGITGRHLWETWYTVSRLLQSGKLNLDPIITHKYKGFDKYEEAFELMRAGKT 340 +++ G+ GR E V + L+ G+ L ITH G D EAF+LM GK+ Sbjct: 312 RVWRGSAFGGVKGRS--ELPGIVEQYLR-GEFALSDFITHT-MGLDAINEAFDLMHEGKS 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: 335 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: 377 Length adjustment: 29 Effective length of query: 319 Effective length of database: 348 Effective search space: 111012 Effective search space used: 111012 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 Apr 09 2024. 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