Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate Echvi_0507 Echvi_0507 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Cola:Echvi_0507 Length = 337 Score = 107 bits (266), Expect = 7e-28 Identities = 83/245 (33%), Positives = 124/245 (50%), Gaps = 33/245 (13%) Query: 51 EKPT----EIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFSGVVVEA-G 105 EKPT IIK+K GICG+D+H + + + +P LGHE SG +VE G Sbjct: 18 EKPTLSPGRAIIKIKRIGICGTDLHAYEGTQPFF-------NYPRVLGHELSGELVEVDG 70 Query: 106 PEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGFNVDGAFAEYVKV 165 E F G+ V CG C C G PN C ++ G + DG E++ V Sbjct: 71 AEG--------FVPGDLVTIIPYFNCGECVACKAGKPNCCATISVFGVHEDGGMKEFISV 122 Query: 166 DAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVILGGGPIGL 225 + SL + EG+ ++L LA EP ++ + V R G++PG+ VV++G GPIGL Sbjct: 123 PSS---SLVKQEGL-SLEQLALA----EPLAIGAHGV--RRAGVQPGEFVVVMGAGPIGL 172 Query: 226 AAVAILKHAGASKVILSEPSEVRRNLAKE-LGADHVIDPTKENFVEAVLDYTNGLGAKLF 284 + + AG KVI + +E R +E LG ++ ++ K +F A+ D T G A+ Sbjct: 173 GVMEFARIAG-GKVIAMDINEDRLAFCRETLGVEYTVN-AKGDFKAAIADITGGSFAESV 230 Query: 285 LEATG 289 ++ATG Sbjct: 231 IDATG 235 Lambda K H 0.319 0.138 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: 322 Number of extensions: 24 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: 395 Length of database: 337 Length adjustment: 30 Effective length of query: 365 Effective length of database: 307 Effective search space: 112055 Effective search space used: 112055 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 (21.7 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