Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate GFF875 Psest_0895 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__psRCH2:GFF875 Length = 379 Score = 109 bits (273), Expect = 1e-28 Identities = 82/264 (31%), Positives = 127/264 (48%), Gaps = 35/264 (13%) Query: 39 EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPV--TLGHE 96 +V V+ VP+ +IE+PT+ +++V + ICGSD+HM Y G T F GHE Sbjct: 11 DVSVQNVPDAKIERPTDALVRVTSTNICGSDLHM----------YEGRTTFETGRVFGHE 60 Query: 97 FSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLN------- 149 G VVE G +R ++G+ VC + CG C C +G +C N Sbjct: 61 NLGEVVEVGAGV------ERVKVGDMVCLPFNIGCGFCENCEKGLTGYCLTANPGSAGAA 114 Query: 150 ----ELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVR 205 E+G DG AE ++V L E E + ++ S + PT ++A R Sbjct: 115 YGFAEMG-TYDGGQAELLRVPFADFNCLVLPEDAKEREDDYVMLSDIFPT--GWHA--TR 169 Query: 206 GGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTK 265 G++PG+++ I G GP+GL A GAS+V + + R LA ++GA I+ + Sbjct: 170 LAGLQPGESIAIYGAGPVGLMAAHSALIQGASQVFVIDDQPDRLKLAAQMGAT-PINSVE 228 Query: 266 ENFVEAVLDYTNGLGAKLFLEATG 289 + V+ +L+YT+G G E G Sbjct: 229 QKAVDEILNYTDGKGTDRGCECVG 252 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: 343 Number of extensions: 26 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: 379 Length adjustment: 30 Effective length of query: 365 Effective length of database: 349 Effective search space: 127385 Effective search space used: 127385 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: 50 (23.9 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