Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_086509112.1 BZY95_RS06260 formaldehyde dehydrogenase, glutathione-independent
Query= SwissProt::Q9WYP3 (395 letters) >NCBI__GCF_002151265.1:WP_086509112.1 Length = 397 Score = 80.1 bits (196), Expect = 1e-19 Identities = 80/252 (31%), Positives = 113/252 (44%), Gaps = 50/252 (19%) Query: 39 EVRVEEVPEPRIEKPTE-----IIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFP--V 91 +V VE +P P + +I+KV ICGSD HM + G T P + Sbjct: 15 KVDVESIPYPELALGNRKCDHGVILKVVTTNICGSDQHMVR----------GRTTAPAGL 64 Query: 92 TLGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLN-- 149 LGHE +G+VVE G R + + G+ V + CG CR C EG C N+N Sbjct: 65 VLGHEITGLVVECG------RDVEFIKPGDLVSVPFNIACGRCRNCKEGRTGICLNVNPA 118 Query: 150 ---------ELGFNVDGAFAEYVKVD------AKYAWSLRELEGVYEGDRLFLAGSLVEP 194 ++G V G EYV V K+ S + +E + + L S + P Sbjct: 119 RPGAAYGYVDMGGWVGGQ-TEYVMVPYADFNLLKFPDSDQAMEKIRDLTLL----SDIFP 173 Query: 195 TSVAYNAVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKE 254 T ++ + G G PG V I G GP+GLAA A + GA+ VI+ + E R A+ Sbjct: 174 TG--FHGCVTAGVG--PGSTVYIAGAGPVGLAAAASAQLLGAACVIVGDMIEERLAQARS 229 Query: 255 LGADHVIDPTKE 266 G + ID T+E Sbjct: 230 FGCE-TIDLTQE 240 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: 372 Number of extensions: 19 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: 397 Length adjustment: 31 Effective length of query: 364 Effective length of database: 366 Effective search space: 133224 Effective search space used: 133224 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 24 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