Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate SMc01214 SMc01214 zinc-containing alcohol dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Smeli:SMc01214 Length = 347 Score = 150 bits (379), Expect = 5e-41 Identities = 112/344 (32%), Positives = 175/344 (50%), Gaps = 38/344 (11%) Query: 40 VRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFSG 99 VR +PEP P ++++KV+ACGICG+D H+ + +P PVTLGHEF G Sbjct: 14 VRNVGIPEPG---PDDLLVKVEACGICGTDRHLLHGE------FPSTP--PVTLGHEFCG 62 Query: 100 VVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGFNVDGAF 159 +VVEAG + G + + + CG C C G N C NL +G + DG F Sbjct: 63 IVVEAGSAV------RDIAPGARITGDPNISCGRCPQCQAGRVNLCRNLRAIGIHRDGGF 116 Query: 160 AEYVKVDAKYAWSLR-ELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVIL 218 AEYV V K A+ + L+ V+ G+ EP + + V + GI+ G V IL Sbjct: 117 AEYVLVPRKQAFEIPLTLDPVH--------GAFCEPLACCLHGVDL--SGIKAGSTVAIL 166 Query: 219 GGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTKENFVEAVLDYTNG 278 GGG IGL V + + AGA+ VILS +R LA+E+GA +DP+ + VEA+ G Sbjct: 167 GGGVIGLLTVQLARLAGATTVILSTRQATKRRLAEEVGATATVDPSAGDVVEAIAGPV-G 225 Query: 279 L---GAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARADAKIPLTGEVFQVRRAQ 335 L G + +E GV + V + +A G + ++ + + K+ + R + Sbjct: 226 LVPGGVDVVIECAGVAETVKQSTR--LAKAGGTVVILGVLPQGE-KVEIEPFDILFRELR 282 Query: 336 IVGSQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEIPEYI 378 ++GS R L+A+G +++ ++IS+ +S++E P+ I Sbjct: 283 VLGS--FINPFVHRRAADLVATGAIEIDRMISRRISLDEAPDVI 324 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: 345 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: 347 Length adjustment: 30 Effective length of query: 365 Effective length of database: 317 Effective search space: 115705 Effective search space used: 115705 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