Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein
Query= SwissProt::Q9WYP3 (395 letters) >NCBI__GCF_000330705.1:WP_017549841.1 Length = 338 Score = 151 bits (382), Expect = 2e-41 Identities = 107/356 (30%), Positives = 175/356 (49%), Gaps = 31/356 (8%) Query: 39 EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFS 98 ++ + E+ +P IE E+I+K+K GICGSDVH+ T +P +GHE S Sbjct: 11 QLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNP-------FTSYPRVIGHEVS 63 Query: 99 GVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGFNVDGA 158 G+V + G EA+ G+ V E + +CG C C G PN C++L G + DG Sbjct: 64 GIVEQVG-EAVTSLAP-----GDLVALEPITYCGECYACRNGQPNVCDSLEVFGVHRDGG 117 Query: 159 FAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVIL 218 AEY+K D + ++ G + A +L+EP ++ A G +R GD V ++ Sbjct: 118 MAEYLKADEN---NWHKVPGNVSEE----AAALMEPMTIGAQATY--RGDVREGDTVFVI 168 Query: 219 GGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTKENFVEAVLDYTNG 278 G GP G+A + K GA KV +S+ ++ R + AK +GAD I P + E + TNG Sbjct: 169 GAGPTGIACLLQAKQRGA-KVFISDFNQNRLDYAKSIGADATIQPDGVHVEEEINRLTNG 227 Query: 279 LGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARADAKIPLTGEVFQVRRAQIVG 338 A + ++A G+PQ +E R + + + LT + +V +++ Sbjct: 228 ELANVVIDAVGLPQTFQQAVELASIAGRVVTLGFNEQPSSIPSLLLTKKELKVAGSRLQT 287 Query: 339 SQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEIPEYIKRLQTDKSLVKVTML 393 Q FP+VI + G +D T+IIS+ SM++I + + L+ + + +L Sbjct: 288 HQ-------FPKVIDQVGRGEIDPTQIISQRYSMDQIHDAFELLENNPEAARKIVL 336 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: 333 Number of extensions: 20 Number of successful extensions: 6 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: 338 Length adjustment: 30 Effective length of query: 365 Effective length of database: 308 Effective search space: 112420 Effective search space used: 112420 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 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