Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__azobra:AZOBR_RS13230 Length = 340 Score = 90.9 bits (224), Expect = 5e-23 Identities = 70/221 (31%), Positives = 100/221 (45%), Gaps = 21/221 (9%) Query: 42 VEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFSGVV 101 +EEVP P + P +I++K++A G+C +D+H A D +P P GHE G V Sbjct: 19 IEEVPVPEVG-PGQILVKIEASGVCHTDLHAADGD------WPVKPNPPFIPGHEGVGTV 71 Query: 102 VEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGFNVDGAFAE 161 G + R +G P CGHCR C G+ C+ G++V+G FAE Sbjct: 72 AAVGTGVTAVKEGDR--VGVPWLHTA---CGHCRQCLAGWETLCDLQQNTGYSVNGGFAE 126 Query: 162 YVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVILGGG 221 Y D Y L + + AG V Y ++ +PGD VVI G G Sbjct: 127 YTLADPNYVGHLPDRLDWEMAAPILCAGVTV------YKG--LKETDTKPGDTVVISGIG 178 Query: 222 PIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVID 262 +G AV K G VI + S+ + LA+ +GAD I+ Sbjct: 179 GLGHIAVQYAKAMGLD-VIAVDISDEKLALARAMGADAAIN 218 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: 339 Number of extensions: 17 Number of successful extensions: 3 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: 340 Length adjustment: 30 Effective length of query: 365 Effective length of database: 310 Effective search space: 113150 Effective search space used: 113150 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