Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate CA265_RS12005 CA265_RS12005 glutathione-dependent formaldehyde dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Pedo557:CA265_RS12005 Length = 385 Score = 101 bits (252), Expect = 3e-26 Identities = 78/267 (29%), Positives = 123/267 (46%), Gaps = 30/267 (11%) Query: 39 EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFS 98 ++RV+ VP+P+I P ++I+KV + ICGSD+H+ G + P+ +GHEF Sbjct: 11 DIRVDYVPDPKILDPRDVILKVTSTAICGSDLHILS----GAVPQKD----PLIMGHEFM 62 Query: 99 GVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGH-CRPCAE--GFPNHCEN-------- 147 G+V E G N + R + P+ + +C H P E F N+ N Sbjct: 63 GIVEEVGASITNLKRGDRVVVPFPISCGKCFFCTHEASPACETSNFKNYGPNGDMMSQKG 122 Query: 148 -----LNELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAV 202 +L G A+YV+V E + + LFL + PT + Sbjct: 123 AALFGYTDLYGGYSGGQAQYVRVPYADISPRIVPEHLSDEQALFLTD--IFPTGWS---- 176 Query: 203 IVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVID 262 + ++ G+ V I G GP+GL A GAS+VI +P + R AK + +++ Sbjct: 177 AIDWAQLKGGEVVAIFGSGPVGLMAQKAAWINGASRVIAIDPLDYRLEKAKAVNNVDILN 236 Query: 263 PTKENFVEAVLDYTNGLGAKLFLEATG 289 P K + VEA+ + T G GA L ++A G Sbjct: 237 PHKVDVVEAIREMTGGRGADLCVDAVG 263 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: 370 Number of extensions: 19 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: 385 Length adjustment: 31 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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