Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_110751435.1 C7477_RS09440 L-iditol 2-dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_003217235.1:WP_110751435.1 Length = 258 Score = 132 bits (331), Expect = 9e-36 Identities = 89/263 (33%), Positives = 136/263 (51%), Gaps = 10/263 (3%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 MS + GK +TGA IG A A A EG +AL D++ L++A+ S + G A + Sbjct: 1 MSGRLEGKSAFITGAARGIGFAFAEAFAREGATVALADID---LDRAQESAAKIGERAYA 57 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 DVT ++ V V G ID L NNA AP+ + + F R+ +NV G Sbjct: 58 VQIDVTDIASIERAVAEAVAKTGGIDILVNNAALFD-MAPMVEITRESFERLYAVNVHGV 116 Query: 121 FHVLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179 ++AV+R MI + G +I+N AS AG +G +A Y ++K A+I+LT++A LDL + Sbjct: 117 LFTMQAVARAMIARGRGGKIINMASQAGRRGEALVAVYCSTKAAVISLTQSAGLDLIRHG 176 Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 I VNAI+PG + G W L AK ++ ++V + +VP R G ++ G Sbjct: 177 INVNAIAPGVV-DGEHWAGVDALFAKHENRPLGEKKRLVGE----AVPFGRMGRPEDLTG 231 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 + FL G +S ++ + GG Sbjct: 232 MAIFLAGPESDYVVAQTYNVDGG 254 Lambda K H 0.318 0.135 0.384 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: 158 Number of extensions: 16 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: 262 Length of database: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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