Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ga0059261_1900 Ga0059261_1900 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Korea:Ga0059261_1900 Length = 250 Score = 129 bits (325), Expect = 5e-35 Identities = 94/262 (35%), Positives = 132/262 (50%), Gaps = 20/262 (7%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEA-SVREKGVEARSYV 62 +F KV +VTG G +IG + +LRLA EG + + + EA KA ++ G A Sbjct: 2 RFKDKVAIVTGGGRDIGKSISLRLAAEGAKVVINYRSDEAAAKATLDAIEAAGGTALLAR 61 Query: 63 CDVTSEEAVIGTVDSVVRDFG-KIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121 DVT + V+ V + FG K+D L N AG A + + F V+ +N+ AF Sbjct: 62 ADVTKADEVVALVKAATDAFGGKVDILVNCAGGMVARKTLAEMDEAFFDTVMDLNLKSAF 121 Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGP-PNMAAYGTSKGAIIALTETAALDLAPYNI 180 V KAV + ++ IVN AS AG G P + Y SKGA++ LT + A +L P I Sbjct: 122 LVTKAVLPHL--ESGAAIVNIASQAGRDGGGPGASIYAASKGALMTLTRSWAKELGPQGI 179 Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240 RVNA++PG +G F FS A + G+ P+RR G +E+ Sbjct: 180 RVNALNPGLIGTSF-------------HDIFSKPEGRAA--VAGNTPLRREGHPDEVAAA 224 Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262 VAFL D+SF+TG N+ I GG Sbjct: 225 VAFLASGDASFLTGTNVDINGG 246 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: 168 Number of extensions: 8 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: 262 Length of database: 250 Length adjustment: 24 Effective length of query: 238 Effective length of database: 226 Effective search space: 53788 Effective search space used: 53788 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 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