Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 3607850 Dshi_1258 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Dino:3607850 Length = 247 Score = 127 bits (318), Expect = 3e-34 Identities = 87/255 (34%), Positives = 131/255 (51%), Gaps = 22/255 (8%) Query: 9 VCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTSE 68 + L+TG IG A A LA EG I L D+ ++++++A A + G Y+CD+ Sbjct: 6 LALITGGAQGIGYACAEALAAEGARIILADI-QDSVQEAAARLGGAG-----YLCDMGDA 59 Query: 69 EAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKAVS 128 AV D + + G + +L NNAG A DY F RVL IN+ G F + Sbjct: 60 AAVGALFDRIEAEHGAVTYLVNNAGI-AAPGDFLDYDLATFDRVLDINLRGVFVATQRAG 118 Query: 129 RQMITQNY-GRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAISP 187 R M+ G +VN +S+ P++ AY SKG ++ LT+ AAL LAP+ IRVNA+ P Sbjct: 119 RSMVAHGIKGAVVNMSSINAQVAIPSIPAYCASKGGLMQLTKVAALALAPHGIRVNAVGP 178 Query: 188 GYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLGD 247 G + E+ A V + +P+ + ++ P++R G EI VVAFL D Sbjct: 179 GSI--------DTEMMAGV-----NANPEAM-NMVLSRTPLKRVGTAQEIANVVAFLCSD 224 Query: 248 DSSFMTGVNLPIAGG 262 +S++TG + + GG Sbjct: 225 KASYVTGETIYVDGG 239 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: 167 Number of extensions: 11 Number of successful extensions: 5 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: 247 Length adjustment: 24 Effective length of query: 238 Effective length of database: 223 Effective search space: 53074 Effective search space used: 53074 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