Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate H281DRAFT_00358 H281DRAFT_00358 Aldo/keto reductase
Query= BRENDA::P31867 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_00358 Length = 312 Score = 196 bits (497), Expect = 8e-55 Identities = 114/300 (38%), Positives = 170/300 (56%), Gaps = 18/300 (6%) Query: 7 NSGYDMPAVGFGCWKVDVDTCSEQIYRAIKTGYRLFDGAEDYANEKLVGAGVKKAIDEGI 66 + G MPA+GFG D A++ GYR FD AE Y NE+ VG ++ + G Sbjct: 16 HGGGSMPAIGFGTLIADAAITISATKDALEAGYRHFDCAERYRNEREVGDALQAGLAAGG 75 Query: 67 VKREDLFLTSKLWNNYHHPDNVEKALNRTLSDLQVDYVDLFLIHFPVTFKFVPLEEKYPP 126 + RED+F+T+KLWN+ H P+ V+ A + +L L++DY+DL+LIH P F F +E+ P Sbjct: 76 IAREDIFVTTKLWNSNHRPERVKPAFDASLERLRLDYLDLYLIHTP--FAFQAGDEQDPR 133 Query: 127 GFYCGKGDNFDYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLLRGATIKPSVL 186 G+ E V +L+TW+A+E LV G+ R+IG+S+ L+ L A IKP+V+ Sbjct: 134 D---ANGNVLYDEGVTLLDTWRAMEDLVDGGRCRAIGLSDIGLDDLVPLYESARIKPAVV 190 Query: 187 QVEHHPYLQQPRLIEFAQSRGIAVTAYSSFGPQSFVELNQGRALNTSPLFENETIKAIAA 246 QVE HPYL + L+EF + + I A++ G + PL E+ + IAA Sbjct: 191 QVEAHPYLPESELLEFCKKKEIVFLAFAPL----------GHGIRPGPL-EDPVVSRIAA 239 Query: 247 KHGKSPAQVLLRWSSQRGIAIIPKSNTVPRLLENKDVNSFDLDEQDFADIAKLDINLRFN 306 + GK+PAQVLL W+ QRG A++ T R EN D+++ D F +I +++ RFN Sbjct: 240 RIGKTPAQVLLAWAVQRGTAVLTTPKTAARARENFDISALPADA--FDEINRIETRQRFN 297 Lambda K H 0.320 0.139 0.423 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: 279 Number of extensions: 12 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: 318 Length of database: 312 Length adjustment: 27 Effective length of query: 291 Effective length of database: 285 Effective search space: 82935 Effective search space used: 82935 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 (21.8 bits) S2: 48 (23.1 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