Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BWI76_RS11560 BWI76_RS11560 oxidoreductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Koxy:BWI76_RS11560 Length = 327 Score = 179 bits (454), Expect = 9e-50 Identities = 112/313 (35%), Positives = 173/313 (55%), Gaps = 17/313 (5%) Query: 14 ISIKGIDKSATRVALGTWAIGGW-MWGGTDD-DASIKTIHRAIDLGINIIDTAPAYGRGH 71 I + D +R+ LGTWAIGG W G D I TI A GIN+IDTAP Y G+ Sbjct: 4 IPLGSTDIRLSRMGLGTWAIGGGPAWNGDLDLRICIDTIIEAHRCGINLIDTAPGYNFGN 63 Query: 72 AEEVVGKAIKG-QRDNLIIATKVGLDWTLTP-------DQSMRRNSSASRIKKEIEDSLR 123 +E +VG+A+K R ++++ TK G+ W T D+ + +N + I++E++ SL+ Sbjct: 64 SEVIVGQALKQLPRRDIVVETKCGIVWERTGSLFNKVGDRQLYKNLTPESIREEVDASLQ 123 Query: 124 RLGTDYIDLYQVHWPDP---LVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYA 180 RLG D ID+Y HW PI ET L AL+KEGKIR+IG +N + E+ K+ Sbjct: 124 RLGIDTIDIYMTHWQSVEPCFTPIAETVATLNALKKEGKIRAIGAANVDAGHIREYLKHG 183 Query: 181 ELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKT 240 EL + Q+ Y++ +R ++ ++LP ++N +VV Y L +GLLSG +T D + R Sbjct: 184 ELDIVQAKYSILDRALEAELLPLCQQNGIVVQVYSPLEQGLLSGTITRD--YVPGGARAN 241 Query: 241 DPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGPTLALW-GACKPEQIDG 299 FQ+ + +E+ + L E Y ++ ALA+ W+L+Q + L GA PEQ+ Sbjct: 242 KVWFQRENMLRVIDMLEQWQPLC-EKYRCAIPALALAWILKQSDLITLLSGATAPEQVRE 300 Query: 300 IDEVFGWQISDED 312 + ++D+D Sbjct: 301 NIDALTIALTDDD 313 Lambda K H 0.317 0.136 0.407 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: 264 Number of extensions: 14 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: 340 Length of database: 327 Length adjustment: 28 Effective length of query: 312 Effective length of database: 299 Effective search space: 93288 Effective search space used: 93288 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 (21.6 bits) S2: 49 (23.5 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