Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate N515DRAFT_4192 N515DRAFT_4192 Predicted oxidoreductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Dyella79:N515DRAFT_4192 Length = 314 Score = 122 bits (306), Expect = 1e-32 Identities = 96/318 (30%), Positives = 154/318 (48%), Gaps = 36/318 (11%) Query: 26 VALGTWAIGGWMWG-GTDDDASIKTIHRAIDLGINIIDTAPAYGR-------GHAEEVVG 77 +++ A GG ++G D+ S + + + +D G N+IDTA Y G +E ++G Sbjct: 11 LSIAPLAFGGNVFGWSVDEKRSFELLDQFVDAGFNLIDTADVYSAWAPGNRGGESETIIG 70 Query: 78 KAIK--GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQV 135 K +K G+RD ++IATKV W + + I++ +E SL+RL TD+IDLYQ Sbjct: 71 KWLKQSGKRDRVLIATKVA-KWV------EHKGLAPLNIQQAVEGSLKRLQTDHIDLYQA 123 Query: 136 HWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDE---------FKKYAELAVSQ 186 H D VP+ ET L ++GK+R IG SNY + E +Y L Q Sbjct: 124 HEDDASVPLHETLGAFARLIEQGKVRVIGASNYGADRFAEALDVSARHNLPRYESL---Q 180 Query: 187 SPYNLFER-EIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTD-PKF 244 YNL R + +K + P K + V+ Y AL G LSG+ ++ R KF Sbjct: 181 PEYNLMVRGDYEKYLEPLVTKEQVGVINYYALASGFLSGKYRSETDLGKSAARAAAVRKF 240 Query: 245 QKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQ-GPTLALWGACKPEQIDGIDEV 303 PR LAA++++ K + + +A+ W++ + T + A EQ++ + Sbjct: 241 LNPRGMGVLAALDDVAKT----HRATPSQVALAWLMARPSITAPIASATSAEQLNDLIGA 296 Query: 304 FGWQISDEDLKQIDAILA 321 Q+S ++ Q+DA A Sbjct: 297 ARLQLSATEIAQLDAASA 314 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: 263 Number of extensions: 20 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: 340 Length of database: 314 Length adjustment: 28 Effective length of query: 312 Effective length of database: 286 Effective search space: 89232 Effective search space used: 89232 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: 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