Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate CA265_RS00955 CA265_RS00955 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Pedo557:CA265_RS00955 Length = 327 Score = 181 bits (460), Expect = 2e-50 Identities = 115/314 (36%), Positives = 170/314 (54%), Gaps = 20/314 (6%) Query: 26 VALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKG-QR 84 +A G +AIGG MWGG + SI+++ +ID GI IDTAP YG G +E ++G+AIKG R Sbjct: 16 IAYGAFAIGGNMWGGNEKKDSIESVKASIDNGITTIDTAPFYGFGLSEALIGEAIKGYDR 75 Query: 85 DNLIIATKVGLDWTLTPDQS---------------MRRNSSASRIKKEIEDSLRRLGTDY 129 + + TK GL W + + + + R ++ + I KE+EDSL+RL TDY Sbjct: 76 TKIQLLTKFGLVWDGSNNGAGEHFFDAQNDGKAVPIYRYATKASIIKEVEDSLKRLHTDY 135 Query: 130 IDLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPY 189 IDL Q HWPDP I+E + L K+GKI + G+SN +++ A +Q P+ Sbjct: 136 IDLLQQHWPDPTTEIDEVMEAMAQLIKDGKILAAGLSNADHALLEKAAAVNLPASNQVPF 195 Query: 190 NLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRF 249 ++ R I D++PY +N++ ++ Y + RGLLSG+ DD R + F + Sbjct: 196 SMLNRAIQDDLIPYTLENNIGIIAYSPMERGLLSGKYFEKEKLKADDHR--NGYFSQFDL 253 Query: 250 EHYLAAVEELKKLAKEHYNKSVLALAIRW-MLEQGPTLALWGACKPEQIDGIDEVFGWQI 308 + +E + LAKE N S+ L +RW L+QG T+ L GA EQ ++I Sbjct: 254 DAVKTFLERISPLAKEK-NASIAQLVLRWTTLQQGITVVLAGARNAEQAVSNAAAMDFEI 312 Query: 309 SDEDLKQIDAILAK 322 S E+L ID L K Sbjct: 313 SKEELAFIDGELGK 326 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: 255 Number of extensions: 9 Number of successful extensions: 4 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