Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate GFF871 Psest_0890 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= BRENDA::P22144 (363 letters) >FitnessBrowser__psRCH2:GFF871 Length = 369 Score = 89.7 bits (221), Expect = 1e-22 Identities = 106/350 (30%), Positives = 148/350 (42%), Gaps = 44/350 (12%) Query: 30 DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKGVTSLKVGDNVA 89 +VLV++ TG+C +D F G V P VLGHE AG VV+VG+GVTS+K GD+V Sbjct: 29 EVLVRITNTGVCHTDA-FTLSGEDPEGVF--PAVLGHEGAGIVVEVGEGVTSVKPGDHV- 84 Query: 90 IEPGIPSRFSD-----EYKSGHYNLCPH---------MAFAATPNSKEGEP----NPPGT 131 IP ++ KSG NLC M T S G+P T Sbjct: 85 ----IPLYTAECGECLFCKSGKTNLCVAVRATQGKGVMPDGTTRFSYNGQPIYHYMGCST 140 Query: 132 LCKYFKSPEDFLVKL-----PDHVSLELGALVEPLSVGVHASKLGSVAFGDYVAVFGAGP 186 +Y E L K+ P+HV L LG V VH V GD VA+FG G Sbjct: 141 FSEYTVVAEVSLAKINPDANPEHVCL-LGCGVTTGIGAVH--NTAKVQPGDSVAIFGLGG 197 Query: 187 VGLLAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGGS---EELIKAFGGN 243 +GL A A+ A +I +D K ++A+ G AT N K E LI+ G Sbjct: 198 IGLAAIQGARQAKAGRIIAIDTNPAKFELARTFG-ATECLNPKDFDKPIHEVLIEMTGWG 256 Query: 244 VPNVVLECTGAEPCIKLGVDAIAPG-GRFVQVGNAAGPVSFPITVFAMKELTLFGSFRYG 302 V + EC G ++ ++A G G+ + +G A F + + +G Sbjct: 257 VDH-TFECIGNVNVMRSALEAAHRGWGQSIVIGVAGAGKEISTRPFQLITGRTWKGSAFG 315 Query: 303 FNDYKTAVGIFDTNYQNGRENAPIDFEQLITHRYKFKDAIEAYDLVRAGK 352 +T + + G ID +TH D +A+DL+ GK Sbjct: 316 GVKGRTQLPGMVEDAMKGE----IDLAPFVTHTMGLDDINKAFDLMHEGK 361 Lambda K H 0.318 0.138 0.411 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: 375 Number of extensions: 21 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: 363 Length of database: 369 Length adjustment: 30 Effective length of query: 333 Effective length of database: 339 Effective search space: 112887 Effective search space used: 112887 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: 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