Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 6935786 Sama_0004 alcohol dehydrogenase, zinc-binding (RefSeq)
Query= BRENDA::P22144 (363 letters) >FitnessBrowser__SB2B:6935786 Length = 377 Score = 89.7 bits (221), Expect = 1e-22 Identities = 106/347 (30%), Positives = 151/347 (43%), Gaps = 38/347 (10%) Query: 30 DVLVQVKKTGICGSDIHFYAHGRIGNFVLTKPMVLGHESAGTVVQVGKGVTSLKVGDNVA 89 +VLV++ TG+C +D F G V P +LGHE G V VG+GVTS+ VGD+V Sbjct: 34 EVLVRIVATGVCHTDA-FTLSGDDPEGVF--PAILGHEGGGIVEMVGEGVTSVAVGDHV- 89 Query: 90 IEPGIPSRFSDEYK-----SGHYNLCPH---------MAFAATPNSKEGEP----NPPGT 131 IP ++ K SG NLC M T K+GEP T Sbjct: 90 ----IPLYTAECGKCKFCTSGKTNLCSAVRATQGKGLMPDGTTRFYKDGEPIYHYMGCST 145 Query: 132 LCKYFKSPEDFLVKLPDHVSLELGALVE-PLSVGVHAS-KLGSVAFGDYVAVFGAGPVGL 189 +Y PE L K+ LE L+ ++ G+ A K V GD VA+FG G +GL Sbjct: 146 FSEYTVLPEISLAKVNPEAPLEEVCLLGCGVTTGMGAVLKTAKVKKGDTVAIFGLGGIGL 205 Query: 190 LAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGG---SEELIKAFGGNVPN 246 A A GA +I +DI D+K ++AK +G AT N K + +++ G V + Sbjct: 206 SAVIGATMAGASRIIGIDINDSKFELAKKLG-ATDCINPKDYDKPIQDVIVEMTDGGV-D 263 Query: 247 VVLECTGAEPCIKLGVDAIAPG-GRFVQVGNAAGPVSFPITVFAMKELTLFGSFRYGFND 305 EC G ++ ++ G G V +G A F + ++ +G Sbjct: 264 FSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTRPFQLVTGRVWRGSAFGGVK 323 Query: 306 YKTAVGIFDTNYQNGRENAPIDFEQLITHRYKFKDAIEAYDLVRAGK 352 ++ + Y G E A DF ITH EA+DL+ GK Sbjct: 324 GRSELPGIVEQYLRG-EFALSDF---ITHTMGLDAINEAFDLMHEGK 366 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: 356 Number of extensions: 18 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: 377 Length adjustment: 30 Effective length of query: 333 Effective length of database: 347 Effective search space: 115551 Effective search space used: 115551 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