Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate PP_3970 PP_3970 putative oxidoreductase, Zn-dependent and NAD(P)-binding
Query= BRENDA::Q86ZV0 (358 letters) >FitnessBrowser__Putida:PP_3970 Length = 400 Score = 107 bits (268), Expect = 4e-28 Identities = 87/268 (32%), Positives = 124/268 (46%), Gaps = 33/268 (12%) Query: 17 GIHKVKFEDRPIPQLRDAHDVLVDVRFTGICGSDVHYWEHGSIGQFVVKDPMVLGHESSG 76 G + V+ + P P L+DA D+++ V T ICGSD+H + G I + D + GHE G Sbjct: 8 GANDVRVDSVPDPILQDADDIILRVTATAICGSDLHLYR-GKIPETEQGD--IFGHEFMG 64 Query: 77 VISKVGSAVTTLKVGDHVAMEPGIPCRRCEPCKEGKYNLCEKMAFA--------ATPP-- 126 ++ +VG VTTL+VGD V + I C C C++ + CE PP Sbjct: 65 IVEEVGRDVTTLQVGDRVVIPFVIACGSCFFCQQDLFAACETTNTGRGSIINKKGIPPGA 124 Query: 127 -----------YDGTLAKYYVLPEDFC--YKLPENINLQEAAVMEP-LSVAVHIVKQANV 172 G A Y +P+ +K+P + + + L A V A + Sbjct: 125 ALFGYSHLYGGIPGGQADYVRVPKGNVGPFKVPTTLADDKVLFLSDILPTAWQAVINAEI 184 Query: 173 APGQSVVVFGAGPVGLLCCAVARAFGSPKVIAVDIQKGRLEFAKK-YAATAI-FEPSKVS 230 G SV ++GAGPVGLL A AR G+ V VD RL +A++ Y I FE Sbjct: 185 GEGSSVAIYGAGPVGLLSAACARMLGAHTVFMVDDNDYRLAYAQEAYGVIPINFEKDD-- 242 Query: 231 ALENAERIVNENDLGRGADIVIDASGAE 258 + A+ I+ + RG D VIDA G E Sbjct: 243 --DPADSIIRQTPGMRGVDAVIDAVGFE 268 Lambda K H 0.319 0.137 0.406 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: 398 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 400 Length adjustment: 30 Effective length of query: 328 Effective length of database: 370 Effective search space: 121360 Effective search space used: 121360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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