Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 18382 b4358 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (RefSeq)
Query= BRENDA::S6BFC0 (363 letters) >FitnessBrowser__Keio:18382 Length = 340 Score = 159 bits (402), Expect = 1e-43 Identities = 108/353 (30%), Positives = 172/353 (48%), Gaps = 20/353 (5%) Query: 11 NSFVLQKQDEISFEDRPVPVAGPGQVIVNIKATGICGSDVHYWTHGRIGHFVCNGPMVLG 70 N + Q+ E+ ++ R +P+ G + ++ IK+ GICG+D+H W G F + P VLG Sbjct: 5 NVLICQQPKELVWKQREIPIPGDNEALIKIKSVGICGTDIHAWG-GNQPFF--SYPRVLG 61 Query: 71 HESAGIVTSLGEGVIDLKVGDRVALEPGVPCGRCEMCKIGKYNLCPDMAFAATPPYDGTL 130 HE G + LG+ + DLK G +VA+ P V C +C CK G+ N C ++ DG Sbjct: 62 HEICGEIVGLGKNIADLKNGQQVAVIPYVACQQCPACKSGRTNCCEKISVIGV-HQDGGF 120 Query: 131 CDYYRHSADFCYKLP-DNVSLEEGALIEPLSVGIHAARRGEVRLGDRVFVFGAGPVGLLT 189 +Y S LP D + + ALIEP ++ HA RR + G++V V GAGP+GL Sbjct: 121 SEYL--SVPVANILPADGIDPQAAALIEPFAISAHAVRRAAIAPGEQVLVVGAGPIGLGA 178 Query: 190 AAAARAAGASHITMADISESRLKFAKSYIADETVHMTSKPPRDVDTNEFAKAEAEKLFQS 249 AA A+A GA + +AD S +R + ++A P D +F +A+ Q Sbjct: 179 AAIAKADGA-QVVVADTSPAR----REHVATR----LELPLLDPSAEDF---DAQLRAQF 226 Query: 250 GITPANVVFDCTGVEVCVQMSVYLVKNNGKIILVGMGASVQSISVADVSAREVDVRGVMR 309 G + A V D TG + + +V L+++ G ++ VG+ S + +E + G Sbjct: 227 GGSLAQKVIDATGNQHAMNNTVNLIRHGGTVVFVGLFKGELQFSDPEFHKKETTMMGSRN 286 Query: 310 YC-NTYPTAIEVLASEKVDLKSLITHRYKFEDSIKAFQHVKEGREGTIKVVIT 361 + ++A K+ ++THRY F + ++ IK VIT Sbjct: 287 ATPEDFAKVGRLMAEGKITADMMLTHRYPFATLAETYERDVINNRELIKGVIT 339 Lambda K H 0.319 0.136 0.405 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: 303 Number of extensions: 18 Number of successful extensions: 5 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: 340 Length adjustment: 29 Effective length of query: 334 Effective length of database: 311 Effective search space: 103874 Effective search space used: 103874 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 (21.8 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