Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__Btheta:351439 Length = 259 Score = 116 bits (291), Expect = 4e-31 Identities = 74/263 (28%), Positives = 122/263 (46%), Gaps = 19/263 (7%) Query: 3 KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62 K+F KV ++TGA G IG AT R+ EG + + D+++E +K A + + G + R Sbjct: 2 KRFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPIY 61 Query: 63 CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAP--VQDYPSDDFARVLTINVTGA 120 T ++ VD ++++G+ID L NN G ++ D F V +N+ Sbjct: 62 FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180 ++ + V M T G IVN AS++G+ N YG SK +I LT+ A + NI Sbjct: 122 MYLSQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKNI 181 Query: 181 RVNAISPG-YMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239 R NA++PG + P + E V +G G+ ++ Sbjct: 182 RCNAVAPGLVLTPAALDNLNEE----------------VRNIFLGQCATPYLGEPEDVAA 225 Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262 +AFL +D+ ++TG + + GG Sbjct: 226 TIAFLASNDARYITGQTIVVDGG 248 Lambda K H 0.318 0.135 0.384 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: 158 Number of extensions: 7 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: 262 Length of database: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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: 47 (22.7 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