Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_038857207.1 AFK65_RS09920 SDR family oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_001277175.1:WP_038857207.1 Length = 254 Score = 131 bits (330), Expect = 1e-35 Identities = 81/262 (30%), Positives = 136/262 (51%), Gaps = 24/262 (9%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVRE-KGVEARSYV 62 +F KV +VTGAG IG A A R A EG ++ L+ +E L+K A++ + K + A Sbjct: 3 RFQEKVVVVTGAGSGIGAAAARRFAREGASVVLVGRTKEKLDKVAATLAQGKHLVAP--- 59 Query: 63 CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQDYPSDDFARVLTINVTGA 120 CDV+ V V +FG++D + NNAG QG + + +D+ ++ ++ G Sbjct: 60 CDVSDAAQVQALAQRVTDEFGRVDVVVNNAGVIVQGK---IHEITLEDWETLMGTDLNGV 116 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180 F+ L A ++ + G ++N +S++G+ G M+ Y +KGA+ T + A+D + Sbjct: 117 FYCLHAFMPGLL-KTKGNVINISSVSGLGGDWGMSVYNAAKGAVTNFTRSLAMDYGADGV 175 Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240 RVNAI PG+ + + + + Q+ +PM+R G+ +I Sbjct: 176 RVNAICPGFTFTDLTEDTKQD--------------DALLQKFYERIPMKRAGEPEDIADA 221 Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262 +AFL DD+ ++TGVNLP+ GG Sbjct: 222 IAFLASDDARYITGVNLPVDGG 243 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: 168 Number of extensions: 12 Number of successful extensions: 4 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: 254 Length adjustment: 24 Effective length of query: 238 Effective length of database: 230 Effective search space: 54740 Effective search space used: 54740 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 24 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