Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_011914237.1 PST_RS15785 KR domain-containing protein
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_000013785.1:WP_011914237.1 Length = 252 Score = 119 bits (297), Expect = 8e-32 Identities = 88/265 (33%), Positives = 139/265 (52%), Gaps = 31/265 (11%) Query: 8 KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67 KV +VTG G +G A A LA G +AL+D+N++ L++A A+ + G EAR+Y+C+V S Sbjct: 6 KVIIVTGGGQGLGRAMAEHLAGRGARLALVDLNQDRLDEAVAACKAAGGEARAYLCNVAS 65 Query: 68 EEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQD-----YPSDDFARVLTINVTGA 120 EE V V V DFG + L NNAG G V+D + V+ +N+TG Sbjct: 66 EEQVCEMVARVAEDFGGLHGLVNNAGILRDGLLLKVKDGEISKMSLAQWQAVIDVNLTGV 125 Query: 121 FHVLKAVSRQMI-TQNYGRIVNTASM--AGVKGPPNMAAYGTSKGAIIALTETAALDLAP 177 F + V+ +M+ ++ G I+N +S+ AG G N Y +K + + T A +LA Sbjct: 126 FLCTREVAAKMVELKSEGAIINISSISRAGNMGQTN---YSAAKAGVASATVVWAKELAR 182 Query: 178 YNIRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEI 237 Y IRV ++PG++ + E+ A S P+ + ++M +P++R G EI Sbjct: 183 YGIRVAGVAPGFI--------ETEMVA-------SMKPEAL-EKMTAGIPLKRMGKPAEI 226 Query: 238 PGVVAFLLGDDSSFMTGVNLPIAGG 262 VA++ +D + TG L + GG Sbjct: 227 AHSVAYIFEND--YYTGRILELDGG 249 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: 162 Number of extensions: 9 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: 252 Length adjustment: 24 Effective length of query: 238 Effective length of database: 228 Effective search space: 54264 Effective search space used: 54264 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