Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_106712313.1 CU102_RS17075 L-iditol 2-dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_003010955.1:WP_106712313.1 Length = 258 Score = 130 bits (327), Expect = 3e-35 Identities = 84/262 (32%), Positives = 137/262 (52%), Gaps = 13/262 (4%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTA-IALLDMNREALEKAEASVREKGVEARSYV 62 + GK +TG+ IG A A E A + + D+N LE+A+ + RE G A + Sbjct: 3 RLEGKTAFITGSARGIGRAFAEAYLRESAAHVVIADIN---LERAQETARELGAGAYAVR 59 Query: 63 CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFH 122 DVT + ++ V V FG ID L NNA AP+ + + + ++ +N +G Sbjct: 60 LDVTDQASIDAAVSETVTKFGGIDVLINNAALFD-LAPIVEITRESYEKLFAVNFSGTLF 118 Query: 123 VLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181 L+AV++ MI + G +I+N AS AG +G P +A Y +K A+I+LT++A L+L + I Sbjct: 119 TLQAVAKAMIARGKGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIEHGIN 178 Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIG-SVPMRRYGDINEIPGV 240 VNA++PG + G WE L AK + P+ ++++G +VP R G ++ G+ Sbjct: 179 VNAMAPGVV-DGEHWEGVDALFAK-----YENRPRGEKKRLVGEAVPYGRMGTAEDLTGM 232 Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262 FL +S ++ + GG Sbjct: 233 AIFLASSESDYIVAQTYNVDGG 254 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: 159 Number of extensions: 12 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: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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