Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Pf1N1B4_5039 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5039 Length = 257 Score = 150 bits (379), Expect = 3e-41 Identities = 90/261 (34%), Positives = 144/261 (55%), Gaps = 10/261 (3%) Query: 3 KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62 K+ GK L+TG+ IG A EG +A+ D+N LE+A+A+ E A + Sbjct: 2 KRLEGKSALITGSARGIGRTFAQAYIREGATVAIADIN---LERAQATAAELWPNAYAVE 58 Query: 63 CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFH 122 DVT ++++ G + +V+ GK+D L NNA AP+ + D + R+ +INV+G Sbjct: 59 MDVTDQQSIDGAIAAVIATTGKLDILINNAALFD-LAPITEISRDSYERLFSINVSGTLF 117 Query: 123 VLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181 L+A ++QMI Q +G +I+N AS AG +G +A Y +K A+I+LT++A L+L P+NI Sbjct: 118 TLQAAAKQMIRQGHGGKIINMASQAGRRGEALVAVYCATKAAVISLTQSAGLNLIPHNIN 177 Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241 VNAI+PG + G W+ L AK ++ K+ Q+ VP R G +++ G+ Sbjct: 178 VNAIAPGVV-DGEHWDGVDALFAKYENRPLGEKKKLAGQE----VPYGRMGTADDLVGMA 232 Query: 242 AFLLGDDSSFMTGVNLPIAGG 262 FL +S ++ + GG Sbjct: 233 IFLASAESDYIVAQTYNVDGG 253 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: 163 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: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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