Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS02925 Length = 244 Score = 142 bits (358), Expect = 7e-39 Identities = 85/261 (32%), Positives = 130/261 (49%), Gaps = 27/261 (10%) Query: 2 SKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSY 61 S F V +VTG G IG A + RLA G + + D + +A + R++ + Sbjct: 7 SYDFGDCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQHHDAA----SPYRQQSI----- 57 Query: 62 VCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121 D+T AV+ ++ D G+IDFL NNAGY G P+ +Y ++ R++ +N+ G F Sbjct: 58 --DITDAPAVMQAAQELLADTGRIDFLINNAGYAGPTVPLDEYDVGEWHRIVQVNLLGVF 115 Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181 H ++V+ M GRIVN AS+AG +G PN +AY +K ++ALT++ +LA + Sbjct: 116 HACRSVTPAMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVL 175 Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241 VNAI+P A V + Q MI PM R G ++E+ + Sbjct: 176 VNAIAP----------------AAVKTALLGQMSPAHVQTMIAKSPMHRLGSVDEVADMC 219 Query: 242 AFLLGDDSSFMTGVNLPIAGG 262 A+L SF TG ++GG Sbjct: 220 AWLCSGSCSFNTGAVFDLSGG 240 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: 150 Number of extensions: 8 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: 244 Length adjustment: 24 Effective length of query: 238 Effective length of database: 220 Effective search space: 52360 Effective search space used: 52360 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: 46 (22.3 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