Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate PP_2368 PP_2368 2,5-diketo-D-gluconate reductase
Query= BRENDA::A0MTG4 (323 letters) >FitnessBrowser__Putida:PP_2368 Length = 267 Score = 142 bits (359), Expect = 7e-39 Identities = 106/304 (34%), Positives = 146/304 (48%), Gaps = 50/304 (16%) Query: 15 LEMPSIGFGCWKLGKSTAADQVYNAIKAGYRLFDGAEDYGNEQEVGEGVKRAIDEGIVTR 74 + +PS G G ++L T D V +A+ GYR+ D A+ Y NE EVG+ AI E V R Sbjct: 1 MSVPSFGLGTFRLTGQTVIDSVKSALAVGYRVIDTAQIYKNEAEVGQ----AIAESGVPR 56 Query: 75 EEIFLTSKLWNNYHDPKNVETALNKTLKDLKVDYVDLFLIHFPIAFKFVPIEEKYPPGFY 134 E+F+T+K+W + + + +L +L+ L+ DYVDL LIH+P PG Sbjct: 57 SELFITTKIWVDNYAADKLIPSLRDSLQKLRTDYVDLLLIHWP------------APG-- 102 Query: 135 CGDGDNFVYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLFRGATI-----KPA 189 V + E KAL + G R IGVSNF ++L R A + A Sbjct: 103 ---------NGVELPEYMKALADAKQQGLARQIGVSNFN----IELTRQAIAVVGKGEIA 149 Query: 190 VLQVEHHPYLQQPKLIEYAQKVGITVTAYSSFGPQSFVEMNQGRALNTPTLFEHDVIKAI 249 Q+E PYLQ KL + ++ GITVT+Y + + G+ L P V+ I Sbjct: 150 TNQIELSPYLQNSKLTAFLKEQGITVTSY--------MTLAYGKVLKDP------VLAQI 195 Query: 250 AAKHNKVPAEVLLRWSAQRGIAVIPKSNLPERLVQNRSFNDFELTKEDFEEISKLDINLR 309 AAKH A+V L W+ Q G AVIP S E L N L +D I+KL+ N R Sbjct: 196 AAKHKATVAQVALAWALQLGYAVIPSSTKRENLASNLLARGLTLDTDDMARIAKLERNGR 255 Query: 310 FNDP 313 P Sbjct: 256 EVSP 259 Lambda K H 0.319 0.139 0.422 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: 205 Number of extensions: 11 Number of successful extensions: 5 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: 323 Length of database: 267 Length adjustment: 26 Effective length of query: 297 Effective length of database: 241 Effective search space: 71577 Effective search space used: 71577 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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