Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate GFF854 HP15_833 2,5-diketo-D-gluconic acid reductase B
Query= BRENDA::A0MTG4 (323 letters) >FitnessBrowser__Marino:GFF854 Length = 269 Score = 147 bits (372), Expect = 2e-40 Identities = 103/305 (33%), Positives = 149/305 (48%), Gaps = 47/305 (15%) Query: 17 MPSIGFGCWKLGKSTAADQVYNAIKAGYRLFDGAEDYGNEQEVGEGVKRAIDEGIVTREE 76 +P IG G ++L + A D V +A+ GYR D A+ YGNE EVG+G I + R E Sbjct: 6 LPKIGMGTFRLKGNDARDAVKSALSLGYRHIDTAQMYGNEAEVGDG----ITSSGIPRRE 61 Query: 77 IFLTSKLWNNYHDPKNVETALNKTLKDLKVDYVDLFLIHFPIAFKFVPIEEKYPPGFYCG 136 IFLT+K+W++ ++ +L+ +L LK D+VDL LIH+P PG Sbjct: 62 IFLTTKIWHDQLHASDLINSLHDSLARLKTDHVDLALIHWP------------SPG---- 105 Query: 137 DGDNFVYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLFRGATIKPAVL-QVEH 195 ++VP+ E AL + G IG+SNF A + + P QVE Sbjct: 106 -------DEVPMKEYLGALRDSQREGLAEHIGISNFTCAQMDEAKAILGDTPIFTNQVEV 158 Query: 196 HPYLQQPKLIEYAQKVGITVTAYSSFGPQSFVEMNQGRALNTPTLFEHDVIKAIAAKHNK 255 HP+L K++ +AQK+GITVT Y L + E + ++ IAA+ N Sbjct: 159 HPFLANRKVVAHAQKLGITVTGYMP--------------LAVGKVMEDETLQRIAAERNL 204 Query: 256 VPAEVLLRWSAQRGIAVIPKSNLPERLVQNRSFNDFELTKEDFEEISKLDINLRFNDP-- 313 PA+V + W A RG+ IP S P N + EL++E+ I +LD N R +P Sbjct: 205 TPAQVAIAWVASRGVVPIPSSTRPGHQKANLEALEVELSEEEIRAIDELDRNERIANPDF 264 Query: 314 ---WD 315 WD Sbjct: 265 APSWD 269 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: 225 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: 269 Length adjustment: 26 Effective length of query: 297 Effective length of database: 243 Effective search space: 72171 Effective search space used: 72171 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