Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__PV4:5210422 Length = 248 Score = 135 bits (341), Expect = 6e-37 Identities = 87/262 (33%), Positives = 122/262 (46%), Gaps = 18/262 (6%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 M F GKV L+TGA G A RLA +G + L D+N AL+ + + E V R Sbjct: 1 MQSNFEGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDINDTALDALCSELGECAVGLR- 59 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120 CDV+ E + FG++D NNAG + D IN G Sbjct: 60 --CDVSIEAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGV 117 Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180 F +KA M G I+N ASMAG+ G P + Y +K A++ +T TAAL+ A I Sbjct: 118 FFGMKAQIPLMQKHKCGAILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGI 177 Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240 +VNAI P + + E DP ++ +Q+ +VPMRR D NE+ Sbjct: 178 QVNAICPFFTPTPMVTE--------------GVDPALI-EQLTRAVPMRRLADPNEVVSA 222 Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262 + ++ D+ FMTG + I GG Sbjct: 223 MLHMVNPDNGFMTGQAIAIDGG 244 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: 160 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: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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