Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_085218348.1 B9N75_RS08190 3-hydroxybutyrate dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_900177405.1:WP_085218348.1 Length = 261 Score = 130 bits (328), Expect = 2e-35 Identities = 82/259 (31%), Positives = 133/259 (51%), Gaps = 9/259 (3%) Query: 7 GKVCLVTGAGGNIGLATALRLAEEGTAIALLDM-NREALEKAEASVREKGVEARSYV-CD 64 GK L+TG+ IGLA A LA G I L +R+A+ K + + Y D Sbjct: 5 GKAALITGSTSGIGLAYAKTLAGAGAHIMLNGFGDRDAIAKIQREIEGLSGARTDYSDAD 64 Query: 65 VTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVL 124 +T+ A+ + G +D L NNAG Q APV ++P D + ++ +N++ AFH + Sbjct: 65 LTNPAAIEAMIGQAKSSLGGVDILINNAGMQHV-APVDEFPIDKWNAIIALNLSAAFHAI 123 Query: 125 KAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNA 184 + M + +GRI++TAS + PN +AY +K I LT+T AL++A + I VN Sbjct: 124 RLAVPHMKEKKWGRIISTASAHSLVASPNKSAYVAAKHGIAGLTKTVALEVATHGITVNC 183 Query: 185 ISPGYMGPGFMWERQVELQ-AKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243 ISPGY +W + VE Q T +V+ ++ + P +++ ++ + + Sbjct: 184 ISPGY-----VWTQLVEDQIPDTMKSRGLTREQVMNDVLLAAQPTKQFVTPEQVASLALY 238 Query: 244 LLGDDSSFMTGVNLPIAGG 262 L DD++ +TG NL + GG Sbjct: 239 LCSDDAAAITGANLSMDGG 257 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: 139 Number of extensions: 6 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: 262 Length of database: 261 Length adjustment: 25 Effective length of query: 237 Effective length of database: 236 Effective search space: 55932 Effective search space used: 55932 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 24 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