Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate Dsui_2312 Dsui_2312 3-hydroxybutyrate dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__PS:Dsui_2312 Length = 260 Score = 118 bits (295), Expect = 1e-31 Identities = 84/260 (32%), Positives = 131/260 (50%), Gaps = 25/260 (9%) Query: 9 AGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVV-------- 60 +G+ A+VTG SG+G VA + G AV L NG AA + A Sbjct: 3 SGKIALVTGSTSGIGLAVARALARNGAAVML---NGSRPAAEAEGLRAAMAAEFGVKVAY 59 Query: 61 -ALDVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGL 119 + D++D A+V A A + LG VDIL+ +AGI V EFP + + ++I INL+ + Sbjct: 60 TSADLADAASVRALAAAAEKQLGVVDILVNNAGIQHVAA-VDEFPEEKWDQLIAINLSSV 118 Query: 120 FYCNREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGV 179 F+ + V+P M +GRIVN+AS G +P + Y+ASK V+GF+K++ E+A G+ Sbjct: 119 FHATKAVLPGMKARNWGRIVNIASAHGLVASPFKAPYTASKHAVVGFSKAVALEVAETGI 178 Query: 180 IANALTPATFESPILDQ----------LPQSQV--DYMRSKIPMGRLGLVEESAAMVCFM 227 NA+ P +P++++ LP+ QV D + + P R ++ A V F+ Sbjct: 179 TCNAVCPGYVRTPLVEKQVAAQAKVHNLPEDQVIRDVILAAQPNKRFLEADDLAEFVLFL 238 Query: 228 ASEECSFTTASTFDTSGGRT 247 S + T + G T Sbjct: 239 CSPAGAGMTGAALPMDGAWT 258 Lambda K H 0.318 0.132 0.381 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: 146 Number of extensions: 5 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: 249 Length of database: 260 Length adjustment: 24 Effective length of query: 225 Effective length of database: 236 Effective search space: 53100 Effective search space used: 53100 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