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 AO353_20700 AO353_20700 oxidoreductase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20700 Length = 258 Score = 117 bits (292), Expect = 3e-31 Identities = 78/244 (31%), Positives = 127/244 (52%), Gaps = 11/244 (4%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEI--DATHVVALDVSDH 67 GR A+VTG A G+G +AA +++EG V L DL+ A + A++ D + +DV+D Sbjct: 13 GRVALVTGAARGIGLGIAAWLVSEGWQVVLTDLDR-ARGSKVAKVLGDNACFIGMDVADE 71 Query: 68 AAVAAAAKDSAAALGKVDILICSAGITGA-TVPVWEFPVDSFQRVIDINLNGLFYCNREV 126 VA + G++D L+C+A + + + + + RV+ +NL+G + Sbjct: 72 QQVAQGVAEVLGQFGRIDALVCNAAVADPHNITLESLDLAYWNRVLAVNLSGPMLLAKHC 131 Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186 P++ + G IVNLAS + P+ AY+ASK G++ T +L L G + NA++P Sbjct: 132 APYLRAHS-GAIVNLASTRAAQSEPDTEAYAASKGGLLALTHALAISL-GPEIRVNAVSP 189 Query: 187 ATFES--PILDQL-PQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTS 243 ++ P + P S D+ + P GR+G VE+ AAMV ++ S+ F T F Sbjct: 190 GWIDTRDPATRRAEPLSDADHAQH--PAGRVGTVEDVAAMVAWLLSKNAGFVTGQEFVVD 247 Query: 244 GGRT 247 GG T Sbjct: 248 GGMT 251 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: 145 Number of extensions: 7 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: 258 Length adjustment: 24 Effective length of query: 225 Effective length of database: 234 Effective search space: 52650 Effective search space used: 52650 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