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 3608022 Dshi_1429 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Dino:3608022 Length = 256 Score = 142 bits (359), Expect = 5e-39 Identities = 85/248 (34%), Positives = 135/248 (54%), Gaps = 8/248 (3%) Query: 7 RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHV-VALDVS 65 R +G+ AIVTG ASG G+++A R + EG VA+ DLNG+ A + + V DVS Sbjct: 9 RLSGKTAIVTGAASGFGREIARRFVREGARVAIVDLNGEGAKAVADALQQNAIAVTCDVS 68 Query: 66 DHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNRE 125 A V+ A +++ A G+VDI I +AG + P + ++F+RV ++N++ +F+ Sbjct: 69 KGADVSRAVQETIDAFGRVDIAINNAGWSHRNQPALDVDFETFKRVYEVNVDSIFHATHA 128 Query: 126 VVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALT 185 +VP + G G ++N+ S AG P S Y++SK V TK+L ELA V L Sbjct: 129 LVPHWRDIGGGVMINVGSTAGIRPRPGLSWYNSSKGAVNMMTKTLAVELAPDRVRVCGLA 188 Query: 186 PATFESPILD------QLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTAST 239 P +P+L+ P+++ ++ IP+GRL E+ A ++AS+E +F T Sbjct: 189 PVMGATPLLETFMGMPDTPENRAKFL-GTIPLGRLCEPEDMANAALYLASDEANFITGVI 247 Query: 240 FDTSGGRT 247 + GGRT Sbjct: 248 LEVDGGRT 255 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: 153 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: 249 Length of database: 256 Length adjustment: 24 Effective length of query: 225 Effective length of database: 232 Effective search space: 52200 Effective search space used: 52200 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: 46 (22.3 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