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 HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__HerbieS:HSERO_RS02925 Length = 244 Score = 209 bits (531), Expect = 5e-59 Identities = 111/241 (46%), Positives = 155/241 (64%), Gaps = 8/241 (3%) Query: 10 GRC-AIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDHA 68 G C A+VTGG G+G ++AR+ A G V +WD + DA + + + ++D++D Sbjct: 11 GDCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQHHDAASPYRQQ-------SIDITDAP 63 Query: 69 AVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVP 128 AV AA++ A G++D LI +AG G TVP+ E+ V + R++ +NL G+F+ R V P Sbjct: 64 AVMQAAQELLADTGRIDFLINNAGYAGPTVPLDEYDVGEWHRIVQVNLLGVFHACRSVTP 123 Query: 129 FMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPAT 188 M GRIVN+AS+AGKEG PNASAYSA+KAGV+ TKSLGKELA GV+ NA+ PA Sbjct: 124 AMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVLVNAIAPAA 183 Query: 189 FESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGRTT 248 ++ +L Q+ + V M +K PM RLG V+E A M ++ S CSF T + FD SGGR T Sbjct: 184 VKTALLGQMSPAHVQTMIAKSPMHRLGSVDEVADMCAWLCSGSCSFNTGAVFDLSGGRAT 243 Query: 249 F 249 + Sbjct: 244 Y 244 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: 174 Number of extensions: 10 Number of successful extensions: 2 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: 244 Length adjustment: 24 Effective length of query: 225 Effective length of database: 220 Effective search space: 49500 Effective search space used: 49500 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