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 RR42_RS21790 RR42_RS21790 short-chain dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Cup4G11:RR42_RS21790 Length = 252 Score = 136 bits (343), Expect = 4e-37 Identities = 82/248 (33%), Positives = 134/248 (54%), Gaps = 10/248 (4%) Query: 9 AGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATH------VVAL 62 AG+ + TGGASG+G+ +A G + L DL+ LA+ +AE++A + +V Sbjct: 2 AGKVVLNTGGASGIGRAMAHGFARHGARLMLLDLDAQGLASAKAELEAAYPEVQVEIVKA 61 Query: 63 DVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYC 122 ++D AV A + A G++DIL+ +AGI+ P E D ++R IDI+L+G+F+C Sbjct: 62 SITDPDAVEQACAATEARFGRIDILLNNAGIS-MNKPSLELTPDDWRRAIDIDLSGVFFC 120 Query: 123 NREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIAN 182 + M+ G G I++ AS+ G + AY A+KAGV+ TKSL E A + N Sbjct: 121 TQAAARRMVRQGGGSILSTASMWGLASSARRLAYCAAKAGVVSLTKSLAAEWAEYNIRVN 180 Query: 183 ALTPATFESPILDQLPQSQV---DYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTAST 239 A+ P + +++ L S+ + + ++ P+ R G EE A + F+AS+ +F T Sbjct: 181 AVCPGYTSTALMETLLASKAIDGEALLARTPLRRFGAPEEMAEVALFLASDSAAFITGHA 240 Query: 240 FDTSGGRT 247 + GG T Sbjct: 241 LVSDGGWT 248 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: 133 Number of extensions: 5 Number of successful extensions: 4 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: 252 Length adjustment: 24 Effective length of query: 225 Effective length of database: 228 Effective search space: 51300 Effective search space used: 51300 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