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 GFF3457 Psest_3522 3-hydroxybutyrate dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__psRCH2:GFF3457 Length = 256 Score = 115 bits (289), Expect = 7e-31 Identities = 86/252 (34%), Positives = 128/252 (50%), Gaps = 20/252 (7%) Query: 10 GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEID-----ATHVVALDV 64 G+ A+VTG SG+G +A ++ AE GA + + GDA AA AE+ H A DV Sbjct: 5 GKTALVTGSTSGIGLGIALKL-AEAGADLILNGFGDASAAL-AEVGRHGRKVGHHGA-DV 61 Query: 65 SDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNR 124 SD A +A + G VDIL+ +AGI PV EFPV+ + +I INL+ F+ R Sbjct: 62 SDPAQIAELFAYAERDFGGVDILVNNAGIQHVA-PVEEFPVERWDAIIAINLSSAFHTTR 120 Query: 125 EVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANAL 184 +P M + G+GRI+N+ASV G G+ +AY A+K G++G TK + E A + NA+ Sbjct: 121 LALPGMRQRGWGRIINIASVHGLVGSEQKAAYVAAKHGLVGLTKVVALETATTPITCNAI 180 Query: 185 TPATFESPILDQL-----------PQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECS 233 P +P++ Q Q++ D + K P + AM F+ SE Sbjct: 181 CPGWVLTPLVQQQIDERARESGDEQQARHDLLAEKQPSLDFVTPAQLGAMALFLCSEAGD 240 Query: 234 FTTASTFDTSGG 245 + ++ GG Sbjct: 241 QVRGAAWNMDGG 252 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: 157 Number of extensions: 9 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