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 PP_1946 PP_1946 Oxidoreductase, short chain dehydrogenase/reductase family
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Putida:PP_1946 Length = 262 Score = 142 bits (359), Expect = 5e-39 Identities = 80/242 (33%), Positives = 126/242 (52%), Gaps = 4/242 (1%) Query: 8 YAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGD----ALAATQAEIDATHVVALD 63 ++G+ +VTG SG+G+ A G +VA+ D++ D + +AE +D Sbjct: 7 FSGKVVLVTGAGSGIGRATALAFAQSGASVAVADISTDHGLKTVELVKAEGGEATFFHVD 66 Query: 64 VSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCN 123 V +V + A G +DI +AGI VP+ E D+++RVID+NL+ +FYC Sbjct: 67 VGSEPSVQSMLAGVVAHYGGLDIAHNNAGIEANIVPLAELDSDNWRRVIDVNLSSVFYCL 126 Query: 124 REVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANA 183 + +P ML+ G G IVN AS +G G S Y+A+K GV+G TK+ + A + + NA Sbjct: 127 KGEIPLMLKRGGGAIVNTASASGLIGGYRLSGYTATKHGVVGLTKAAAIDYANQNIRINA 186 Query: 184 LTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTS 243 + P +SP L +PQ D + P+GRL EE A V ++ S++ + + Sbjct: 187 VCPGPVDSPFLADMPQPMRDRLLFGTPIGRLATAEEIARSVLWLCSDDAKYVVGHSMSVD 246 Query: 244 GG 245 GG Sbjct: 247 GG 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: 179 Number of extensions: 9 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: 262 Length adjustment: 24 Effective length of query: 225 Effective length of database: 238 Effective search space: 53550 Effective search space used: 53550 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