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 WP_028314742.1 G491_RS0111750 NAD(P)-dependent oxidoreductase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000429905.1:WP_028314742.1 Length = 265 Score = 128 bits (321), Expect = 1e-34 Identities = 89/254 (35%), Positives = 125/254 (49%), Gaps = 17/254 (6%) Query: 7 RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAAT--QAEIDATHVV--AL 62 R G+ AI+TG ASG+G A G ++ L D+ +ALAA QAE VV Sbjct: 6 RLQGKTAIITGAASGIGAATATLFAEHGASLVLADVVEEALAAVAAQAEEKGAKVVYKTT 65 Query: 63 DVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYC 122 DVSD V A + G++D+L +AGITG + ++++RV+ +NL G Sbjct: 66 DVSDEEQVKALVDLALDTYGQIDVLCNNAGITGDFTDMNSEDQENWKRVLAVNLIGPVLL 125 Query: 123 NREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIAN 182 + P+M + G G IVN ASVAG ++AYSASKA +I FTK+ +L V N Sbjct: 126 TKYAAPYMKDRGCGSIVNTASVAGIRAGAGSNAYSASKAALINFTKTAACDLGSFNVRVN 185 Query: 183 ALTPATFESPILDQLPQSQVDYMR---------SKIPMGRLGLVEESAAMVCFMASEECS 233 A+ P E+ + + DY R S+ M R GL E A + F+A +E S Sbjct: 186 AVCPGLIETGMTKMV----FDYARDAGKEAKLGSRCEMKRYGLPHEIAFAILFLACDESS 241 Query: 234 FTTASTFDTSGGRT 247 + T GG T Sbjct: 242 YVTGQHLAVDGGNT 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: 144 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: 265 Length adjustment: 24 Effective length of query: 225 Effective length of database: 241 Effective search space: 54225 Effective search space used: 54225 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 24 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