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_037570504.1 BS73_RS07230 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000744815.1:WP_037570504.1 Length = 254 Score = 127 bits (319), Expect = 2e-34 Identities = 93/229 (40%), Positives = 125/229 (54%), Gaps = 14/229 (6%) Query: 7 RYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDL---NGDALAATQAEIDATHVVALD 63 + AG A++TGGASGLG+ A R++A GG V L DL +G+A+AA E A D Sbjct: 2 KIAGSTAVITGGASGLGRATAERLLAAGGNVLLLDLPSSDGEAVAAKLGERAA--FAPAD 59 Query: 64 VSDHAAVAAAAKDSAAALGKVDILICSAGI-TGATV--PVWEFPVDSFQRVIDINLNGLF 120 V D A V+AA + A G + I + AGI T A V FP+D F RV++INL G F Sbjct: 60 VRDEAQVSAALDAAQALGGDLRIAVNCAGIGTPARVLGKNGPFPLDVFTRVVEINLIGTF 119 Query: 121 YCNREVVPFM-----LENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELA 175 R M L+ G IVN ASVA +G +AYSASK GV+G T + ++LA Sbjct: 120 NVIRLAAERMAANEPLDGDRGVIVNTASVAAFDGQIGQAAYSASKGGVVGMTLPIARDLA 179 Query: 176 GKGVIANALTPATFESPILDQLPQSQVDYMRSKIP-MGRLGLVEESAAM 223 G+ + + P F +P+L LPQ D + ++P RLG E AA+ Sbjct: 180 GRSIRVMTIAPGLFATPMLAGLPQEAQDSLGEQVPHPPRLGNPVEYAAL 228 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: 175 Number of extensions: 10 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: 254 Length adjustment: 24 Effective length of query: 225 Effective length of database: 230 Effective search space: 51750 Effective search space used: 51750 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 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