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_015930314.1 MNOD_RS17780 3-oxoacyl-ACP reductase FabG
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_000022085.1:WP_015930314.1 Length = 268 Score = 151 bits (381), Expect = 1e-41 Identities = 95/248 (38%), Positives = 135/248 (54%), Gaps = 10/248 (4%) Query: 8 YAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATH----VVALD 63 +AGR +VTG G+G+ +A A G V + D+N D + T A I+ + LD Sbjct: 17 HAGRRVLVTGAGRGIGRAIAMGFAARGATVGVADVNRDDVEGTVAAIEGAGGRALALLLD 76 Query: 64 VSDHAAVAAAAKDSAAALG-KVDILICSAGIT----GATVPVWEFPVDSFQRVIDINLNG 118 V+D+A V ++A A+G D +I +AGI+ G VWE + RVI +NL+G Sbjct: 77 VADYAEVETRLAEAALAMGGPFDTVINNAGISPKHDGVAHKVWEMDPAEWNRVIAVNLSG 136 Query: 119 LFYCNREVVPFMLENGYGRIVNLASVAGKEGNPNASA-YSASKAGVIGFTKSLGKELAGK 177 F R + P M E G G IVNL+SVAGK +P + Y+ASKAG+IG TK L EL Sbjct: 137 AFNTVRALSPAMREAGSGWIVNLSSVAGKTYSPIVACHYAASKAGLIGLTKHLAAELGPF 196 Query: 178 GVIANALTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTA 237 G+ NA+ P E+P++ + + + P+GRLG EE A + ++ S E SF T Sbjct: 197 GIRVNAIAPGRIETPMVRAVGAAVNEEQARLTPLGRLGAPEEVADLALYLTSAEASFVTG 256 Query: 238 STFDTSGG 245 T D +GG Sbjct: 257 QTVDVAGG 264 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: 180 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: 268 Length adjustment: 24 Effective length of query: 225 Effective length of database: 244 Effective search space: 54900 Effective search space used: 54900 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