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_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG
Query= SwissProt::Q1NEI6 (249 letters) >NCBI__GCF_003063475.1:WP_108358580.1 Length = 255 Score = 153 bits (386), Expect = 4e-42 Identities = 85/247 (34%), Positives = 136/247 (55%), Gaps = 5/247 (2%) Query: 5 AGRYAGRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVAL-- 62 A R G+ +++TG A G+G A + EG V + D+ A+ + A AL Sbjct: 9 AQRLQGKVSLITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALGF 68 Query: 63 --DVSDHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLF 120 DV+ V A K G++D+L+ +AGIT + + ++ F RVID+NL G+F Sbjct: 69 VVDVTQRDMVDATVKAVLDKFGRIDVLVNNAGIT-QDARLQKMTLEQFDRVIDVNLRGVF 127 Query: 121 YCNREVVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVI 180 +C + V M+ G G I+N +SV G GN + Y+A+K GVIGFTK+ +EL KG+ Sbjct: 128 HCAQAVTEAMVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIR 187 Query: 181 ANALTPATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTF 240 NA+ P ++PIL +P+ + M ++P+ RLG E+ A + F+AS+E ++ + Sbjct: 188 VNAVAPGFIQTPILSTIPEKVIHEMTDRVPLKRLGQPEDIANVYAFLASDEAAYINGTVI 247 Query: 241 DTSGGRT 247 + +GG T Sbjct: 248 EVAGGLT 254 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: 255 Length adjustment: 24 Effective length of query: 225 Effective length of database: 231 Effective search space: 51975 Effective search space used: 51975 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