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 Ga0059261_1451 Ga0059261_1451 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q1NEI6 (249 letters) >FitnessBrowser__Korea:Ga0059261_1451 Length = 240 Score = 142 bits (358), Expect = 6e-39 Identities = 85/236 (36%), Positives = 126/236 (53%), Gaps = 1/236 (0%) Query: 11 RCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDHAAV 70 R AIVTGG G+G+ ++ + G VA D AA E DV+D+ A Sbjct: 3 RVAIVTGGTRGIGEAISVALKDMGMTVAANYAGNDQRAAEFTERTGIKAFKWDVADYDAC 62 Query: 71 AAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVPFM 130 D AALG VD+++ +AGIT + + ++ V+D NL G F + P M Sbjct: 63 QQGVADVEAALGPVDVVVNNAGITRDGT-ILKMTYQMWKEVMDTNLGGCFNMAKATFPGM 121 Query: 131 LENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPATFE 190 E +GRIVN+ S+ G+ G Y+A+K+G+ GFTK+L +E A GV NA+ P + Sbjct: 122 RERKWGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGARAGVTVNAIAPGYID 181 Query: 191 SPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGR 246 + ++ +P ++ + +KIP+GRLG E A V F+ SEE F T ST +GG+ Sbjct: 182 TDMVAAVPAEVLEKIVAKIPVGRLGQANEIARGVAFLCSEEGGFVTGSTLSINGGQ 237 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: 173 Number of extensions: 9 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: 240 Length adjustment: 24 Effective length of query: 225 Effective length of database: 216 Effective search space: 48600 Effective search space used: 48600 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 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