Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate 203460 SO4382 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__MR1:203460 Length = 241 Score = 92.8 bits (229), Expect = 7e-24 Identities = 75/247 (30%), Positives = 114/247 (46%), Gaps = 21/247 (8%) Query: 61 RCLITAAGAGIGRESALACARAGAHVI--------ATDIDAAALQALAAESDAITTQLLD 112 R L+T + GIG+ AL A AG + A D AA L+AL + + D Sbjct: 4 RVLVTGSSRGIGKAIALKLAAAGHDIALHYHSNQAAADASAAELRALGVNVSLLKFDVAD 63 Query: 113 -VTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCK-AV 170 V AA+ A + A+G + + AG + E W N+D Y V Sbjct: 64 RVAVRAALEADIEANGAYYGVVLNAGINRDNAFPAMSEAEWDSVIHTNLDGFYNVIHPCV 123 Query: 171 LPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAIC 230 +P + R G II ++SV S I G + Y +KA +IG +KA++ + + + N I Sbjct: 124 MPMVQARKGGRIITLASV-SGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVNCIA 182 Query: 231 PGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQ 290 PG I+T + + + EQ V PM R+G P EIA L +L SD++++ T Q Sbjct: 183 PGLIETDMVADIPKDM--VEQLV--------PMRRMGKPNEIAALAAFLMSDDAAYITRQ 232 Query: 291 THIIDGG 297 ++GG Sbjct: 233 VISVNGG 239 Lambda K H 0.320 0.133 0.395 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: 110 Number of extensions: 6 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: 300 Length of database: 241 Length adjustment: 25 Effective length of query: 275 Effective length of database: 216 Effective search space: 59400 Effective search space used: 59400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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