Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_066329720.1 BLR17_RS09410 SDR family oxidoreductase
Query= SwissProt::Q8P3K4 (300 letters) >NCBI__GCF_900100165.1:WP_066329720.1 Length = 255 Score = 132 bits (331), Expect = 1e-35 Identities = 81/252 (32%), Positives = 140/252 (55%), Gaps = 12/252 (4%) Query: 56 RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESDAITTQLL---- 111 R + K CL+T A +GIGR +A++ A+ GA+V+ +D++ AA + + E A+ + Sbjct: 3 RFENKVCLVTGASSGIGRATAISFAKEGANVVVSDVNEAAGELVVNEIKALGKEAFFVKC 62 Query: 112 DVTDAAAITAL----VAAHGPFDVLFNCAGYVHQGSI--LDCDEPAWRRSFSINVDAMYY 165 D++ A + + V G D N AG S+ + E AW + +IN+ +Y Sbjct: 63 DISQRAEVENMIQKTVKTFGRLDCAVNSAGIAGTLSLPTHEYPEDAWLQQININLTGTWY 122 Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225 K L ML++G G+I+ +SS A+ + G P+ Y +K VIG+ K+ A + + +R Sbjct: 123 CVKYQLIEMLKQGGGNIVCVSS-AAGLVGQPDNVPYCASKHGVIGIVKSAAIENATKNIR 181 Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285 NAICP I+TP + + + L + +A+ ++ + Q M R+G P E+A + +++ SD+S+ Sbjct: 182 INAICPTAIETPMIMEGRRKLAHNPEAL-EAAINLQRMKRMGQPLEVADVALWMCSDQST 240 Query: 286 FTTGQTHIIDGG 297 F TG +DGG Sbjct: 241 FITGHAMAVDGG 252 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: 142 Number of extensions: 9 Number of successful extensions: 4 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: 255 Length adjustment: 25 Effective length of query: 275 Effective length of database: 230 Effective search space: 63250 Effective search space used: 63250 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 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