Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate Synpcc7942_1596 Synpcc7942_1596 short chain dehydrogenase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__SynE:Synpcc7942_1596 Length = 245 Score = 96.7 bits (239), Expect = 5e-25 Identities = 77/242 (31%), Positives = 124/242 (51%), Gaps = 29/242 (11%) Query: 63 LITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESD-----AITTQLLDVTDAA 117 LIT A +GIG +A A A+AG ++ D LQ++A + A+ T LD+T+ Sbjct: 13 LITGASSGIGAATAHAFAQAGWSLLLLGRDRGRLQSVAESARSQGAAAVATYSLDLTNLT 72 Query: 118 AI----TALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKAVLPG 173 AI LV G DVL N AG G + F++NV + +A+LPG Sbjct: 73 AIGPAIAQLVEQFGVPDVLINNAGTAQTGPLATLSLSDLECIFALNVHSPLLVVQALLPG 132 Query: 174 MLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAICPGT 233 M +R RG I+N++S+A+ + P+ Y +K+A+ S+ +AA+ + G+R + ICPG+ Sbjct: 133 MRQRQRGLILNVASIAAQ-QAFPDWGAYCASKSALAAWSRVLAAEERSHGIRVSLICPGS 191 Query: 234 IKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQTHI 293 + T D+ +V +F DRQ M R P +AQ+++ +A T +T + Sbjct: 192 VDTAL---------WDQPSVGANF-DRQAMLR---PETVAQVLLQVA------TLPETAV 232 Query: 294 ID 295 +D Sbjct: 233 VD 234 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: 140 Number of extensions: 7 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: 245 Length adjustment: 25 Effective length of query: 275 Effective length of database: 220 Effective search space: 60500 Effective search space used: 60500 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