Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate N515DRAFT_2873 N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Dyella79:N515DRAFT_2873 Length = 247 Score = 125 bits (314), Expect = 1e-33 Identities = 85/246 (34%), Positives = 127/246 (51%), Gaps = 18/246 (7%) Query: 63 LITAAGAGIGRESALACARAGAHVIATDIDA-----AALQALAAESD-AITTQLLDVTDA 116 ++T G+G E A AG VIA D+ A AA QA A+ D A+ + +DV+D Sbjct: 6 IVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPVDVSDF 65 Query: 117 AAITALVA----AHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKAVLP 172 A+ + L+A AHG DVL N AG ++ D W+ +N+D ++ C+ V+ Sbjct: 66 ASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMCRHVVE 125 Query: 173 GMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAICPG 232 GM RG G I+N+SSV + G + Y KA V G A+A + +GV N + PG Sbjct: 126 GMSARGFGRIVNLSSV-NGQTGQFGQTNYAAAKAGVHGFGMALARETARKGVTVNTVSPG 184 Query: 233 TIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQTH 292 TP L RV A + + P+GRLG P +IA+ V +LA+D++ + TG Sbjct: 185 YCDTP-LVARVPA------EIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGANL 237 Query: 293 IIDGGW 298 ++GG+ Sbjct: 238 PVNGGY 243 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: 146 Number of extensions: 5 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: 247 Length adjustment: 25 Effective length of query: 275 Effective length of database: 222 Effective search space: 61050 Effective search space used: 61050 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