Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate N515DRAFT_2198 N515DRAFT_2198 Tropinone reductase 1
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Dyella79:N515DRAFT_2198 Length = 280 Score = 108 bits (269), Expect = 2e-28 Identities = 76/255 (29%), Positives = 125/255 (49%), Gaps = 16/255 (6%) Query: 56 RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESD---------AI 106 +LQG LIT A GIG A A GA+++ D L+ + E A Sbjct: 29 QLQGHTALITGASKGIGYAVARELAGLGANLLLVARDDDHLEQVRVELADDFDHIEVLAF 88 Query: 107 TTQLLDVTDAAAITALVAAHG-PFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYY 165 L D A+ +A G P +L N AG ++L+ E +R F +N+ + + Sbjct: 89 AADLSMQEDRLAVFDWIADLGAPLSLLVNNAGGNTPAAVLEYSERDYRAIFELNLFSAFE 148 Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225 C+ P +++ +I+N+ SV S I V YG++KAA+ L++ +AA++ G+R Sbjct: 149 MCRLAHPQLVQHANAAIVNVGSV-SGITHVRTGAAYGMSKAALHQLTRNLAAEWATDGIR 207 Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285 NA+ P I+T QR + D++ + D P+ R+G+P E+A + +L +S Sbjct: 208 VNAVAPWYIRT----QRSEPALADDEYL-DEVLDHTPLRRIGEPEEVAAAIAFLCLPAAS 262 Query: 286 FTTGQTHIIDGGWSN 300 + TGQ +DGG+ N Sbjct: 263 YITGQVLAVDGGFLN 277 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: 139 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: 280 Length adjustment: 26 Effective length of query: 274 Effective length of database: 254 Effective search space: 69596 Effective search space used: 69596 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: 48 (23.1 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