Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate N515DRAFT_1253 N515DRAFT_1253 2-dehydro-3-deoxy-L-fuconate dehydrogenase (EC 1.1.1.-)
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Dyella79:N515DRAFT_1253 Length = 248 Score = 362 bits (928), Expect = e-105 Identities = 173/245 (70%), Positives = 205/245 (83%) Query: 56 RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESDAITTQLLDVTD 115 RL GK L+TAAGAGIGR +ALA AR GA V+ATDID AL AL+AE+ + T+ LDVTD Sbjct: 4 RLAGKHALVTAAGAGIGRATALAFAREGARVLATDIDEQALAALSAEAPELRTERLDVTD 63 Query: 116 AAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKAVLPGML 175 I LVA+H PFDVLFNCAGYVH G+ILD D+ AW+RSF+INVD+M++ C+ VLP ML Sbjct: 64 PVQIDRLVASHPPFDVLFNCAGYVHAGTILDTDDAAWKRSFAINVDSMFHLCQRVLPAML 123 Query: 176 ERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAICPGTIK 235 ERG GSI+NMSSVASSIKGVPNRF Y TKAAVIGL+K++AAD+V +G+RCNAICPGT+K Sbjct: 124 ERGGGSIVNMSSVASSIKGVPNRFAYSTTKAAVIGLTKSVAADFVGRGIRCNAICPGTVK 183 Query: 236 TPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQTHIID 295 TPSLG RV+ALGGDE AVW+ F +RQPMGRLG+P EIA L +YLASDE++FTTG HI+D Sbjct: 184 TPSLGDRVRALGGDEDAVWRGFVERQPMGRLGNPEEIAMLALYLASDEAAFTTGTVHIVD 243 Query: 296 GGWSN 300 GGWSN Sbjct: 244 GGWSN 248 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: 253 Number of extensions: 6 Number of successful extensions: 1 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: 248 Length adjustment: 25 Effective length of query: 275 Effective length of database: 223 Effective search space: 61325 Effective search space used: 61325 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