Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_035481637.1 B3C1_RS09380 acetoacetyl-CoA reductase
Query= SwissProt::Q8P3K4 (300 letters) >NCBI__GCF_000299915.1:WP_035481637.1 Length = 246 Score = 106 bits (264), Expect = 6e-28 Identities = 74/248 (29%), Positives = 122/248 (49%), Gaps = 16/248 (6%) Query: 58 QGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAESDAITTQ----LLDV 113 +G L+T A GIG A A+ G V A + + + A + D+ Sbjct: 3 KGNVALVTGANGGIGTAICRALAKEGYQVAALCRCPSRAEPWLEQEKAQGYNPHLVIADI 62 Query: 114 TDA----AAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKA 169 D +A++ + A G +++ N AG ++ E W N+ Y+ C+A Sbjct: 63 KDQDGIFSAVSVVEAELGAINLVVNNAGITRDKTLKRMQEDDWLEVIQTNLTGAYHLCRA 122 Query: 170 VLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAI 229 V+P MLER G I+N+SS+ + KG + Y KA + GL+ ++A + ++G+ N I Sbjct: 123 VVPLMLERQYGRIVNISSI-NGEKGQMGQTNYAAAKAGLHGLTMSLAQEVASKGITVNTI 181 Query: 230 CPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTG 289 PG I T V A+ + + +S ++ P+GRLG+P EIA++V +LAS ++ F TG Sbjct: 182 SPGYIAT----DMVMAV---PEEIRQSIINQIPVGRLGEPSEIARIVTFLASPDAGFITG 234 Query: 290 QTHIIDGG 297 +GG Sbjct: 235 SNLSANGG 242 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: 136 Number of extensions: 6 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: 246 Length adjustment: 25 Effective length of query: 275 Effective length of database: 221 Effective search space: 60775 Effective search space used: 60775 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