Align BadH (characterized)
to candidate N515DRAFT_1104 N515DRAFT_1104 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_1104 Length = 246 Score = 159 bits (401), Expect = 7e-44 Identities = 93/247 (37%), Positives = 141/247 (57%), Gaps = 6/247 (2%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63 + +TA++TGG GGIG A R A++G ++A + A+ AI G V+ D Sbjct: 1 MTQRTALVTGGTGGIGTAIVRYLARQGHRVATNYRDPARADAWRAAIAQEGIEVAMVQGD 60 Query: 64 IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123 ++D S +A + + LG V+ILVNNAG F K +W ++ NL ++ Sbjct: 61 VSDPASCEAMVRELESKLGAVEILVNNAGITRDTTFHKMSYQQWTDVVNTNLNACFNVTR 120 Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183 V+ GM R+ GRIV I+S + G G+A YAA K G+ F+ +LA+E+A+ GITVN V Sbjct: 121 PVIDGMRGRKWGRIVQISSINGQKGQYGQANYAAAKAGMHGFTISLAQENAKFGITVNTV 180 Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243 PG T ++ V PE++ E IP+GRLGKP+++A A+AF ++A +ITG Sbjct: 181 SPGYVATDMVMAV------PEEVREKIVAQIPVGRLGKPEEIAHAVAFLTGEEAAWITGT 234 Query: 244 VLSVSGG 250 L+++GG Sbjct: 235 NLAINGG 241 Lambda K H 0.318 0.135 0.398 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: 154 Number of extensions: 7 Number of successful extensions: 2 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: 255 Length of database: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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