Align BadH (characterized)
to candidate N515DRAFT_2873 N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_2873 Length = 247 Score = 166 bits (419), Expect = 5e-46 Identities = 97/250 (38%), Positives = 131/250 (52%), Gaps = 8/250 (3%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDL--NLDAAEKVAGAIRDAGGTAEAVRCDI 64 + A++TGG GG+G CR+ A G ++ DL D + D G D+ Sbjct: 3 RIAIVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPVDV 62 Query: 65 ADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHA 124 +D S IA G VD+LVN AG K +P W+ L+ +NL G +M Sbjct: 63 SDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMCRH 122 Query: 125 VLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVC 184 V+ GM R GRIVN++S + G G+ YAA K G+ F LARE AR G+TVN V Sbjct: 123 VVEGMSARGFGRIVNLSSVNGQTGQFGQTNYAAAKAGVHGFGMALARETARKGVTVNTVS 182 Query: 185 PGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244 PG DT L+A V P ++ + IP+GRLG P D+A A+ F +DDAG+ITG Sbjct: 183 PGYCDTPLVARV------PAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGAN 236 Query: 245 LSVSGGLTMN 254 L V+GG M+ Sbjct: 237 LPVNGGYFMS 246 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: 179 Number of extensions: 8 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: 255 Length of database: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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