Align BadH (characterized)
to candidate 6939300 Sama_3393 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__SB2B:6939300 Length = 241 Score = 142 bits (357), Expect = 8e-39 Identities = 87/247 (35%), Positives = 133/247 (53%), Gaps = 11/247 (4%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65 K ++TG GIG A R A +G +AV + NL AAE A I D G ++ D+A Sbjct: 3 KRVLVTGSSRGIGKAIALRLASQGYDVAVHYHSNLTAAEATASEIADLGVKVSLLKFDVA 62 Query: 66 DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHM-HHA 124 DR +V AAI G +V NAG + F +W+ +I NL G ++ Sbjct: 63 DRAAVRAAIEADIEANGAYYGVVLNAGINRDTAFPAMTDDDWDSVIHTNLDGFYNVVQPT 122 Query: 125 VLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVC 184 V+P + R+ GRI+ +AS + G+ G+ Y+A K GL+ +K L+ E A+ ITVN + Sbjct: 123 VMPMIQSRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVNCIA 182 Query: 185 PGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244 PG +T ++++ S E + +P+ R+GKP+++A F SDDA +IT QV Sbjct: 183 PGLIETDMVSEFPS---------EMVDQLVPMRRMGKPEEIAALAGFLMSDDAAYITRQV 233 Query: 245 LSVSGGL 251 +SV+GG+ Sbjct: 234 ISVNGGM 240 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: 142 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: 241 Length adjustment: 24 Effective length of query: 231 Effective length of database: 217 Effective search space: 50127 Effective search space used: 50127 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