Align BadH (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Cola:Echvi_4610 Length = 248 Score = 138 bits (347), Expect = 1e-37 Identities = 79/252 (31%), Positives = 134/252 (53%), Gaps = 7/252 (2%) Query: 1 MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIA-VFDLNLDAAEKVAGAIRDAGGTAEA 59 M L KTA+ITG GIG A ++AQEGA +A F +++ + + + + G A+ Sbjct: 1 MGLLTGKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKG 60 Query: 60 VRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGAL 119 R D +D + + + G +D+L+NNAG + W+ ++ INL Sbjct: 61 FRSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCF 120 Query: 120 HMHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGIT 179 + A +++++ G I+NI S G++G+A YAA K G++ F+K++A E GI Sbjct: 121 NTVKAATRTLMKQKAGSIINITSVVGIKGNAGQANYAASKAGIIGFTKSVALELGSRGIR 180 Query: 180 VNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGF 239 N V PG +T + + EK ++ + AIP+ R G+P+++A A F GSD + + Sbjct: 181 SNAVAPGFIETEMTEVL------DEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSY 234 Query: 240 ITGQVLSVSGGL 251 ++GQV+ V G + Sbjct: 235 VSGQVIQVDGAM 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: 142 Number of extensions: 7 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: 255 Length of database: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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