Align BadH (characterized)
to candidate WP_048081445.1 EJ01_RS05790 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000745485.1:WP_048081445.1 Length = 258 Score = 146 bits (368), Expect = 5e-40 Identities = 84/254 (33%), Positives = 134/254 (52%), Gaps = 7/254 (2%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63 L+ K AV+TG GG+G R +AQEGA +A+ + E +A I AG A AV+CD Sbjct: 7 LKGKVAVVTGASGGLGADAARAYAQEGADVALLARRKERLESLAEEIESAGVKALAVQCD 66 Query: 64 IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123 +AD SV+ AI G +DIL+NNAG + +W++ + +N+ G + Sbjct: 67 VADEESVENAIDEVIKYFGKIDILLNNAGIAVRGGVHSLSVEDWDKGMDVNVKGIFLVSK 126 Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEA----VYAACKGGLVAFSKTLAREHARHGIT 179 VLP M++ +G+IVN +S + G E VY A K + + +A + ++GIT Sbjct: 127 YVLPHMMKNNYGKIVNTSSINSIAGDKSEMFIRHVYNASKAAVRGLTMGMACSYGKYGIT 186 Query: 180 VNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGF 239 VN V P ++ + ++ E+ +E ++ +PL R K +L G I F S+ + + Sbjct: 187 VNAVAPALFESEMTSNT---LFKSEEFLERYSNVVPLNRPAKKGELNGPIIFLSSEASSY 243 Query: 240 ITGQVLSVSGGLTM 253 ITGQ + V GG ++ Sbjct: 244 ITGQTIFVDGGFSV 257 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: 151 Number of extensions: 9 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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: 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