Align BadH (characterized)
to candidate Pf6N2E2_1323 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1323 Length = 255 Score = 148 bits (374), Expect = 9e-41 Identities = 91/250 (36%), Positives = 133/250 (53%), Gaps = 10/250 (4%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66 +T ++TGG GIG A FA GA++ + DL L AE VA + G +AV D+AD Sbjct: 10 QTVLVTGGAQGIGRAIVEAFALRGARVVIADLGLARAEAVADELTAEGCQVQAVGVDLAD 69 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 T+V +A LG +DIL++NAG+ PF + P +R +A+NL+ + A L Sbjct: 70 ATAVFGMMAELEQRLGRLDILIHNAGYFPLTPFAEITPSMLDRTLAVNLSALFWLTQAAL 129 Query: 127 PGMVERRHGR---IVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183 P + RR G+ +V + RV G + YAA K G+ F + A E A + VN V Sbjct: 130 P--MFRRQGQGCVLVTSSVTGPRVAYPGLSHYAASKAGVNGFIRNAALELAAENVRVNGV 187 Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243 PG T +A++ N + + +PLGRLG+P D+AGA+ + S A ++TGQ Sbjct: 188 EPGMIATPAMANLGDDEVNQD-----IARRVPLGRLGQPSDIAGAMLYLASSLASYVTGQ 242 Query: 244 VLSVSGGLTM 253 L V GG T+ Sbjct: 243 TLVVDGGSTL 252 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: 176 Number of extensions: 11 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 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