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Interestingly, UBA4 has only a single UBA motif, but does have a rhodanese homology domain (RHD) [63].
The FnbpA D3 segment contains a well defined 4F1 5F1 binding motif, but does not bind to F3 modules nor does it induce Fn aggregation.
The human 2-kinase contains an FXFP motif, but does not contain a D-domain (Table 1).
OtrC-ORF2 contains the G−2…R4 conserved motif, but does not possess the EAA conserved motif.
This finding suggests that CiaD does not need to be phosphorylated at this motif, but does not exclude the possibility CiaD is phosphorylated at another site.
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First, from the Nanog ChIP-seq positive regions, we randomly selected five sequences that match the new Nanog motif but do not match the Oct4-Sox2 joint motif (Table S2).
In contrast to most primate PSG N domains, rodent PSG N1 domains do not contain an RGD tri-peptide motif, but do contain RGD-like sequences, which are not conserved in rodent N2 and N3 domains.
Our attempts to systematically remove the protonable side chains Glu22 and Glu25 on TM1, which form part of the conserved ExxERF motif but do not interact with either of the di-peptide or tri-peptide in the crystal structures (Lyons et al., 2014), resulted in inactive transporters.
Based on cell toxicity studies (for bioactivity of ACVL2a and ACVL2b, see ESI Fig. 2 †) three groups of important chemical tool compounds were discovered: (i) compounds that contain the privileged 4-bromo-isoxazole motif but do not exhibit any bioactivity (ACVL1, ACVL2a, ACVL2b), (ii) ACV1 with moderate activity and (iii) ACV2 with comparable activity to ACV.
Structural analysis of the chloroplast D1 degrading protease (D1P) (Liao et al., 2000), a member of this protease family involved in the biogenesis of photosystem II, revealed a Ser-Lys dyad as the catalytic motif but did not elucidate further regulatory properties.
The consensus sequence we have deduced does not appear to be homologous to the published motifs, but does contain the common invariant glycine residue and is predicted to adopt the typical α-helical structure [ 42].
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