There is a single example of an “”IRREKO”" domain from a eukaryote and a single example from a virus. The eukaryote protein is TVAG_084780 from Trichomonas vaginalis G3 (Figure 1Q and Additional file 2, Figure S1). TVAG_084780 contains 10 LRRs. Two of the 10 repeats are clearly “”IRREKO”" domains.
KU-57788 nmr The virus protein is MSV251 from Melanoplus sanguinipes entomopoxvirus [Q9YVJ1]. This protein contains 11 LRRs with the consensus of LkyLdCsNNxLxnLxiN(n/d)n (Additional file 1, Table 1). The repeating unit length is 19 residues and thus shorter than that of typical “”IRREKO”" LRR. Two subtypes of IRREKO@LRR domains IRREKO@LRRs that are 21 residues long may be classified into two subtypes (Figure 1). The first subtype has the consensus of LxxLxLxxNxLxxLDLxx(N/L/Q/x)xx, while the second has the consensus of LxxLxCxxNxLxxLDLxx(N/L/x)xx, where “”L”" is
Leu, Val, Ile, Phe, Met or Ala, “”N “” is Asn, Thr or Ser, “”D”" is Asp or Asn, “”Q”" is Gln, and “”x”" is nonconserved residues. As well as the other seven classes, “”x”" is generally hydrophilic or neutral residues (Figure 1 and Additional files 1 and 2: Table 1 and Figure S1, respectively). In these two subgroups, “”L”" at positions 1, 4, 14 and 16 is predominantly Leu, while “”L”" or “”C”" at position 6 is not only Leu or Cys but also Val or Ile, and frequently Ala and Phe. “”N”" at position 9 is predominantly Asn and often Thr, Ser or Cys. “”D”" at position 15 is check details predominantly occupied by Asp and frequently SDHB by Asn. Position 19 is often occupied by Leu, Asn, or Gln. Some IRREKO@LRR proteins such as Listeria internalin-J homologs and four Bacteroides proteins include LRRs in which the HCS part consists of a twelve residue stretch, LxxLxLxx(N/C)xxL As LRRs with 20
or 22 residues sometimes keep the most conserved segments of Lx(L/C) in both HCS and VS parts, we regard those as IRREKO@LRR. IRREKO@LRR domains that mainly consist of the first subtype are observed in 61 proteins (Additional file 1, Table 1). Some proteins have the consensus of LxxLxLxxNxLxxLDLxxNxx. These include BIFLAC_05879 and BLA_0865 from Bifidobacterium animalis, A1Q_3393, VAS14_09189, VAS14_14509, and CPS_2313 from Vibrio species, SwooDRAFT_0647, SwooDRAFT_0647, and Shal_3481 from Shewanella species, and SKA34_06710 and SKA34_09358 from Photobacterium sp. SKA34 (Figures 1B, C and 1D, and Additional file 2, Figure S1). Also, the consensus of LxxLxLxxNxLxxLDLxxLxx is observed in a few proteins including SCB49_09905 from unidentified eubacterium SCB49 (Figure 1E). The pattern of LxxLxLxxNxLxxLDLxxQxx is observed in only CPS_3882 from Vibrio psychroerythus (Figure 1F).