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Fig. 4 | BMC Molecular and Cell Biology

Fig. 4

From: Remote homology searches identify bacterial homologues of eukaryotic lipid transfer proteins, including Chorein-N domains in TamB and AsmA and Mdm31p

Fig. 4

All–vs.–all HHsearches for TULIPs. MSAs were made from 3 rounds of PSI-BLAST of each of four eukaryotic TULIPs (BPI-N and BPI-C, Juvenile Hormone Binding Protein (JHBP) from arthropods and the SMP domain of Nvj2p) and six bacterial proteins (P47/OrfX2, YceB/DUF1439, DUF4403-N and -C, DUF2140 and DUF2993). Hydrophobic signals were removed from BPI, DUF4403, YceB, and DUF2140, and the whole N-terminus of DUF2993 was removed. BPI and DUF4403 MSAs were divided into N- and C-terminal domains. For each of the 10 MSAs, the HHpred server returned 1000 hits from PFAM (v32.0). The diagram shows the ppSS (and number of aligned columns) of the highest target in each of the 10 PFAM families for the ten domains. Hits are colour-coded according to ppSS as indicated. “0” indicates ppSS < 0.5%, or no match in the top 1000 hits. The search with P47 matched both halves of the DUF4403 pseudodimer. The results between two domains are in many cases asymmetric depending on which is query and which template, which is caused by HHsearch making query and target templates differently, as reported previously [11, 29]. The strongest homology between eukaryotic and bacterial proteins occurred with (i) the combination of JHBP < > DUF4403-C (either as query; outlined in red) and (ii) DUF4403-N as query with BPI-N as target, outlined in blue

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