Fig. 3
Homologies between YceB and 4 other bacterial TULIP domains. a All vs. all pairwise alignments of bacterial TULIP YceB (#1) with four newly proposed bacterial TULIPs (#2–5): DUF4403 N and C-terminus; DUF2140; and Rv0817c, a DUF2993 protein in M. tuberculosis. The arthropod protein Takeout (#6) is also included. The strength of alignments is colour coded according to the predicted probability of shared structure (ppSS, large numbers), with the number of aligned columns shown in brackets. b Arrangement of secondary structural elements predicted in DUF4403. Each TULIP domain core is a superhelix (coloured in rainbow order blue to red), and three additional β-strands: one before the core 1 (“-1” - white) and two after the core (“+ 1” & “+ 2” - black). A loop links the two domains (gray). c I-TASSER model of DUF4403 (residues 17–423), each core domain rainbow coloured (N = blue <− > C = red), and interface strands coloured as in B (“-1” white, “+ 1” “+ 2” black). d DUF4403-N and -C structures predicted by contact co-evolution in GREMLIN [24, 25]. Colouring as in c. This method predicts helices immediately following the core of both domains. e & f DUF2140 and DUF2993C predicted and coloured as in d. In both cases, the initial α-helix and β-strand are short. DUF2993C includes the final 15 residues of Rv0817c, beyond the end of DUF2993, predicted as an extra short strand and helix