Retrieved results were further analyzed with selleck products HHpred and HMMER (Additional file 5), transmembrane helices were predicted with TMHMM, protein family matches were identified via Pfam, and conserved motifs together with critical residues were identified manually. Regarding the
motif search, GDC-0449 mouse symbol (✓) denotes identification of the canonical motif as known from the literature (CcsA: WAXX(A/δ)WGX(F/Y)WXWDXKEXX and CcsB: VNX1-4P), letter (M) denotes presence of the CcsA modified heme-binding motif as found in the anammox genera tested (WGXXAWGXYFLWDAK(V/L)(V/L)W), and letter (T) denotes presence of the truncated CcsB motif (VN). TMHs: transmembrane Selleckchem PFT�� helices; (*): E-value cut
off set at 10-6; (**): E-value cut off set at 10-3; (✓): significant annotation and/or identification; (✗): absence of significant hits and/or protein matches. Published: W A X X (A/S) W G X (F/Y) W X W D X K E X X Modified: W G X X A W G X Y F L W D A K (V/L) (V/L) W In the latter, the observed amino acid substitutions may suggest a structurally different heme-binding configuration and/or implications for protein functionality. Nonetheless, the identified CcsA and CcsB homologs are coded adjacent to each other in all anammox genomes. Phylogenetic relationships among the anammox CcsA and CcsB homologs are illustrated in Figure 2A and 2B, respectively. Figure 2 Unrooted phylogenetic trees, constructed based on the Maximum Likelihood algorithm, indicating the relationships of CcsA (A) and CcsB (B) homologs of four anammox genera. Anammox CcsA and CcsB homologs were used as queries for blastP annotation and five (for CcsA) or three
(for CcsB) significant hits were included in the construction of the tree. NCBI accession numbers of reference sequences are shown in parentheses. The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model . The tree with the highest DOK2 log likelihood (-6044.3478 for CcsA; -11148.2432 for CcsB) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a JTT model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All ambiguous positions were removed for each sequence pair. There were a total of 401 and 685 positions in the final dataset for CcsA and CcsB, respectively. Evolutionary analyses were conducted in MEGA 5.0 .