HHblits hits against PDB database for alternative-frame ORFs.

HHblits hits were grouped by PDB ID or putative ORF. E-value, sequence identity and probability were provided by averaging ones from HHblits hits. The alignments between putative ORFs and structures were generated by HHblits tool. The number in parenthesis following a sequence alignment is the length of either query or subject. Consensus sequences are shown in HMM format for both the query and the subject, in which capital and lowercase letters are used to represent conserved columns with ≥60 and ≥40 probabilities, respectively, and a tilde “∼” is used to represent non-conserved column. Based on default settings with two iterations, HHblits tool adds significant hit(s) from the previous search/iteration to the HMM query for the next search/iteration. It results to that our query may not be single sequence. Five symbols are used to show the alignment quality, in which “|”, “+”, “.”, “−” and “ = ” each represents a quality from the perfect to the worst.
aTwo groups of putative ORFs from PB1 and NP genes hit to 1WRG structure.
HHblits hits against PDB database for alternative-frame ORFs.