Number of gaps N_gaps is a quality characteristics of Ca-alignment. Gap is defined as a consequitive sequence section (containing 1 or more residues) of query chain that cannot be matched to any part of target chain, found between two sections of matched residues. An ideal alignment contains no gaps, i.e. a consecutive sequence section of query structure may be matched to a same-length sequence section of target structure.

NOTE 1: The above definition of gap differs from that accepted in sequence alignment. In sequence alignment, a gap is defined as one or more consequitive spaces which need to be inserted in the aligned string.
 
NOTE 2: The above definition of gaps results in that number of gaps is equal for both query and target structures.