They are not very useful however in providing an actual alignment between the two sequences. To do this, other algorithms are required. First, a word on terminology. People in the field shudder when the terms similarity and homology are used indiscriminately. Similarity simply means that sequences are in some sense similar and has no evolutionary connotations.
Homology refers to evolutionary related sequences stemming from a common ancestor.
The ability to calculate the correct alignment is crucial to many types of studies. An explicit and precise algorithm is also required. They obviously did this alignment by eye and did not use an explicit algorithm. This alignment not only increases the number of base matches by 133 per cent, but also decreases the number of gaps by 50 per cent and reduces the number of gapped residues by 80 per cent. Hence, if the number of base matches can be increased by reducing the number of gaps, then clearly the original author's insertion of gaps did not maximize that number.