ARB uses dots ('.') as a special gap type. The meaning of a dot is "might be a gap or a nucleotide/aa". It indicates the lack of any information about the sequence data at the position where they are used.
Opposed to that, a normal gap ('-') clearly states that it is KNOWN that the sequence does NOT CONTAIN any bases at the positions of the gaps - the gaps have only been inserted for alignment purposes.
And - opposed to gap - a 'N' (or 'X' for amino acid sequences) clearly states, that it is KNOWN that the sequence CONTAINS some nucleotide/aa at that position.
In ARB databases you should use dots at both ends of the alignment. Doing so means: you know that the sequence continues in both directions - it just has not been sequenced completely.
Also you may use dots in the middle of the alignment, whenever you have stronger indications, that some gap might in fact be a sequencing error.