Protein's physical and chemical parameters calculator

Protparam
http://web.expasy.org/protparam/

Sequence alignment

MultAlin:
http://multalin.toulouse.inra.fr/multalin/

ClustalW
http://embnet.vital-it.ch/software/ClustalW.html

T-coffee
http://www.ebi.ac.uk/Tools/msa/tcoffee/T-coffee

Similarity search

BLAST protein search
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins