You could use e.g. Jalview (http://www.jalview.org/) and obtain similar figures. Protein multiple alignments can be also made in Uniprot (http://www.uniprot.org/). It's easy to do there and can be used for preliminary evaluations.

For comparison of two proteins its better to use pairwise sequence alignment, e.g. one of these http://www.ebi.ac.uk/Tools/psa/ . You can get the similarity and identity % there and some other criteria too.

Good luck!

You will have to use ESsPript to produce the figure given in the paper.

http://espript.ibcp.fr/ESPript/ESPript/

Thank you so much Vasily

Thanks Yusuf

The following books may help:

@BOOK{Jon-04,

title = {An introduction to bioinformatics algorithms},

author = {N.C. Jones and P.A. Pevzner},

publisher = {MIT Press},

year = {2004},

address = {Cambridge, London},

isbn = {978-0-262-10106-6},

language = {eng},

price = {US$ 45.-},

}

 @BOOK{Bok-03,

author = {H.-J. Böckenhauer and D. Bongartz},

title = {Algorithmische Grundlagen der Bioinformatik},

year = {2003},

publisher = {Teubner},

address = {Wiesbaden},

edition = {1},

language = {ger},

isbn = {978-3-519-00398-8},

price = {€ 38.-},

}

You could generate similar figure using Multiple Sequence Viewer Panel in Schrödinger.  The Multiple Sequence Viewer is an alignment, visualization, and manipulation toolkit for multiple sequences. You could change colour w.r.t. 

Residue Type Color the residues by residue type. The colors are:

ACFILMPVW  blue (hydrophobic)

DE red (acidic)

HKR green-yellow (basic)

GNQSTY orange (other)

Residue SimilarityColor residues by similarity. Identical residues are red, similar residues (positive BLOSUM62 pairwise score) are orange, other residues are white.

Taylor SchemeColor residues with the Aminochromography color scheme developed by William Taylor (Protein Engineering 1997, 10, 743–746). In this scheme, well conserved parts of the alignment exhibit bright, clear colors, while parts that are not well conserved have brownish, dull colors.

Secondary StructureColor the sequence by the secondary structure assignment. If no SSA is available but one or more secondary structure predictions are available, the predictions are used to color the sequence. The colors for multiple predictions are averaged, so positions where all predictions agree have bright colors, and the positions of disagreement are more gray. If no SSP nor SSA is available, the color of the sequence is not changed.

B FactorColor the residues by their temperature factor (PDB B factor), on a green-white-red scale, with green for the lowest values and red for the highest.

Residue PropensitiesColor residues by the residue propensities. The schemes that are available on the submenu are described in the table below.

Example figure given as attachment:

Protein family refers to a group of structurally similar proteins which are mutually evolutionary and encoded in corresponding gene families.

A classification of proteins in families due to their amino acid sequence and the architecture of the sequence-internal protein domains helps in the theoretical understanding of the evolutionary development of these protein families.