BLAST and similarity search

Last updated: 9-05-2017.

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Task 1. Homology of proteins found by similarity

To search for homology, 9 proteins were taken from BLAST output (Swiss-Prot database was used, word size was changed from 6 to 3). As a result of their comparison, Table 1 was created. Figure 1 contains alignment of them with 'blocks' bordered. According to Figure 1, first 8 of 9 sequences are seeming like homologous, but I am still not sure about eighth one (P0AG81.1). Assuming Q926H8.1 and P0AG81.1 are homologous, so P0AG81.1 should be homologous to the rest of observed proteins (according to the criterion of transition forms) Conclusions about homology were based on data about E-value and identity from Table 1 and on information about blocks from Figure 1. Notes for Figure 1'2: even selected block has gaps, they are the same for both sequences, so it is possible not to take them into account.

Figure 1. The most informative part of multiple alignment of sequences from Table 1. Borders of blocks are colored blue.

Figure 1'2. The most informative part of multiple alignment of sequences from Table 1. Borders of blocks are colored black. Corrected variant.

Uniprot AC	Protein name	Coverage, %	Identity, %	E-value	Homology
P19576	Maltose-binding periplasmic protein	100	100	0	N/A
P18815.1	Maltose-binding periplasmic protein	100	93	0	+
P59213.1	Maltose/maltodexrin-binding periplasmic protein	97	31	6e-37	+
O07009.1	Cyclodextrin-binding protein	91	31	2e-35	+
Q9V297.1	Maltotriose-binding protein	93	28	6e-31	+
Q7LYW7.2	Trehalose/maltose-binding protein	69	28	2e-13	+
O32156.1	Uncharacterized ABC transporter extracellular-binding protein	53	26	7e-06	+
Q926H8.1	sn-glycerol-3-phosphate-binding periplasmic protein	69	24	8e-06	+
P0AG81.1	sn-glycerol-3-phosphate-binding periplasmic protein	37	27	0.004	+
Q8DD83.1	Protein CyaY	12	31	8.8	-

Table 1. Properties of several sequences from BLAST output.

Task 2. Major rearrangements between a pair of proteins having homologous domains

Family of LIM proteins from Pfam was chosen for this task due to its specific site architecture. Proteins with AC Q24400 and W5N561 were chosen. Their domain structure is shown in Figure 2. Figure 3 contains dot matrix of observed proteins. According to mapping from Figure 4, there are several evolution events could happen: first 'A' plot from W5N561 could be duplicated with insertion mapped as 'B'. Then this plot (A+B mapped as A') could duplicate 4 more times.

Figure 2. Q24400 and W5N561 domain structure.

Figure 3. Hit matrix of Q24400 (vertical axis) and W5N561 (horizontal axis).

Figure 4. Mapped hit matrix of Q24400 (vertical axis) and W5N561 (horizontal axis).