Pfam | JalView

Algorithms for multiple alignments

Task 1

According the task I used 5 homologous proteins which I found in pr12. You can see them characteristics in the table 1. Then I aligned them by programs Tcoffee, Probcons, Muscle and Mafft. Concatenating the result of the alignmenst you can see on picture 1.

Table 1. Characteristics of homologous proteins which were used.
*Line with "my protein" is in bold.

#	ID/AC	Name of protein	Coverage	Identity %	E-value
1	A0A0U3W9X5_9BACI/A0A0U3W9X5	Fructose-1,6-bisphosphatase
4	GLPX_MYCBO/Q7U0N5.2	Fructose-1,6-bisphosphatase class 2	97%	51%	2e-111
5	FBSB_CYAA5/B1WQ07.1	D-fructose 1,6-bisphosphatase class 2	99%	48%	2e-109
6	FBSB_MICAN/B0JKN5.1	D-fructose 1,6-bisphosphatase class 2	99%	47%	3e-109
7	GLPX_MYCLB/B8ZSG6.2	Fructose-1,6-bisphosphatase class 2	97%	50%	1e-107
8	FBSB2_ACAM1/B0BZF8.1	D-fructose 1,6-bisphosphatase class 2	98%	48%	1e-106

Picture 1. The representation of multiple alignment. (You can also see it here)
*You can see list of programs which were used for alignments in the left column.

Differences between programs Tcoffee and Probcons:

• Sequence 4: letters KPG are on the 10-12 positions in Tcoffee's alignment and they are on the 17-19 positions in Probcons' alignment (because of it there is one more conserved position - 18).
• Sequence 1: letter A is on the 279 position in Tcoffee's alignment (because of it there is longer column of functionally conserved residues) and it is on 291 in Probcons' alignment.
• Sequence 1: letter K is on the 368 in Tcoffee's alignment and on 380 in Probcons' alignment.
• Sequence 2: letter K is on the 379 in Tcoffee's alignment and on 369 in Probcons' alignment.

Sum up, there are minor differences between the alignments. Overall they are very similar. I think Probcons' alignments might carry more weight than Tcoffee's alignment.

Task 2

I used Pfam to search for my protein's architecture. Then I found other proteins including the same domain but which have some differences in architecture.

Description of the architecture of my protein:
There is only one domain in my protein: FBPase_glpX (See picture 2, table 2). It includes the part of sequence from the third residue to the 310th residue (the lenght of the whole sequence is 322 residues).

Picture 2. Domain organisation of the Fructose-1,6-bisphosphatase.

Table 2. Some data about FBPase_glpX.

Source	Domain	Start	End
Pfam	FBPase_glpX	3	310
disorder	n/a	20	32
disorder	n/a	34	41
disorder	n/a	79	80
low_complexity	n/a	141	152

Some other architectures including FBPase_glpX domain (see pictures 3, 4, 5, 6):

Picture 3.



• Only one protein has this architecture - A0A077ZKT0_TRITR. Here domain FBPase_glpX has deletions on both ends and on the right side it closely adjacent to the domain MtlR (which has deletions on both ends too).

Picture 4.



• 8 proteins have this architecture. Here is insert in the beginning of the domain's sequence.

Picture 5.



• Only one protein has this architecture - A0A0A2VY08_BEABA. Here is domains: FBPase_glpX, FAD_binding_6, NAD_binding_1 and a coiled_coil. FBPase_glpX has deletion at the right side, FAD_binding_6 has deletions on both ends.

Picture 6.



• 2 proteins have this architecture. Here is domains: Transketolase_N, Transket_pyr, FBPase_glpX. Transketolase_N has deletion at the right side, FBPase_glpX has deletions on both ends.