Gene analogue finder: a GRID solution for finding functionally analogous gene products

Tulipano, Angelica; Donvito, Giacinto; Licciulli, Flavio; Maggi, Giorgio; Gisel, Andreas

doi:10.1186/1471-2105-8-329

BMC Bioinformatics

Table 5 Example with Q88869_MIDDV

From: Gene analogue finder: a GRID solution for finding functionally analogous gene products

Rating	Symbol	UniProt	χ²	Common terms	Pfam	Organism	Local alignment
							Hit length	Identity %
1	Q88869_MIDDV	Q88869	20080,7	54	No	Middelburg virus	37	100.0
2	O75901	O75901	19332,8	54	RA, RasGTP effectors	Homo sapiens	28	25.0
3	Pamci	O88869	17455,7	54	RA, RasGTP effectors	Rattus norvegicus	6	66.7
4	Tb09.244.2760	Q38CZ1	12733,8	44	-, Golgi dynamics	Trypanosoma brucei	36	27.8
5	Tb11.01.6880	Q381R2	12733,8	44	GP25L, Golgi dynamics	Trypanosoma brucei	44	22.7
6	TOM1_HUMAN	O60784	11529,8	35	VHS; membrane targeting	Homo sapiens	42	23.8
7	Vps28	Q9D1C8	11486,0	32	VPS28, Vacuolar protein sorting	Mus musculus	40	32.5
8	AT1G28490.1	Q946Y7	11360,8	32	SNARE, vesicular fusion	Arabidopsis thaliana	33	21.2
9	AT1G28490.2		11360,8	32	SNARE, vesicular fusion	Arabidopsisthaliana	21	23.8
10	AT5G16830	Q39233	11011,1	35	SNARE, vesicular fusion	Arabidopsis thaliana	27	29.6
11	AT5G46860.1	P93654	11011,1	35	SNARE, vesicular fusion	Arabidopsis thaliana	30	30.0
12	CG9308	Q9W2A6	11007,0	36	GP25L, Golgi dynamics	Drosophila melanogaster	14	28.6
13	AT5G26980.1	O65359	10926,6	34	SNARE, vesicular fusion	Arabidopsis thaliana	24	29.2
14	AT4G02195.1	Q9SWH4	10926,6	34	SNARE, vesicular fusion	Arabidopsis thaliana	24	33.3
15	AT5G26980.2		10926,6	34	SNARE, vesicular fusion	Arabidopsis thaliana	24	29.2
16	SPBC4F6.05c	O42707	10881,4	35	Lectin_leg-like	Schizosaccharomyces pombe	31	25.8
17	COPB_HUMAN	P53618	10873,7	39	No	Homo sapiens	23	30.4
18	VPS27	P40343	10803,4	33	VHS; membrane targeting	Saccharomyces cerevisiae	32	31.2
19	tlg1	Q9HGN3	10758,7	32	SNARE, vesicular fusion	Schizosaccharomyces pombe	38	18.4
20	ENT5	Q03769	10505,4	38	ENTH, membrane interacting	Saccharomyces cerevisiae	27	14.8
21	sft2	Q9P6K1	10398,2	33	SFT2, vesicular transport	Schizosaccharomyces pombe	11	36.4
22	Cope	O89079	10365,0	32	Coatomer_E, Golgi to ER transport	Mus musculus	29	27.6
23	Copb1	P23514	10363,2	37	Adaptin_N; coated vesicles	Rattus norvegicus	23	30.4
24	Tgoln2	Q4G0B6	10255,5	34	No	Rattus norvegicus	14	28.6
25	Vps26	P40336	10182,5	29	Vps26, Vacuolar protein sorting	Mus musculus	7	57.1
26	SPAC630.11	Q9UUH1	10182,0	30	Vps55, Vacuolar protein sorting	Schizosaccharomyces pombe	9	44.4
27	apl4	Q9UU81	10141,8	37	Adaptin_N; coated vesicles	Schizosaccharomyces pombe	17	35.3
28	apm1	Q9HFE5	10141,8	37	-, Clathrin coated vesicles	Schizosaccharomyces pombe	24	25
29	apl2	O43079	10141,8	37	Adaptin_N; coated vesicles	Schizosaccharomyces pombe	16	37.5
30	Q6DE70_XENLA	Q6DE70	10135,7	33	C2, Ca2+-dependent membrane-targeting	Xenopus laevis	8	50.0

The table contains the following information: The ranking of the potential functional analogues of Q88869_MIDDV according the χ² - value, the gene name and the UniProt accession number, the χ² - value, the number of common terms between a hit and Q88869_MIDDV, the Pfam name with short domain description the gene product belongs to, the organism the gene products is from, and the local alignment characteristics, such as hit length and the % identity of the hit, of the alignment between Q88869_MIDDV and the hit sequence.

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ISSN: 1471-2105

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