ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

Table 1 Bacterial RecA Homologs

Phyla	1997	Current	Representative Species
Actinobacteria	6	37	Mycobacterium tuberculosis
Aquificae	1	3	Aquifex pyrophilus
Bacteroidetes/Chlorobi	1	8	Bacteroides fragilis
Chlamydiae/Verrucomicrobia	1	8	Chlamydia trachomatis
Chloroflexi	0	2	Dehalococcoides ethenogenes
Cyanobacteria	3	12	Anabaena variabilis
Deinococcus-Thermus	3	5	Deinococcus radiodurans
Dictyoglomi	0	1	Dictyoglomus thermophilum
Fibrobacteres/Acidobacteria	0	2	Fibrobacter succinogenes
Firmicutes	8	73	Bacillus subtilis
Fusobacteria	0	2	Fusobacterium nucleatum
Nitrospirae	0	1	Thermodesulfovibrio yellowstonii
Planctomycetes	0	2	Gemmata obscuriglobus
Proteobacteria	(39)	(133)
Alpha	11	30	Rhodobacter capsulatus
Beta	6	25	Neisseria gonorrhoeae
Delta/Epsilon	3	20	Campylobacter jejuni
Gamma	19	58	Escherichia coli
Spirochaetes	1	8	Borrelia burgdorferi
Thermodesulfobacteria	0	1	Thermodesulfobacterium commune
Thermotogae	1	2	Thermotoga maritima
Total	64	300

Bacterial phylogenetic classification was taken from the NCBI Taxonomy database [33]. Column "1997" depicts the number of bacterial RecA homologs used in the multiple sequence alignment from a previous analysis [17]. The adjacent column shows the number of homologs used in the present work. The last column lists a representative species from the corresponding phyla.

ISSN: 1471-2105