Birth and death of protein domains: A simple model of evolution explains power law behavior

Table 1 Domain families in sequenced genomes and parameters of the best-fit second-order balanced linear BDIM

	No. of ORFs in genome	No. of detected domain families	No. of detected domains	No. of ORFs with RPS-BLAST hits	Maximum size of a family	f₁ (f'₁)	a	b	k	ν/δ = ν/λ	G = λ_if_i/ν
Sce^b	6340	1080	4575	3331	130	420 (436)	1.55	3.27	-2.72	1861.8	[3.28..3.53]
Dme	13605	1405	11734	7262	335	426 (435)	1.62	2.79	-2.17	1648.2	[8.44..15.50]
Cel	20524	1418	17054	11090	662	423 (421)	1.13	2.03	-1.89	1273.0	[16.18..∞ ]
Ath	25854	1405	21238	15006	1535	270 (277)	3.80	4.98	-2.18	1657.7	[17.09..26.89]
Hsa	39883	1681	27844	16755	1151	298 (288)	5.16	6.43	-2.27	2136.2	[17.14..22.88]
Tma	1846	772	1683	1268	97	501 (499)	0.14	2.22	-3.08	1606.4	[1.04..1.06]
Mth	1869	693	1480	1150	43	438 (436)	0.12	2.00	-2.88	1305.3	[1.18..1.27]
Sso	2977	695	1950	1614	81	386 (385)	0.36	2.04	-2.68	1167.8	[1.83..2.00]
Bsu	4100	1002	3413	2502	124	507 (510)	0.48	2.01	-2.53	1534.6	[2.46..2.79]
Eco	4289	1078	3624	2765	140	523 (519)	0.84	2.54	-2.70	1837.0	[2.45..2.61]

a: f₁(f'₁), the observed (predicted) number of domains in class 1 (represented only once in the genome); a, b, parameters of the second-order balanced linear BDIM; k, slope of the power asymptotic; ν/δ = ν/λ, ratio of the innovation rate to the per domain death (birth) rate; G, ratio of the innovation rate to the total (per genome) birth rate. b: Species abbreviations: Sce, Saccharomyces cerevisiae, Dme, Drosophila melanogaster, Cel, Caenorhabditis elegans, Ath, Arabidopsis thaliana, Hsa, Homo sapiens, Tma, Thermotoga maritima, Mth, Methanothermobacter thermoautotrophicum, Sso, Sulfolobus solfataricus, Bsu, Bacillus subtilis, Eco, Escherichia coli.

ISSN: 2730-7182