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

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

  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 i f i
Sceb 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]
  1. 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.