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Supplementary material for the Web.

Estimation of Divergence Times from Multiple Protein Sequences (manuscript).

Table 3. 104 protein sequence data from 5 verterbrate species (data from Hovergen)

	Protein	Estimate (a) of gamma parameter	Number of amino acids used	Accession number^a
1	Insulin-like growth factor I	0.588	112	FAM00007
2	Prepro-insulin	0.811	106	FAM00008
3	Heparin cofactor II	1.139	453	FAM000037
4	Muscarinic acetylcholine receptor M1	0.454	459	FAM000059d
5	Angiotensin II receptor type I	0.994	354	FAM000084
6	Alcohol dehydrogenase-1 (Adh-1)	0.938	228	FAM000111
7	Gastric H+, K+ ATPase beta-subunit	1.144	281	FAM000133
8	Na+, K+ ATPase beta-subunit	0.718	301	FAM000135
9	Acetylcholine receptor delta-subunit	0.886	508	FAM000152a
10	Acetylcholine gamma-subunit	1.307	500	FAM000152b
11	Acetylcholine receptor alpha-subunit	0.409	456	FAM000152e
12	Serum albumin	4.916	596	FAM000192
13	Gap junction protein connexin-4	0.23	377	FAM000242
14	Alpha-A-crystallin	0.887	163	FAM000248a
15	Cu-Zn superoxide dismutase (SOD1)	0.853	150	FAM000256
16	Neural cadherin (N-cadherin)	0.355	900	FAM000258
17	Basic fibroblast growth factor (bFGF)	0.369	152	FAM000274
18	Preproglucagon	1.358	131	FAM000286
19	Bone morphogenetic protein-4 (BMP-4)	0.392	394	FAM000306a
20	Bone morphogenetic protein-2 (BMP-2)	0.581	351	FAM000306b
21	Tissue inhibitor of metalloproteinase-3 (TIMP-3)	0.512	209	FAM000330b
22	Aldehyde dehydrogenase I (ALDH-1)	0.595	499	FAM000337
23	Ornithine decarboxylase (ODC)	0.489	448	FAM000348
24	Osteonectin (Sparc)	0.367	292	FAM000350
25	Poly (ADP-ribose) synthetase	0.634	990	FAM000356
26	Phosphatase 2A-beta (PP2A-beta)	0.039	309	FAM000362
27	Preprosomatostatin	0.398	115	FAM000371
28	ABC transporter (TAP2)	2.661	656	FAM000385
29	Tryptophan hydroxylase (Tph)	0.668	437	FAM000388b
30	Iron binding protein (ferretin) heavy chain	0.403	176	FAM000533
31	Glutamine synthetase	0.46	368	FAM000534
32	Retinol-binding protein (RBP)	0.924	189	FAM000555
33	Type IIA activin receptor	0.286	513	FAM000561a
34	Alpha-enolase (2-phospho-D-glycerate hydrolase)	0.252	434	FAM000627
35	Cyclin D1	0.711	290	FAM000646a
36	Complement component C	1.96	1556	FAM000664
37	Zona pellucida glycoprotein-3 (ZP3)	3.254	397	FAM000667
38	Helix-loop-helix protein (Id-2)	0.243	133	FAM000769
39	Cardiac troponin	0.74	162	FAM000868a
40	Hepatic nuclear factor 1-alpha unit	0.608	585	FAM001004b
41	Retinal degeneration slow (RDS) protein	0.602	343	FAM001091
42	Hepatocyte growth factor (HGF)	0.883	706	FAM001247a
43	Hepatocyte growth factor-like protein	1.243	692	FAM001247c
44	Vimentin (intermediate filament)	0.365	455	FAM001327a
45	Middle weight neurofilament (NF-M)	0.838	748	FAM001328b
46	Cardiac calsequestrin	1.301	380	FAM001355
47	Steroidogenic factor-1 SF-1	0.505	451	FAM001365a
48	Thyroid hormone receptor alpha (c-erbA)	0.288	408	FAM001369a
49	Thyroid hormone receptor beta subunit	0.192	368	FAM001369b
50	Very low density lipoprotein receptor (VLDLR)	0.398	830	FAM001390b
51	Domain transcription factor LIM-1	0.187	401	FAM001396
52	Cyclin-dependent kinase (CDC2)	0.422	296	FAM001432b
53	Neural cell-adhesion molecule (N-CAM)	0.576	716	FAM001444
54	Neural cell surface protein F	0.665	991	FAM001446a
55	Focal adhesion kinase (FAK)	0.182	1051	FAM001463
56	Protein-tyrosine (src) kinase (CSK)	0.224	450	FAM001467
57	Neural receptor protein-tyrosine kinase (trkB)	0.508	797	FAM001471b
58	Insulin-like growth factor I receptor	0.434	1301	FAM001471e
59	c-met oncogene	0.881	1366	FAM001472
60	c-kit receptor tyrosine kinase	0.957	924	FAM001478b
61	Oocyte maturation factor Mos (c-mos)	1.456	324	FAM001493
62	Fibronectin (FN1)	0.839	1069	FAM001519
63	Zinc finger protein slug (SLUG)	0.665	148	FAM001601
64	Wilms tumor protein	0.35	375	FAM001607
65	Integrin beta-1 subunit	0.376	789	FAM001621
66	Muscle regulatory factor (MRF4)	0.38	239	FAM001622c
67	Achaete-scute homologue	0.293	189	FAM001624
68	Collagenase-3 (matrix metalloproteinase-13)	1.02	378	FAM001631c
69	Fos-related antigen-2 (fra-2)	0.336	313	FAM001679a
70	Follistatin (activin antagonist)	0.354	315	FAM001730
71	Structure-specific recognition protein 1 (SSRP1)	0.305	529	FAM001987
72	Gonadotrophin-releasing hormone (GnRH)	3.093	87	FAM002205
73	Alpha 2,8-sialyltransferase-1 (pst-1)	0.577	353	FAM002490
74	Syndecan-3 (Syn-3)	2.598	317	FAM002852
75	Distal-less 3 (Dlx-5) homeobox	0.331	278	FAM002888a
76	Homeobox protein Nkx-2.5 subunit	1.097	285	FAM002890b
77	Corticotrophin-releasing factor type1 receptor	0.375	410	FAM003058b
78	T-cell leukemia (LERK-2)	0.439	326	FAM003670
79	Delta-1 protein	0.584	705	FAM003932a
80	Conductin/axin (AXIN)	0.667	818	FAM006148
81	Transforming growth factor – beta3	0.653	389	FAM000027^b
82	Na, K-ATPase beta-2 subunit (ATP1B2)	1.61	271	FAM000134^b
83	Embryonic beta-type globin	1.364	137	FAM000214^b
84	Alpha globin	1.277	142	FAM000215^b
85	Heat shock protein	0.138	650	FAM000300^b
86	Lactate dehydrogenase-A	0.616	330	FAM000364a^b
87	Histone H2A	0.149	129	FAM000427^b
88	bcl-x regulator of cell death	0.764	200	FAM000506^b
89	c-ets-1 (p54) protein	0.202	437	FAM000514^b
90	Glutamine synthetase	0.471	368	FAM000534a^b
91	Bone morphogenetic receptor	0.28	522	FAM000306d^b
92	Cyclin (D2, D3)	0.291	288	FAM000646^b
93	Furin	0.522	768	FAM000747^b
94	Hepatocyte growth factor (HGF)	1.261	686	FAM001247^b
95	Liver glyceraldehyde-3-phosphate dehydrogenase	0.243	332	FAM001297^b
96	Nucleolin	1.793	605	FAM001318^b
97	Vimentin	0.361	454	FAM001327^b
98	Lamin B1	0.675	578	FAM001331^b
99	Nucleolar phosphoprotein B23 (NPM1)	1.022	285	FAM001359^b
100	N-myc protein	0.698	398	FAM001383^b
101	CDC2 involved in cell cycle control	0.332	296	FAM001432^b
102	Protein tyrosine phosphatase (PTPase-alpha)	0.280	778	FAM001447^b
103	Phosphotyrosil protein phosphatase	0.084	591	FAM001456^b
104	M-sam fibroblast growth factor	0.314	807	FAM001479^b

^a Gene family names from Hovergen database.
^b Entries 81-104 from Hovergen 1996 Release.