Genetic structure and evolution of the Vps25 family, a yeast ESCRT-II component

Slater, Ruth; Bishop, Naomi E

doi:10.1186/1471-2148-6-59

BMC Ecology and Evolution

Table 1 Physical characteristics of Vps25 family and similarity to orthologs from key species.

From: Genetic structure and evolution of the Vps25 family, a yeast ESCRT-II component

Species^a	Length (amino acids)	pI^b	Molecular mass^c (kDa)	BLASTP^d similarity to^e:
				S. cerevisiae	H. sapiens	P. primaurelia	T. brucei	D. discoideum	A. thaliana
CHROMALVEOLATES
Alveolates
Apicomplexans
Theileria annulata	249	8.3	29.0	0.53	0.7	>10^f	>10	>10	1.2
Theileria parva	249	8.1	29.0	4.5	3.5	>10	>10	>10	3.5
Ciliates
Paramecium primaurelia	201	6.3	23.5	0.006	5e-09	-^g	>10	1e-09	4e-04
EXCAVATES
Euglenozoa
Kinetoplasts
Leishmania brazilia	230	6.5	25.2	>10	>10	>10	1e-63	1.0	0.055
Leishmania infantum	230	6.7	25.4	>10	2.3	>10	7e-64	3.9	6e-04
Leishmania major	230	7.0	25.5	>10	3.0	>10	5e-62	2.3	0.005
Trypanosoma brucei	234	6.6	26.1	>10	8e-04	>10	-	2e-04	0.015
Trypanosoma brucei gambiae	234	6.6	26.1	>10	8e-04	>10	4e-73	2e-04	0.015
Trypanosoma congolese	301	7.1	26.1	>10	0.067	>10	8e-77	0.005	7e-04
Trypanosoma cruzi	240	7.5	26.2	>10	>10	>10	3e-73	>10	>10
Trypanosoma vivax	232	6.5	25.6	>10	0.014	>10	3e-73	0.27	0.019
Diplomonads
Giardia lamblia	185	5.8	21.4	>10	3e-08	>10	>10	7e-05	1e-05
Parabasalia
Trichomonas vaginalis(1)	186	6.6	21.7	2e-09	7e-22	8e-07	>10	2e-18	2e-15
Trichomona vaginalis(2)	176	7.7	20.1	3e-16	1e-34	3e-11	0.038	2e-27	1e-25
AMOEBOZOA
Entamoebidae
Entamoeba histolytica	171	6.3	20.2	7e-08	6e-16	3e-05	1.5	6e-13	8e-13
Eumycetozoa
Dictyostelium discoideum	194	7.8	23.3	3e-19	3e-32	5e-08	2e-04	-	3e-28
PLANTAE
Green algae
Chlamydomonas reinhardtii	175	6.8	19.9	9e-12	8e-29	0.013	4e-04	8e-32	3e-48
Rhodophyceae
Cyanidioschyzon merolae	209	8.3	24.2	1e-04	2e-18	>10	0.015	2e-20	3e-17
Land plants e
Bryophyta
Physcomitrella patens	175	5.5	20.6	1e-09	5e-23	1e-04	6.0	3e-24	4e-58
Gnetophyta
Welwitschia mirabilis	181	7.6	21.0	2e-13	6e-30	0.002	9e-05	2e-31	7e-71
Pinophyta
Pinus taeda	176	7.4	20.4	3e-12	3e-30	4e-05	2e-04	6e-29	3e-75
Magnoliophyta
Liliopsida
Asparagales
Asparagus officinalis	179	6.9	20.8	1e-11	4e-27	1e-05	0.002	7e-28	6e-80
Cyperales
Hordeum vulgare	177	6.3	20.7	2e-12	3e-28	4e-05	0.006	2e-25	4e-74
Oryza sativa	179	6.6	20.8	9e-15	9e-29	4e-05	0.005	3e-30	2e-80
Sorghum bicolor	177	6.8	20.6	1e-13	3e-28	0.001	0.003	8e-29	6e-77
Saccharum officinarum	177	6.8	20.6	3e-14	3e-28	0.001	0.003	8e-29	2e-76
Triticum aestivum	177	6.9	20.7	9e-12	2e-27	3e-05	0.013	1e-25	3e-74
Eudicotyledons
Asteridae
Antirrhinum majus	179	6.2	20.8	5e-16	2e-26	1e-04	0.004	5e-30	5e-84
Coffea canephora	179	6.9	20.8	7e-12	1e-26	5e-06	0.04	3e-29	2e-82
Lycopersicon esculentum	179	6.7	20.7	5e-14	3e-28	4e-05	0.008	8e-30	4e-85
Rosidae
Arabidopsis thaliana	179	5.7	20.7	2e-15	8e-27	3e-04	0.008	3e-30	-
Brassica napus	179	9.4	20.7	9e-13	7e-26	4e-05	0.004	1e-28	2e-92
Citrus clementina	179	6.2	20.8	3e-12	2e-24	0.069	0.053	5e-27	3e-79
Fragaria vesca	179	6.9	21.0	2e-14	5e-29	3e-04	0.018	8e-32	2e-84
Glycine max	179	6.1	20.7	4e-16	2e-27	3e-04	0.014	1e-29	3e-84
Medicago truncatula	179	5.9	20.9	7e-15	1e-27	2e-05	0.005	6e-28	2e-83
Populus trichocarpa × Populus nigra	179	6.5	21.0	3e-14	1e-27	0.001	0.011	5e-30	8e-88
Populus tremula	179	6.5	21.0	3e-13	3e-27	0.005	0.053	7e-29	2e-86
Vitis vinifera	179	7.0	20.9	3e-14	3e-28	2e-05	0.006	8e-30	1e-85
OPISTHOKONTS
Fungi
Ascomycetes
Saccharomycotina
Candida albicans	196	6.1	22.8	3e-20	7e-20	>10	0.05	1e-20	4e-15
Candida glabrata	194	5.2	22.0	5e-55	3e-16	>10	>10	1e-12	2e-11
Clavispora lusitaniae (Candida lusitaniae)	187	6.2	21.4	1e-13	4e-16	>10	0.65	1e-13	5e-14
Debaryomyces hansenii	196	6.5	22.5	3e-16	7e-18	>10	>10	9e-15	3e-11
Eremothecium gossypii (Ashbya gossypii)	180	6.7	20.2	1e-39	8e-19	>10	>10	2e-11	9e-10
Kluyveromyces lactis	213	5.4	24.6	1e-35	8e-13	>10	>10	2e-12	7e-08
Kluyveromyce waltii	179	5.6	20.7	5e-50	3e-20	>10	0.2	4e-14	3e-15
Saccharomyces cerevisiae	202	5.5	23.6	-	2e-17	0.071	>10	2e-19	4e-14
Saccharomyces bayanus	203	5.4	23.7	1e-98	4e-20	1.3	>10	1e-20	3e-17
Saccharomyces castellii	179	5.7	20.9	2e-59	5e-18	>10	>10	5e-16	2e-15
Saccharomyces kluyveri	185	5.3	21.5	9e-51	3e-15	>10	>10	9e-13	5e-12
Saccharomyces kudriavzevii	202	5.5	23.4	4e-100	1e-18	>10	>10	3e-21	7e-15
Saccharomyces mikatae	202	5.5	23.4	1e-99	3e-19	>10	>10	6e-22	3e-14
Saccharomyces paradoxus	202	5.3	23.4	4e-108	2e-18	0.093	>10	2e-21	9e-16
Yarrowia lipolytica	169	5.9	19.5	4e-18	2e-24	>10	2e-05	2e-19	1e-17
Schizosaccharomycotina
Schizosaccharomyces pombe	175	7.9	20.8	3e-11	4e-22	>10	7.8	5e-15	1e-15
Pezizomycotina
Aspergillus fumigatus	195	8.1	22.3	5e-12	2e-28	2e-07	>10	6e-24	1e-14
Aspergillus oryzae	186	7.5	21.5	8e-10	5e-27	3e-07	>10	4e-24	5e-14
Botryotinia fuckeliana	213	8.0	24.6	2e-12	6e-29	2e-07	2e-07	8e-28	1e-19
Coccidioides immitis	196	8.0	22.3	>10	1e-27	1e-07	>10	3e-25	6e-16
Neosartorya fischeri	191	7.5	21.9	1e-09	1e-26	7e-06	>10	6e-24	2e-13
Neurospora crassa	225	8.7	25.0	1e-05	7e-17	>10	>10	9e-18	3e-09
Phaeosphaeria nodorum	214	8.4	24.1	1e-14	2e-33	1e-05	5e-05	3e-31	2e-22
Sclerotinia sclerotiorum	192	7.5	22.0	9e-17	7e-33	4e-09	6e-07	4e-32	1e-23
Trichoderma reesei	222	7.7	24.0	7e-12	6e-32	0.001	3e-05	5e-27	2e-17
Uncinocarpus reesii	202	7.6	22.7	2e-12	4e-27	5e-05	0.001	3e-25	5e-16
Basidiomycetes
Coprinus cinereus (Coprinopsis cinerea okayama)	234	7.0	26.4	6e-09	4e-16	>10	0.056	1e-16	1e-09
Phanerochaete chrysosporium	200	6.9	22.8	3e-12	1e-18	>10	0.090	4e-18	3e-11
Ustilago maydis	232	8.1	25.2	2e-17	7e-26	2e-04	3e-04	2e-25	3e-20
Zygomycete
Rhizopus oryzae	183	5.0	21.5	7e-16	6.7	0.16	0.002	8e-27	1e-23
Chytridiomycete
Blastocladiella emersonii	186	7.4	21.2	1e-13	3e-20	0.044	0.49	6e-17	3e-16
Metazoa
Echinodermata
Strongylocentrotus purpuratus	175	6.5	20.6	7e-17	3e-56	1e-10	0.002	2e-39	7e-25
Nematoda
Caenorhabditis briggsae	179	6.2	21.1	2e-17	2e-40	9e-10	2e-05	1e-33	2e-22
Caenorhabditis elegans	183	6.2	21.5	1e-16	5e-41	2e-10	2e-05	2e-33	3e-22
Heterodera glycines	175	6.2	20.7	7e-14	6e-43	5e-10	4e-05	3e-33	2e-24
Platyhelminthes
Trematodes
Paragonimus westermani	178	6.4	20.9	5e-21	4e-45	7e-12	0.001	6e-33	9e-28
Schistosoma japonicum	179	7.8	20.7	2e-19	7e-45	6e-09	4e-04	1e-24	9e-26
Schistosoma mansoni	180	6.5	20.8	2e-22	1e-46	6e-12	3e-04	2e-26	4e-28
Schmidtea mediterranea	176	5.0	20.3	2e-18	3e-51	1e-13	0.017	9e-31	2e-27
Arthropoda
Chelicerata
Amblyomma variegatum	175	6.6	20.8	2e-18	7e-46	1e-09	1e-04	1e-31	3e-25
Boophilus microplus	176	5.3	20.3	1e-17	5e-47	6e-11	1e-04	3e-33	7e-25
Hexapoda
Aedes aegypti	173	5.5	19.9	8e-15	5e-34	1e-05	0.061	6e-27	7e-28
Anopheles gambiae	173	5.2	19.9	9e-14	2e-37	3e-05	0.89	6e-26	9e-27
Apis mellifera	175	5.0	20.5	2e-18	2e-48	3e-10	0.017	2e-28	2e-29
Acyrthosiphon pisum	171	5.4	19.6	2e-17	2e-39	6e-05	0.007	2e-26	6e-28
Bombyx mori	175	4.9	20.4	5e-21	6e-45	3e-12	0.008	4e-34	1e-28
Drosophila melanogaster	174	5.1	20.6	8e-16	1e-39	4e-11	4e-05	4e-27	1e-24
Drosophila pseudoobscura	174	5.2	20.7	6e-19	3e-41	2e-11	0.003	2e-26	2e-25
Lutzomyia longipalpis	171	5.2	20.0	2e-16	5e-36	1e-06	3e-04	1e-28	4e-25
Chordata
Urochordata
Ciona intestinalis	176	7.5	20.7	2e-09	6e-38	4e-09	1e-04	1e-21	1e-21
Molgula tectiformis	173	5.7	20.6	7e-14	7e-41	2e-05	1e-04	4e-24	5e-22
Vertebrata
Chondrichthyes
Leucoraja erinacea	174	7.4	20.8	2e-19	7e-75	3e-08	2e-04	1e-38	1e-30
Neopterygii
Danio rerio	174	6.6	20.7	2e-20	5e-77	2e-10	1e-04	2e-42	2e-32
Fugu rubripes	174	6.0	20.7	7e-20	2e-77	7e-11	0.001	2e-41	3e-32
Gasterosteus aculeatus	174	6.2	20.6	7e-19	2e-76	6e-10	0.006	2e-40	2e-31
Ictalurus punctatus	174	6.1	20.7	3e-21	4e-76	1e-10	2e-04	5e-41	2e-32
Oryzias latipes	174	6.0	20.8	8e-21	3e-75	1e-11	0.006	1e-41	7e-33
Oncorhynchus mykiss	174	5.9	20.7	1e-18	6e-74	7e-11	0.01	2e-41	7e-30
Platichthys flesus	173	5.6	20.6	2e-18	3e-77	8e-10	0.003	2e-40	4e-32
Pimephales promelas	174	6.6	20.7	2e-20	7e-76	6e-10	5e-04	2e-42	2e-31
Salmo salar	174	5.9	20.7	1e-18	6e-74	7e-11	0.01	2e-41	7e-30
Tetraodon nigroviridis	174	6.0	20.7	2e-16	5e-70	1e-07	0.001	6e-37	8e-29
Tetrapoda
Aves
Gallus gallus	174	8.1	20.4	3e-16	1e-70	4e-07	5e-04	1e-29	2e-24
Taeniopygia guttata	174	6.2	20.4	2e-16	6e-71	5e-10	0.022	1e-28	4e-23
Amphibia
Xenopus laevis	174	6.6	20.7	6e-22	1e-78	4e-12	2e-04	3e-40	4e-32
Xenopus tropicalis	174	6.8	20.7	7e-22	5e-78	7e-12	3e-05	6e-40	6e-32
Mammalia
Bos taurus	176	6.3	20.7	2e-16	1e-90	1e-07	4e-04	3e-31	9e-23
Canis familiaris	176	6.3	20.8	2e-16	2e-91	2e-07	3e-04	3e-31	9e-23
Equus caballus	176	6.3	20.8	2e-16	2e-91	2e-07	3e-04	3e-31	9e-23
Homo sapiens	176	6.3	20.7	9e-17	-	1e-06	4e-04	4e-31	1e-22
Macaca mulatta	176	6.3	20.7	9e-17	7e-92	1e-06	4e-04	4e-31	1e-22
Monodelphis domestica	176	6.3	20.8	9e-17	2e-89	5e-07	2e-04	8e-32	7e-23
Mus musculus	176	6.3	20.7	2e-16	6e-91	3e-07	4e-04	1e-30	5e-23
Oryctolagus cuniculus	176	6.3	20.8	1e-16	8e-91	2e-07	4e-04	2e-31	5e-23
Rattus norvegicus	176	6.3	20.8	3e-11	4e-78	2e-05	4e-04	2e-23	2e-18
Sus scrofa	176	6.3	20.8	2e-16	2e-91	2e-07	3e-04	3e-31	9e-23
RHIZARIA
None identified to date.

^aSee Additional File 1 for comments on classification of species into major eukaryotic groupings and accession numbers.
^bIsoelectric point calculated using the assumption that all residues have pKa values equivalent to that of isolated residues, so may not accurately represent the value for the folded protein.
^cIsotopically averaged molecular weight prediction in kiloDaltons.
^dThe BLASTP E-value (Expect value) measures the statistical significance threshold for protein sequence matches. The smaller the number the better the match. Computer shorthand nomenclature is used to present E-values when values are small. For example, 5e-01 = 0.5 and 5e-04 = 0.0005.
^eProteins were compared to Saccharomyces cerevisiae, Homo sapiens, Paramecium primaurelia, Trypanosoma brucei, Dictystelium discoideum, or Arabidopsis thaliana Vps25p by BLASTP. The Vps25 proteins used for comparison were chosen as the representive of fungal, metazoan, chromalveolate, excavate, amoebozoan, or plant species because these sequence are documented on the non-redundant protein database and they are well-known eukaryotic species.
^fWhen E-values were greater than 10, details are not provided.
^gA dash is used when alignments have 100% identity.

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