BioNumbers data base: Difference between revisions
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!property index | !property index |
Revision as of 17:53, 8 September 2007
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<exhibit>
<source id="bionumbers" columns="label:number,propfamily,propsubfamily,property,organism,value:number,units,reference,primaryref,keywords,method,range,comments,enteredby" type="Number" label="Number" pluralLabel="Numbers" /> <facet facetClass="TextSearch" /> <facet expression=".organism" /> <facet expression=".property" /> <facet expression=".propfamily" /> <facet expression=".propsubfamily" /> <view viewClass="Tabular" label="Table" columns=".label,.property,.organism,.value,.units" sortColumn="0" /> <view viewClass="Tile" label="Details" orders=".label" />
</exhibit>
property index | Property family | Property subfamily | Property | Organism | Value | Units | Reference (where data was taken from) | Primary source of reference (if different from previous) | Keywords | measurement method | Standard deviation or range if available | comments (cell type, measurement conditions etc.) | Entered by: |
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1 | Sizes | Lengths | Cell length | E. coli | 2 | microns | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani,Paul Stothard, Michael Ellison,and David S. Wishart "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli" Nucleic Acids Res. 2004 January 1; 32 (Database issue): D293.D295 | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
2 | Sizes | Lengths | Cell diameter | E. coli | 0.8 | microns | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
3 | Sizes | Volumes | Cell total volume | E. coli | 1x10-18 | m^3 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
4 | Sizes | Volumes | Cell total volume | E. coli | 0.44-1.79*10^-18 | m^3 | Determination of bacterial cell volume with the Coulter Counter. HE Kubitschek, JA Friske - Journal of Bacteriology, 1986, p. 1466-1467 | Coulter counter | value depends on medium and growth rate, see ref. | Ron Milo | |||
5 | Sizes | Volumes | Cell aqueous volume | E. coli | 7 x 10-16 | L | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
6 | Sizes | Surface | Cell surface area | E. coli | 6x10-12 | m^2 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
7 | Sizes | Weights | Cell wet weight | E. coli | 1x10-15 | kg | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
8 | Sizes | Weights | Cell dry weight | E. coli | 3.0x10-16 | kg | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
9 | Sizes | Weights | Cell dry weight | E. coli | 6.4x10-16 | kg | Bremer, H., Dennis, P. P. (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Neidhardt, et al. eds. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, Table 2 | Indirect calculation based on the ratio: (dry mass)/OD460 | calculated based on data at 30 minutes cell division time. For other division times see reference. | Ron Milo | |||
10 | Sizes | Volumes | Periplasm volume | E. coli | 6.5x10-17 | L | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
11 | Sizes | Volumes | Cytoplasm volume | E. coli | 6.7x10-16 | L | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
12 | Sizes | Volumes | Envelope volume | E. coli | 1.6x10-16 | L | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
13 | Sizes | Volumes | Nuclear (DNA+protein) volume | E. coli | 1.6x10-16 | L | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
14 | Sizes | Lengths | Inner Membrane thickness | E. coli | 8x10-9 | m | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
15 | Sizes | Lengths | Outer Membrane thickness | E. coli | 8x10-9 - 15x10-9 | m | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
16 | Sizes | Lengths | Periplasm thickness | E. coli | 1x10-8 | m | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
17 | Sizes | Sizes | Average size of protein | E. coli | 360 | aa | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
18 | Sizes | Lengths | Average diameter of ave. protein | E. coli | 5 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
19 | Sizes | Weights | Average MW of protein | E. coli | 40 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
20 | Sizes | Complexes | Average prot. oligomerization state | E. coli | 4 | proteins/complex | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
21 | Sizes | Weights | Average MW of protein entity | E. coli | 160 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
22 | Sizes | mRNA | Average size of mRNA | E. coli | 1100 | bp | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
23 | Sizes | mRNA | Average length of mRNA | E. coli | 370 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
24 | Sizes | Weights | Average MW of all RNAs | E. coli | 400 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
25 | Sizes | Weights | Average MW of single DNA | E. coli | 3.0x10^6 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
26 | Sizes | Weights | Average MW of all DNA | E. coli | 7x10^6 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
27 | Sizes | Lengths | Average length of DNA (chrom.) | E. coli | 1.55 | mm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
28 | Sizes | Lengths | Diameter of chromosome | E. coli | 490 | micron | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
29 | Sizes | Lengths | Diameter of condensed chromosome | E. coli | 17 | micron | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
30 | Sizes | Lengths | Spacing between small organics | E. coli | 3.6 | nm/molecule | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
31 | Sizes | Lengths | Spacing between ions | E. coli | 2.1 | nm/molecule | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
32 | Sizes | Lengths | Ave. spacing between proteins | E. coli | 7 | nm/molecule | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
33 | Sizes | Lengths | Spacing between protein entities | E. coli | 9 | nm/molecule | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
34 | General Statistics | Velocities | Mean Velocity of 70 kD protein (cytoplasm) | E. coli | 3 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
35 | General Statistics | Velocities | Mean Velocity of 40 kD protein (cytoplasm) | E. coli | 5 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
36 | General Statistics | Velocities | Mean Velocity of 30 kD protein (cytoplasm) | E. coli | 7 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
37 | General Statistics | Velocities | Mean Velocity of 14 kD protein (cytoplasm) | E. coli | 10 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
38 | General Statistics | Velocities | Mean Velocity of small molecules (cytoplasm) | E. coli | 50 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
39 | General Statistics | Velocities | Mean Velocity of protein in H2O | E. coli | 27 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
40 | General Statistics | Velocities | Mean Velocity of small molecules in H2O | E. coli | 87 | nm/ms | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
41 | General Statistics | Concentrations | Concentration of protein in cell | E. coli | 200-320 | mg/ml | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
42 | General Statistics | Concentrations | Concentration of RNA in cell | E. coli | 75-120 | mg/ml | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
43 | General Statistics | Concentrations | Concentration of DNA in cell | E. coli | 11 - 18 | mg/ml | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
44 | General Statistics | Volumes | Volume occupied by water | E. coli | 70 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
45 | General Statistics | Volumes | Volume occupied by protein | E. coli | 17 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
46 | General Statistics | Volumes | Volume occupied by all RNA | E. coli | 6 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
47 | General Statistics | Volumes | Volume occupied by rRNA | E. coli | 5 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
48 | General Statistics | Volumes | Volume occupied by tRNA | E. coli | 0.8 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
49 | General Statistics | Volumes | Volume occupied by mRNA | E. coli | 0.2 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
50 | General Statistics | Volumes | Volume occupied by DNA | E. coli | 1 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
51 | General Statistics | Volumes | Volume occupied by ribosomes | E. coli | 8 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
52 | General Statistics | Volumes | Volume occupied by lipid | E. coli | 3 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
53 | General Statistics | Volumes | Volume occupied by LPS | E. coli | 1 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
54 | General Statistics | Volumes | Volume occupied by murein | E. coli | 1 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
55 | General Statistics | Volumes | Volume occupied by glycogen | E. coli | 1 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
56 | General Statistics | Volumes | Volume occupied by ions | E. coli | 0.3 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
57 | General Statistics | Volumes | Volume occupied by small organics | E. coli | 1 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
58 | General Statistics | Rates | Translation rate | E. coli | 40 | aa/sec | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
59 | General Statistics | Rates | Translation rate | E. coli | 20 | aa/sec | Bremer, H., Dennis, P. P. (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Neidhardt, et al. eds. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, Table 3 | Dennis, P. P., and H. Bremer. 1974. Differential rate of ribosomal protein synthesis in Escherichia coli B/r. J. Mol. Biol. 84:407�$-1òó422.;Dennis, P. P., and M. Nomura. 1974. Stringent control of ribosomal protein gene expression in | |||||
Escherichia coli. Proc. Natl. Acad. Sci. USA 71:3819�$-1òó3823. | Indirect calculation based on the number of ribosomes, ribosome activity fraction and protein synthesis rate | calculated based on data at 30 minutes cell division time. For other division times see reference. This value is probably an underestimate based on some newer results | Ron Milo | ||||||||||
60 | General Statistics | Rates | RNA polymerase transcription rate | E. coli | 70 | nt/sec | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | coli B/r. J. Mol. Biol. 84:407�$-1òó422. | Ron Milo, Paul Jorgensen, Mike Springer | ||||
61 | Copy numbers | Large Molecule Copy Numbers | Number of cell walls/cell | E. coli | 1 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
62 | Copy numbers | Large Molecule Copy Numbers | Number of membranes/cell | E. coli | 2 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
63 | Copy numbers | Large Molecule Copy Numbers | Number of chromosomes/cell | E. coli | 2.3 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | at mid log phase | Ron Milo, Paul Jorgensen, Mike Springer | |||
64 | Copy numbers | Large Molecule Copy Numbers | Number of mRNA/cell | E. coli | 4000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
65 | Copy numbers | Large Molecule Copy Numbers | Number of rRNA/cell | E. coli | 18000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
66 | Copy numbers | Large Molecule Copy Numbers | Number of tRNA/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
67 | Copy numbers | Large Molecule Copy Numbers | Number of all RNA/cell | E. coli | 222000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
68 | Copy numbers | Large Molecule Copy Numbers | Number of polysaccharides/cell | E. coli | 39000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
69 | Copy numbers | Large Molecule Copy Numbers | Number of murein molecules/cell | E. coli | 240,000-700,000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
70 | Copy numbers | Large Molecule Copy Numbers | Number of lipopolysaccharide/cell | E. coli | 600000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
71 | Copy numbers | Large Molecule Copy Numbers | Number of lipids/cell | E. coli | 25000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
72 | Copy numbers | Large Molecule Copy Numbers | Number of all lipids/cell | E. coli | 25000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
73 | Copy numbers | Large Molecule Copy Numbers | Number of phosphatidylethanolamine | E. coli | 18500000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
74 | Copy numbers | Large Molecule Copy Numbers | Number of phosphatidylglycerol | E. coli | 5000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
75 | Copy numbers | Large Molecule Copy Numbers | Number of cardiolipin | E. coli | 1200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
76 | Copy numbers | Large Molecule Copy Numbers | Number of phosphatidylserine | E. coli | 500000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
77 | Copy numbers | Large Molecule Copy Numbers | Number of LPS (MW = 10kD) | E. coli | 600000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
78 | Copy numbers | Large Molecule Copy Numbers | Average SA of lipid molecule | E. coli | 25 | Ang2 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
79 | Copy numbers | Large Molecule Copy Numbers | Fraction of lipid bilayer=lipid | E. coli | 40 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
80 | Copy numbers | Large Molecule Copy Numbers | Fraction of lipid bilayer=protein | E. coli | 60 | Percent | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
81 | Copy numbers | Large Molecule Copy Numbers | Number of outer membrane proteins | E. coli | 300000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
82 | Copy numbers | Large Molecule Copy Numbers | Number of porins (subset of OM) | E. coli | 60000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
83 | Copy numbers | Large Molecule Copy Numbers | Number of lipoproteins (OM) | E. coli | 240000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
84 | Copy numbers | Large Molecule Copy Numbers | Number of inner membrane proteins | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
85 | Copy numbers | Large Molecule Copy Numbers | Number of nuclear proteins | E. coli | 100000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
86 | Copy numbers | Large Molecule Copy Numbers | Number of cytoplasmic proteins | E. coli | 1000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | excluding ribosomal proteins | Ron Milo, Paul Jorgensen, Mike Springer | |||
87 | Copy numbers | Large Molecule Copy Numbers | Number of ribosomal proteins | E. coli | 900000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
88 | Copy numbers | Large Molecule Copy Numbers | Number of periplasmic proteins | E. coli | 80000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
89 | Copy numbers | Large Molecule Copy Numbers | Number of all proteins in cell | E. coli | 2600000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
90 | Copy numbers | Large Molecule Copy Numbers | Number of all proteins in cell in amino acids | E. coli | 1.89*10^9 | amino acids | Neidhardt, F.C. et al. (1987) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, Table 2 | For a cell cycle of 30 minutes at 37deg, see reference for value at other division rates | Ron Milo | ||||
91 | Genome | Replication | Time to replicate the chromosome | E. coli | 40-67 | Minutes | Neidhardt, F.C. et al. (1987) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, Table 1, 3 | Value in range depends on division rate | Ron Milo | ||||
92 | Translation | Ribosomes | Average distance between ribosomes on mRNA | E. coli | 41-79 | nucleotides | Neidhardt, F.C. et al. (1987) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. chapter 97, Table 3 | Indirectly calculated from other parameters, see reference | Value in range depends on division rate | Ron Milo | |||
93 | Copy numbers | Large Molecule Copy Numbers | Number of external proteins (flag/pili) | E. coli | 1000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
94 | Copy numbers | Large Molecule Copy Numbers | Number of all proteins | E. coli | 3600000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
95 | Complexes | Statistics on Larger Molecule Complexes | Number of protein types to make flagella | E. coli | 42 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
96 | Sizes | Statistics on Larger Molecule Complexes | Length of flagella | E. coli | 10 - 20 | microns | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
97 | Sizes | Statistics on Larger Molecule Complexes | Diameter of flagella | E. coli | 25 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
98 | Complexes | Statistics on Larger Molecule Complexes | Number of protofilaments in flagellum | E. coli | 11 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
99 | Sizes | Statistics on Larger Molecule Complexes | Diameter of each fliC monomer | E. coli | 5 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
100 | Copy numbers | Statistics on Larger Molecule Complexes | Number of fliC monomers in filament | E. coli | 33000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
101 | Copy numbers | Statistics on Larger Molecule Complexes | Number of flagella/cell | E. coli | 10 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
102 | Copy numbers | Statistics on Larger Molecule Complexes | Number of fliC proteins | E. coli | 330000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
103 | Velocities | Statistics on Larger Molecule Complexes | Speed at which E. coli move | E. coli | 50 | micron/sec | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
104 | Statistics on Larger Molecule Complexes | Number of protein types to make pilus | E. coli | 1 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | |||||
105 | Lengths | Statistics on Larger Molecule Complexes | Length of pili/fimbrae | E. coli | 200-2000 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
106 | Lengths | Statistics on Larger Molecule Complexes | Diamter of pili | E. coli | 6.5 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
107 | Copy numbers | Statistics on Larger Molecule Complexes | Number of papA/nm pilus | E. coli | 1.5 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
108 | Copy numbers | Statistics on Larger Molecule Complexes | Number of papA monomers/pilus | E. coli | 3000-30,000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
109 | Copy numbers | Statistics on Larger Molecule Complexes | Number of pili/cell | E. coli | 100-300 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
110 | Copy numbers | Statistics on Larger Molecule Complexes | Number of papA/cell | E. coli | 300,000-900,000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
111 | Copy numbers | Statistics on Larger Molecule Complexes | Number of ribosomes/cell | E. coli | 18000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
112 | Copy numbers | Statistics on Larger Molecule Complexes | Number of protein types to make ribosome | E. coli | 55 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
113 | Copy numbers | Statistics on Larger Molecule Complexes | Number rRNA types to make ribosome | E. coli | 3 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
114 | Copy numbers | Statistics on Larger Molecule Complexes | Number of proteins in 30S subunit | E. coli | 21 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
115 | Copy numbers | Statistics on Larger Molecule Complexes | Number of proteins in 50S subunit | E. coli | 34 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
116 | Copy numbers | Statistics on Larger Molecule Complexes | Number of rRNA in 30S subunit | E. coli | 1 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
117 | Copy numbers | Statistics on Larger Molecule Complexes | Number of rRNA in 50S subunit | E. coli | 2 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
118 | Lengths | Statistics on Larger Molecule Complexes | Length of all rRNA | E. coli | 5520 | nt | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
119 | Weights | Statistics on Larger Molecule Complexes | MW of ribosome | E. coli | 2700 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
120 | Weights | Statistics on Larger Molecule Complexes | MW of RNA component | E. coli | 1700 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
121 | Weights | Statistics on Larger Molecule Complexes | MW of protein component | E. coli | 1000 | kDalton | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
122 | Lengths | Statistics on Larger Molecule Complexes | Diameter of ribosome | E. coli | 20 | nm | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
123 | Volumes | Statistics on Larger Molecule Complexes | Volume of ribosome | E. coli | 4.2 x 10^-24 | m^3 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
124 | Copy numbers | Small Molecule Copy Numbers | Number of water molecules/cell | E. coli | 2.34x10^10 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
125 | Copy numbers | Small Molecule Copy Numbers | Number of ions/cell | E. coli | 120000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 120,000,000 (300 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
126 | Copy numbers | Small Molecule Copy Numbers | Number of small organics/cell | E. coli | 18000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 18,000,000 (40-50 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
127 | Copy numbers | Small Molecule Copy Numbers | Number of K ions | E. coli | 90000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 90,000,000 (200-250 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
128 | Copy numbers | Small Molecule Copy Numbers | Number of Na ions | E. coli | 2000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 2,000,000 (5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
129 | Copy numbers | Small Molecule Copy Numbers | Na (in): Na (out) | E. coli | 1 : 20 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1:20 (in concentration) | Ron Milo, Paul Jorgensen, Mike Springer | |||
130 | Copy numbers | Small Molecule Copy Numbers | Number of Ca ions | E. coli | 2300000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 2,300,000 (6 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
131 | Copy numbers | Small Molecule Copy Numbers | Number of free Ca ions | E. coli | 40 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 40 (100 nM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
132 | Copy numbers | Small Molecule Copy Numbers | Number of Cl ions | E. coli | 2400000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 2,400,000 (6 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
133 | Copy numbers | Small Molecule Copy Numbers | Number of Mg ions | E. coli | 4000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 4,000,000 (10 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
134 | Copy numbers | Small Molecule Copy Numbers | Number of Fe ions | E. coli | 7000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 7,000,000 (18 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
135 | Copy numbers | Small Molecule Copy Numbers | Number of Mn ions | E. coli | 1700000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,700,000 (4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
136 | Copy numbers | Small Molecule Copy Numbers | Number of Zn ions | E. coli | 1700000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,700,000 (4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
137 | Copy numbers | Small Molecule Copy Numbers | Number of Mo ions | E. coli | 1700000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,700,000 (4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
138 | Copy numbers | Small Molecule Copy Numbers | Number of Cu ions | E. coli | 1700000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,700,000 (4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
139 | Copy numbers | Small Molecule Copy Numbers | Number of PO4 ions | E. coli | 2000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 2,000,000 (5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
140 | Copy numbers | Small Molecule Copy Numbers | Number of glucose/cell | E. coli | 200,000-400,000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000-400,000 (0.5-1 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
141 | Copy numbers | Small Molecule Copy Numbers | Number of PEP/cell | E. coli | 1100000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,100,000 (2.8 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
142 | Copy numbers | Small Molecule Copy Numbers | Number of pyruvate/cell | E. coli | 370000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 370,000 (0.9 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
143 | Copy numbers | Small Molecule Copy Numbers | Number of gluc-6-PO4/cell | E. coli | 20000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 20,000 (0.05 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
144 | Copy numbers | Small Molecule Copy Numbers | Number of ATP/cell | E. coli | 500,000 - 3,000,000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 500,000 - 3,000,000 (1.3-7.0 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
145 | Copy numbers | Small Molecule Copy Numbers | Number of ADP/cell | E. coli | 70000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 70,000 (0.17 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
146 | Copy numbers | Small Molecule Copy Numbers | Number of NADP/cell | E. coli | 240000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 240,000 (0.63 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
147 | Copy numbers | Small Molecule Copy Numbers | Number of NADPH/cell | E. coli | 220000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 220,000 (0.56 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
148 | Copy numbers | Small Molecule Copy Numbers | Number of all amino acids/cell | E. coli | 6000000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 6,000,000 (1.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
149 | Copy numbers | Small Molecule Copy Numbers | Number of free Alanine/cell | E. coli | 350000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 350,000 (0.8 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
150 | Copy numbers | Small Molecule Copy Numbers | Number of free Cysteine/cell | E. coli | 80000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 80,000 (0.2 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
151 | Copy numbers | Small Molecule Copy Numbers | Number of free Aspartate/cell | E. coli | 530000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 530,000 (1.34 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
152 | Copy numbers | Small Molecule Copy Numbers | Number of free Glutamate/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000 (0.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
153 | Copy numbers | Small Molecule Copy Numbers | Number of free Phenylalanine/cell | E. coli | 170000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 170,000 (0.4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
154 | Copy numbers | Small Molecule Copy Numbers | Number of free Glycine/cell | E. coli | 350000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 350,000 (0.8 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
155 | Copy numbers | Small Molecule Copy Numbers | Number of free Histidine/cell | E. coli | 80000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 80,000 (0.2 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
156 | Copy numbers | Small Molecule Copy Numbers | Number of free Isoleucine/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000 (0.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
157 | Copy numbers | Small Molecule Copy Numbers | Number of free Lysine/cell | E. coli | 190000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 190,000 (0.46 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
158 | Copy numbers | Small Molecule Copy Numbers | Number of free Leucine/cell | E. coli | 300000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 300,000 (0.7 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
159 | Copy numbers | Small Molecule Copy Numbers | Number of free Methionine/cell | E. coli | 40000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 40,000 (0.1 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
160 | Copy numbers | Small Molecule Copy Numbers | Number of free Asparagine/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000 (0.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
161 | Copy numbers | Small Molecule Copy Numbers | Number of free Proline/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000 (0.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
162 | Copy numbers | Small Molecule Copy Numbers | Number of free Glutamine/cell | E. coli | 200000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 200,000 (0.5 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
163 | Copy numbers | Small Molecule Copy Numbers | Number of free Arginine/cell | E. coli | 170000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 170,000 (0.4 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
164 | Copy numbers | Small Molecule Copy Numbers | Number of free Serine/cell | E. coli | 300000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 300,000 (0.7 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
165 | Copy numbers | Small Molecule Copy Numbers | Number of free Threonine/cell | E. coli | 1400000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 1,400,000 (3.49 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
166 | Copy numbers | Small Molecule Copy Numbers | Number of free Valine/cell | E. coli | 240000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 240,000 (0.6 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
167 | Copy numbers | Small Molecule Copy Numbers | Number of free Tryptophan/cell | E. coli | 80000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 80,000 (0.2 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
168 | Copy numbers | Small Molecule Copy Numbers | Number of free Tyrosine/cell | E. coli | 300000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | 300,000 (0.7 mM) | Ron Milo, Paul Jorgensen, Mike Springer | |||
169 | Pressure | Small Molecule Copy Numbers | Osmotic pressure (pushing out) | E. coli | 75 | lb/in2 | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | inner, pressure, osmotic, internal | Equivalent to about 5 Atm (50ton/m^2) | Ron Milo, Paul Jorgensen, Mike Springer | ||
170 | Energetic cost | E. coli Metabolism | One glucose generates (total) | E. coli | 36-38 | ATP | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
171 | Energetic cost | E. coli Metabolism | Glycolysis yields | E. coli | 39241 | ATP | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
172 | Energetic cost | E. coli Metabolism | Oxidation of pyruvate yields | E. coli | 6 | ATP | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
173 | Energetic cost | E. coli Metabolism | Krebs cycle/e- transport yields | E. coli | 24 | ATP | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
174 | Energetic cost | E. coli Metabolism | Number ATP to make 1 DNA | E. coli | 72289000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
175 | Energetic cost | E. coli Metabolism | Number ATP to make 1 protein (360 aa) | E. coli | 1500 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
176 | Energetic cost | E. coli Metabolism | Number ATP to make 1 lipid | E. coli | 7 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
177 | Energetic cost | E. coli Metabolism | Number ATP to make 1 polysaccharide | E. coli | 2000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
178 | Energetic cost | E. coli Metabolism | Number ATP to make 1 RNA (1000 nt) | E. coli | 2000 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
179 | Energetic cost | E. coli Metabolism | Number ATP to make 1 cell | E. coli | 55*10^9 | ATP | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
180 | Energetic cost | E. coli Metabolism | Number Glucose molecules consumed | E. coli | 1.4*10^6 | Unitless | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
181 | Growth | E. coli Metabolism | Cell generation time | E. coli | 30 | minutes | http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi | A list of primary sources is given in the reference | Ron Milo, Paul Jorgensen, Mike Springer | ||||
182 | General statistics | DNA | Chromosomal DNA weight | X. laevis | 12 | pg | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | A list of primary sources is given in the reference | Stage VI oocyte | Paul Jorgensen | |||
183 | General statistics | DNA | Nucleolar rDNA weight | X. laevis | 25 | pg | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
184 | General statistics | DNA | Nucleolar rDNA | X. laevis | 2 x 10^6 | rDNA repeats | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
185 | General statistics | DNA | Mitochondrial DNA weight | X. laevis | 4000 | pg | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Igor and Dawid, Dev. Biol 27:504-518 (1972) | Egg | Paul Jorgensen | |||
186 | General statistics | DNA | Mitochondrial DNA | X. laevis | 10^8 | genomes | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
187 | General statistics | RNA | rRNA | X. laevis | 5 | ug | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
188 | General statistics | RNA | 5S RNA | X. laevis | 60 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
189 | General statistics | RNA | 5S RNA | X. laevis | 10^12 | RNAs | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
190 | General statistics | RNA | tRNA | X. laevis | 60 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
191 | General statistics | RNA | tRNA | X. laevis | 1.5 x 10^12 | tRNAs | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
192 | General statistics | RNA | snRNA U1 | X. laevis | 0.07 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
193 | General statistics | RNA | snRNA U1 | X. laevis | 8 x 10^8 | RNAs | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
194 | General statistics | RNA | polyA+ RNA | X. laevis | 80 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
195 | General statistics | RNA | polyA+ RNA | X. laevis | 5 x 10^10 | RNAs | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | if 2500bp long on average | Paul Jorgensen | |||
196 | General statistics | RNA | ribosomal protein mRNA | X. laevis | 10 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
197 | General statistics | RNA | ribosomal protein mRNA | X. laevis | 2 x 10^10 | transcripts | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
198 | General statistics | RNA | actin mRNA | X. laevis | 1 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
199 | General statistics | RNA | actin mRNA | X. laevis | 5 x 10^8 | transcripts | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
200 | General statistics | RNA | Hsp70 mRNA | X. laevis | 0.004 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
201 | General statistics | RNA | Hsp70 mRNA | X. laevis | 10^6 | transcripts | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
202 | General statistics | RNA | Ribosomes | X. laevis | 10^12 | ribosomes | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
203 | General statistics | Protein | Yolk protein | X. laevis | 250 | ug | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
204 | General statistics | Protein | non-yolk protein | X. laevis | 25 | ug | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
205 | General statistics | Protein | non-yolk protein | X. laevis | 5 x 10^14 | proteins | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | if 30K average | Paul Jorgensen | |||
206 | General statistics | Protein | Histones | X. laevis | 140 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
207 | General statistics | Protein | Histones | X. laevis | 5 x 10^12 | histone proteins | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
208 | General statistics | Protein | Nucleoplasmin | X. laevis | 250 | ng | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
209 | General statistics | Protein | Nucleoplasmin | X. laevis | 5 x 10^12 | nucleoplasmin proteins | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
210 | General statistics | Protein | RNA polymerase I and II | X. laevis | 10^5 | greater than a somatic cell | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
211 | General statistics | Protein | RNA polymerase III | X. laevis | 5 x 10^5 | greater than a somatic cell | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
212 | General statistics | Metabolism | Each dNTP | X. laevis | 10 - 15 | pmol | Woodland and Pestell, Biochem J. 127:597-605 (1972) | Stage VI oocyte | Paul Jorgensen | ||||
213 | General statistics | Metabolism | rGTP | X. laevis | 250 | pmol | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
214 | General statistics | Metabolism | Methionine | X. laevis | 40 | pmol | Hausen and Riebesell, The Early Development of Xenopus laevis, 1991 | Stage VI oocyte | Paul Jorgensen | ||||
215 | General statistics | Genome | Genome Size | Escherichia coli (Bacterium) | 4.6*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
216 | General statistics | Genome | Genome Size | Sacchromyces cerevisiae (Yeast) | 12156678 | Base pairs | http://www.yeastgenome.org/cache/genomeSnapshot.html | Ron Milo | |||||
217 | General statistics | Genome | Genome Size | Neurospora crassa (Fungus) | 39.9*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
218 | General statistics | Genome | Genome Size | C. elegans (Nematode) | 100*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
219 | General statistics | Genome | Genome Size | C. briggsae (Nematode) | 104*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
220 | General statistics | Genome | Genome Size | Drosophila melanogaster (Fruit fly) | 120*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
221 | General statistics | Genome | Genome Size | Anapheles gambiae (Mosquito) | 280*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
222 | General statistics | Genome | Genome Size | Gallus gallus (Chicken) | 120*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
223 | General statistics | Genome | Genome Size | Fugu rubripes (Pufferfish) | 365*10^6 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
224 | General statistics | Genome | Genome Size | Danio rario (Zebrafish) | 1.7*10^9 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | (?) | Ron Milo | ||||
225 | General statistics | Genome | Genome Size | Mouse | 3*10^9 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
226 | General statistics | Genome | Genome Size | Xenopus laevis (Frog) | 3*10^9 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | ~ | Ron Milo | ||||
227 | General statistics | Genome | Genome Size | Human | 3*10^9 | Base pairs | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
228 | General statistics | Genome | Number of genes | Escherichia coli (Bacterium) | 3000 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
229 | General statistics | Genome | Number of genes | Yeast | 6609 | ORF | http://www.yeastgenome.org/cache/genomeSnapshot.html | Ron Milo | |||||
230 | General statistics | Genome | Number of genes | Neurospora crassa (Fungus) | 10000 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | (Release Apr 2003) | Ron Milo | ||||
231 | General statistics | Genome | Number of genes | C. elegans (Nematode) | 20621 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | (Release WS108) | Ron Milo | ||||
232 | General statistics | Genome | Number of genes | C. briggsae (Nematode) | 19507 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | (Release Sept 2003) | Ron Milo | ||||
233 | General statistics | Genome | Number of genes | Drosophila melanogaster (Fruit fly) | 13647 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | (Release 3.1) | Ron Milo | ||||
234 | General statistics | Genome | Number of genes | Anapheles gambiae (Mosquito) | 13600 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
235 | General statistics | Genome | Number of genes | Fugu rubripes (Pufferfish) | 38000 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
236 | General statistics | Genome | Number of genes | Mouse | 30000 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
237 | General statistics | Genome | Number of genes | Human | 31000 | Genes | http://wormlab.caltech.edu/briggsae/genomeSize.html | Ron Milo | |||||
238 | General statistics | Genome | Number of tRNA | Yeast | 299 | unitless | http://www.yeastgenome.org/cache/genomeSnapshot.html | Ron Milo | |||||
239 | General statistics | Genome | Number of rRNA | Yeast | 27 | unitless | http://www.yeastgenome.org/cache/genomeSnapshot.html | Ron Milo | |||||
240 | Growth | Generation time | Minimal generation time | Vibrio natriegens | 9.8 | Minutes | R. G. Eagon, J. Bacteriol. 83:736-737, 1962 | Optimal growth occurred at 37 C in brain heart infusion broth supplemented with 1.5% sea salt. | Ron Milo | ||||
241 | Growth | Generation time | Minimal generation time | Escherichia coli | 17 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Glucose-salts | Ron Milo | ||||
242 | Growth | Generation time | Minimal generation time | Bacillus megaterium | 25 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Sucrose-salts | Ron Milo | ||||
243 | Growth | Generation time | Minimal generation time | Streptococcus lactis | 26 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Milk | Ron Milo | ||||
244 | Growth | Generation time | Minimal generation time | Streptococcus lactis | 48 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Lactose broth | Ron Milo | ||||
245 | Growth | Generation time | Minimal generation time | Staphylococcus aureus | 27-30 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Heart infusion broth | Ron Milo | ||||
246 | Growth | Generation time | Minimal generation time | Lactobacillus acidophilus | 66-87 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Milk | Ron Milo | ||||
247 | Growth | Generation time | Minimal generation time | Rhizobium japonicum | 344-461 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Mannitol-salts-yeast extract | Ron Milo | ||||
248 | Growth | Generation time | Minimal generation time | Mycobacterium tuberculosis | 792-932 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Synthetic | Ron Milo | ||||
249 | Growth | Generation time | Minimal generation time | Treponema pallidum | 1980 | Minutes | http://textbookofbacteriology.net/growth.html | medium: Rabbit testes | Ron Milo | ||||
250 | copy numbers | Chemotaxis | Number of chemoreceptors (total) | E. coli | 15000 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | strain RP437 grown in TB medium | Tom Shimizu | ||||
251 | copy numbers | Chemotaxis | Number of major receptors (Tsr+Tar) | E. coli | 14000 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
252 | copy numbers | Chemotaxis | Number of minor receptors (Trg+Tap+Aer) | E. coli | 1000 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
253 | copy numbers | Chemotaxis | Number of kinases (CheA) | E. coli | 4500 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
254 | copy numbers | Chemotaxis | Number of receptor-kinase couplers (CheW) | E. coli | 6700 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
255 | copy numbers | Chemotaxis | Number of output response regulators (CheY) | E.coli | 8200 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
256 | copy numbers | Chemotaxis | Number of phosphatases (CheZ) | E. coli | 3200 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
257 | copy numbers | Chemotaxis | Number of feedback response regulators (CheB) | E. coli | 240 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
258 | copy numbers | Chemotaxis | Number of methyltransferases | E. coli | 140 | proteins | http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html | Li & Hazelbauer (PNAS, 2004) | strain RP437 grown in TB medium | Tom Shimizu | |||
259 | Rates | Chemotaxis | Time constant for sub-saturating response | E. coli | 4 | seconds | Segall, Block & Berg (PNAS, 1986) | Li & Hazelbauer (PNAS, 2004) | Tom Shimizu | ||||
260 | Dynamic range | Chemotaxis | Dynamic range for gradient sensing of alpha-methylaspartate | E.coli | 5 | orders of magnitude | Mesibov, Ordal & Adler (J. Gen. Physiol., 1973) | this is minimal estimation, i.e. larger than 5 orders of magnitude | Tom Shimizu | ||||
261 | Biophysical parameters | Diffusion rates | Diffusion rate of small molecule | Generic | 50 | 10^-7*cm^2/sec | "Cell movements - from molecules to motility", pp. 6, Dennis Bray, 2nd ed. Garland, 2001 | Hille (1992), Berg (1993), Atkins (1994) | order of magnitude. ~1msec for a distance of 1 micron | Ron Milo | |||
262 | Biophysical parameters | Diffusion rates | Diffusion rate of protein molecule | Generic | 5 | 10^-7*cm^2/sec | "Cell movements - from molecules to motility", pp. 6, Dennis Bray, 2nd ed. Garland, 2001 | Hille (1992), Berg (1993), Atkins (1994) | order of magnitude. ~10msec for a distance of 1 micron | Ron Milo | |||
263 | Biophysical parameters | Diffusion rates | Diffusion rate of virus particle | Generic | 0.5 | 10^-7*cm^2/sec | "Cell movements - from molecules to motility", pp. 6, Dennis Bray, 2nd ed. Garland, 2001 | Hille (1992), Berg (1993), Atkins (1994) | order of magnitude. ~0.1sec for a distance of 1 micron | Ron Milo | |||
264 | Biophysical parameters | Diffusion rates | Diffusion rate of bacterial cell | Generic | 0.05 | 10^-7*cm^2/sec | "Cell movements - from molecules to motility", pp. 6, Dennis Bray, 2nd ed. Garland, 2001 | Hille (1992), Berg (1993), Atkins (1994) | order of magnitude. ~1sec for a distance of 1 micron | Ron Milo | |||
265 | Biophysical parameters | Diffusion rates | Diffusion rate of animal cell | Generic | 0.005 | 10^-7*cm^2/sec | "Cell movements - from molecules to motility", pp. 6, Dennis Bray, 2nd ed. Garland, 2001 | Hille (1992), Berg (1993), Atkins (1994) | order of magnitude. ~10sec for a distance of 1 micron | Ron Milo | |||
266 | Biophysical parameters | Diffusion rates | Diffusion rate of Pancreatic trypsin inhibitor | Bovine | 12.9 | 10^-7*cm^2/sec | "Proteins", Creighton 1984 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | ||||
267 | Biophysical parameters | Diffusion rates | Diffusion rate of cytochrome c | Equine | 13 | 10^-7*cm^2/sec | "Proteins", Creighton 1985 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1979 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
268 | Biophysical parameters | Diffusion rates | Diffusion rate of Ribonuclease A | Bovine | 10.7 | 10^-7*cm^2/sec | "Proteins", Creighton 1986 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1980 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
269 | Biophysical parameters | Diffusion rates | Diffusion rate of Lysozyme | Hen | 11.3 | 10^-7*cm^2/sec | "Proteins", Creighton 1987 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1981 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
270 | Biophysical parameters | Diffusion rates | Diffusion rate of Myoglobin | Sperm whale | 11.3 | 10^-7*cm^2/sec | "Proteins", Creighton 1988 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1982 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
271 | Biophysical parameters | Diffusion rates | Diffusion rate of Adenylate kinase | Porcine | 10.2 | 10^-7*cm^2/sec | "Proteins", Creighton 1989 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1983 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
272 | Biophysical parameters | Diffusion rates | Diffusion rate of Trypsin | Bovine | 9.3 | 10^-7*cm^2/sec | "Proteins", Creighton 1990 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1984 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
273 | Biophysical parameters | Diffusion rates | Diffusion rate of Bence Jones REI | Porcine | 10 | 10^-7*cm^2/sec | "Proteins", Creighton 1991 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1985 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
274 | Biophysical parameters | Diffusion rates | Diffusion rate of Chymotrypsinogen | Human | 9.48 | 10^-7*cm^2/sec | "Proteins", Creighton 1992 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1986 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
275 | Biophysical parameters | Diffusion rates | Diffusion rate of Elastase | Bovine | 9.5 | 10^-7*cm^2/sec | "Proteins", Creighton 1993 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1987 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
276 | Biophysical parameters | Diffusion rates | Diffusion rate of Subtilisin novo | Porcine | 9.04 | 10^-7*cm^2/sec | "Proteins", Creighton 1994 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1988 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
277 | Biophysical parameters | Diffusion rates | Diffusion rate of Carbonic anhydrase | B. amyloliq. | 10.7 | 10^-7*cm^2/sec | "Proteins", Creighton 1995 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1989 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
278 | Biophysical parameters | Diffusion rates | Diffusion rate of Superoxide dismutase | Human | 8.92 | 10^-7*cm^2/sec | "Proteins", Creighton 1996 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1990 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
279 | Biophysical parameters | Diffusion rates | Diffusion rate of Carboxypeptidase A | Bovine | 9.2 | 10^-7*cm^2/sec | "Proteins", Creighton 1997 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1991 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
280 | Biophysical parameters | Diffusion rates | Diffusion rate of Phosphoglycerate kinase | Bovine | 6.38 | 10^-7*cm^2/sec | "Proteins", Creighton 1998 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1992 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
281 | Biophysical parameters | Diffusion rates | Diffusion rate of Concanavalin A | Yeast | 6.34 | 10^-7*cm^2/sec | "Proteins", Creighton 1999 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1993 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
282 | Biophysical parameters | Diffusion rates | Diffusion rate of Hemoglobin, oxy | Equine | 6.02 | 10^-7*cm^2/sec | "Proteins", Creighton 2000 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1994 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
283 | Biophysical parameters | Diffusion rates | Diffusion rate of Malate dehydrogenase | Porcine | 5.76 | 10^-7*cm^2/sec | "Proteins", Creighton 2001 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1995 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
284 | Biophysical parameters | Diffusion rates | Diffusion rate of Alcohol dehydrogenaseh | Equine | 6.23 | 10^-7*cm^2/sec | "Proteins", Creighton 2002 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1996 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
285 | Biophysical parameters | Diffusion rates | Diffusion rate of Lactate dehydrogenase | Dogfish | 4.99 | 10^-7*cm^2/sec | "Proteins", Creighton 2003 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1997 | Translational diffusion coefficient at 20degC in water, extraploated to zero protein concentration | Ron Milo | |||
286 | Biophysical parameters | Molecular weights | Molecular weight of Pancreatic trypsin inhibitor | Bovine | 6520 | Dalton | "Proteins", Creighton 2004 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1998 | Calculated from covalent structure | Ron Milo | |||
287 | Biophysical parameters | Molecular weights | Molecular weight of cytochrome c | Equine | 12310 | Dalton | "Proteins", Creighton 2005 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 1999 | Calculated from covalent structure | Ron Milo | |||
288 | Biophysical parameters | Molecular weights | Molecular weight of Ribonuclease A | Bovine | 13690 | Dalton | "Proteins", Creighton 2006 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2000 | Calculated from covalent structure | Ron Milo | |||
289 | Biophysical parameters | Molecular weights | Molecular weight of Lysozyme | Hen | 14320 | Dalton | "Proteins", Creighton 2007 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2001 | Calculated from covalent structure | Ron Milo | |||
290 | Biophysical parameters | Molecular weights | Molecular weight of Myoglobin | Sperm whale | 17800 | Dalton | "Proteins", Creighton 2008 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2002 | Calculated from covalent structure | Ron Milo | |||
291 | Biophysical parameters | Molecular weights | Molecular weight of Adenylate kinase | Porcine | 21640 | Dalton | "Proteins", Creighton 2009 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2003 | Calculated from covalent structure | Ron Milo | |||
292 | Biophysical parameters | Molecular weights | Molecular weight of Trypsin | Bovine | 23200 | Dalton | "Proteins", Creighton 2010 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2004 | Calculated from covalent structure | Ron Milo | |||
293 | Biophysical parameters | Molecular weights | Molecular weight of Bence Jones REI | Porcine | 23500 | Dalton | "Proteins", Creighton 2011 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2005 | Calculated from covalent structure | Ron Milo | |||
294 | Biophysical parameters | Molecular weights | Molecular weight of Chymotrypsinogen | Human | 25670 | Dalton | "Proteins", Creighton 2012 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2006 | Calculated from covalent structure | Ron Milo | |||
295 | Biophysical parameters | Molecular weights | Molecular weight of Elastase | Bovine | 25900 | Dalton | "Proteins", Creighton 2013 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2007 | Calculated from covalent structure | Ron Milo | |||
296 | Biophysical parameters | Molecular weights | Molecular weight of Subtilisin novo | Porcine | 27530 | Dalton | "Proteins", Creighton 2014 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2008 | Calculated from covalent structure | Ron Milo | |||
297 | Biophysical parameters | Molecular weights | Molecular weight of Carbonic anhydrase | B. amyloliq. | 28800 | Dalton | "Proteins", Creighton 2015 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2009 | Calculated from covalent structure | Ron Milo | |||
298 | Biophysical parameters | Molecular weights | Molecular weight of Superoxide dismutase | Human | 33900 | Dalton | "Proteins", Creighton 2016 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2010 | Calculated from covalent structure | Ron Milo | |||
299 | Biophysical parameters | Molecular weights | Molecular weight of Carboxypeptidase A | Bovine | 34500 | Dalton | "Proteins", Creighton 2017 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2011 | Calculated from covalent structure | Ron Milo | |||
300 | Biophysical parameters | Molecular weights | Molecular weight of Phosphoglycerate kinase | Bovine | 45800 | Dalton | "Proteins", Creighton 2018 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2012 | Calculated from covalent structure | Ron Milo | |||
301 | Biophysical parameters | Molecular weights | Molecular weight of Concanavalin A | Yeast | 51260 | Dalton | "Proteins", Creighton 2019 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2013 | Calculated from covalent structure | Ron Milo | |||
302 | Biophysical parameters | Molecular weights | Molecular weight of Hemoglobin, oxy | Equine | 64610 | Dalton | "Proteins", Creighton 2020 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2014 | Calculated from covalent structure | Ron Milo | |||
303 | Biophysical parameters | Molecular weights | Molecular weight of Malate dehydrogenase | Porcine | 74900 | Dalton | "Proteins", Creighton 2021 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2015 | Calculated from covalent structure | Ron Milo | |||
304 | Biophysical parameters | Molecular weights | Molecular weight of Alcohol dehydrogenaseh | Equine | 79870 | Dalton | "Proteins", Creighton 2022 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2016 | Calculated from covalent structure | Ron Milo | |||
305 | Biophysical parameters | Molecular weights | Molecular weight of Lactate dehydrogenase | Dogfish | 146200 | Dalton | "Proteins", Creighton 2023 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2017 | Calculated from covalent structure | Ron Milo | |||
306 | DNA | Mutation Rates | Mutation rate per base pair per replication | Bacteriophage M13 | 7.2 x 10-7 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1998 | Squire & Himmel, Arch. Biochem. Biophys. 196:165-177, 2018 | Ron Milo | ||||
307 | DNA | Mutation Rates | Mutation rate per base pair per replication | Bacteriophage {lambda} | 7.7 x 10-8 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1999 | Ron Milo | |||||
308 | DNA | Mutation Rates | Mutation rate per base pair per replication | Bacteriophages T2 and T4 | 2.4 x 10-8 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2000 | Ron Milo | |||||
309 | DNA | Mutation Rates | Mutation rate per base pair per replication | Escherichia coli | 5.4 x 10-10 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2001 | Ron Milo | |||||
310 | DNA | Mutation Rates | Mutation rate per base pair per replication | Saccharomyces cerevisiae | 2.2 x 10-10 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1998 | Ron Milo | |||||
311 | DNA | Mutation Rates | Mutation rate per base pair per replication | Neurospora crassa | 7.2 x 10-11 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1999 | Ron Milo | |||||
312 | DNA | Mutation Rates | Mutation rate per base pair per replication | C. elegans | 2.3 x 10-10 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1998 | Ron Milo | |||||
313 | DNA | Mutation Rates | Mutation rate per base pair per replication | Drosophila | 3.4 x 10-10 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 1999 | Ron Milo | |||||
314 | DNA | Mutation Rates | Mutation rate per base pair per replication | Mouse | 1.8 x 10-10 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2000 | Ron Milo | |||||
315 | DNA | Mutation Rates | Mutation rate per base pair per replication | Human | 5.0 x 10-11 | mutation/bp/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2001 | Ron Milo | |||||
316 | DNA | Mutation Rates | Mutation rate per genome per replication | Bacteriophage M13 | 0.0046 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2001 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
317 | DNA | Mutation Rates | Mutation rate per genome per replication | Bacteriophage {lambda} | 0.0038 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2002 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
318 | DNA | Mutation Rates | Mutation rate per genome per replication | Bacteriophages T2 and T4 | 0.004 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2003 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
319 | DNA | Mutation Rates | Mutation rate per genome per replication | Escherichia coli | 0.0025 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2004 | Ron Milo | |||||
320 | DNA | Mutation Rates | Mutation rate per genome per replication | Saccharomyces cerevisiae | 0.0027 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2005 | Ron Milo | |||||
321 | DNA | Mutation Rates | Mutation rate per genome per replication | Neurospora crassa | 0.003 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2006 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
322 | DNA | Mutation Rates | Mutation rate per genome per replication | C. elegans | 0.018 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2007 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
323 | DNA | Mutation Rates | Mutation rate per genome per replication | Drosophila | 0.058 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2008 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
324 | DNA | Mutation Rates | Mutation rate per genome per replication | Mouse | 0.49 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2009 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
325 | DNA | Mutation Rates | Mutation rate per genome per replication | Human | 0.16 | mutation/genome/replication | Drake et. al., Genetics, Vol. 148, 1667-1686, April 2010 | Notice that this is per gemone replication not per sexual generation | Ron Milo | ||||
326 | Growth | Growth | Generation time | Chlamydomonas reinhardtii | 5 | Hours | http://www.yale.edu/rosenbaum/green_yeast.html | Ron Milo | |||||
327 | DNA | Genome | Number of chromosomes/cell | Chlamydomonas reinhardtii | 17 | Unitless | http://www.yale.edu/rosenbaum/green_yeast.html | Ron Milo | |||||
328 | DNA | Genome | Genome Size | Chlamydomonas reinhardtii | 120*10^6 | Base pairs | http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii | Ron Milo | |||||
329 | Composition | Water | percentage of the total wet weight of cells | bacteria | 70 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
330 | Composition | Water | percentage of the total wet weight of cells | chicken heart fibroblasts | 77 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
331 | Composition | Water | percentage of the total wet weight of cells | rat kidney cells | 74 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
332 | Composition | Water | percentage of the total wet weight of cells | HeLa cells | 70 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
333 | Composition | Water | percentage of the total wet weight of cells | axon | 87 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
334 | Composition | Protein | Percentage by Weight | bacteria | 20-32 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
335 | Composition | Protein | Percentage by Weight | muscle cells | 23 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
336 | Composition | Protein | Percentage by Weight | red blood cells | 35 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
337 | Composition | Protein | Percentage by Weight | mammalian tissue cells | 17-26 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
338 | Composition | Protein | Percentage by Weight | squid axoplasm | 5 | Percent | "Cell movements - from molecules to motility", pp. 303, Dennis Bray, 2nd ed. Garland, 2001 | not given | Ron Milo | ||||
339 | Sizes | Volume | median cell volume | Yeast | 42 | micron^3 | http://yeastpheromonemodel.org/wiki/Cell_volume | Jorgensen et al. 2002 PMID 120894449 | The median volume of a haploid yeast cell in exponential phase growing in YPD at 30°C | Ron Milo | |||
340 | Sizes | Volume | median cell volume | Yeast | 37 | micron^3 | http://yeastpheromonemodel.org/wiki/Cell_volume | Tyson et al. 1979 PMID 374379 | The mean volume of a haploid yeast cell in exponential phase growing in YPD at 30°C | Ron Milo | |||
341 | Transcription | Ribosome | Percent of total transcription devoted to ribosomal RNA | Yeast | 60 | Percent | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | |||||
342 | Transcription | RNA to DNA ratio | Yeast | 50 | Unitless | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | ||||||
343 | Transcription | Percent of total RNA that is ribosomal RNA | Yeast | 80 | Percent | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | ||||||
344 | Transcription | Percent of total RNA that is tRNA | Yeast | 15 | Percent | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | ||||||
345 | Transcription | Percent of total RNA that is ribosomal mRNA | Yeast | 5 | Percent | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | ||||||
346 | Complexes | copy number | Number of ribosomes | Yeast | 200000 | Unitless | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Based on comparison of the size of the genome (1.4 3 107 bp) with the RNA in a ribosome (5469 nucleotides), and using ratio of DNA to rRNA | Ron Milo | ||||
347 | Growth | Generation time | Yeast | 100 | minutes | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Ron Milo | ||||||
348 | mRNA | copy number | Number of mRNAs in cell | Yeast | 15000 | Unitless | The economics of ribosome biosynthesis in yeast, JR Warner - Trends Biochem. Sci, 1999 | Holstege, F. C. P. et al. (1998) Cell 95, 717�$-1òó728 | Ron Milo | ||||
349 | Weight | genome | Weight of DNA base pair | generic | 665 | Dalton | http://www.roche-applied-science.com/PROD_INF/MANUALS/napi_man/pdf/chapter9/page_212-215.pdf | Ausubel et al., 1988 | Notice this is a base PAIR | Itai Yanai | |||
350 | Weight | genome | Weight of single stranded DNA base | generic | 325 | Dalton | http://www.roche-applied-science.com/PROD_INF/MANUALS/napi_man/pdf/chapter9/page_212-215.pdf | Ausubel et al., 1988 | Itai Yanai | ||||
351 | Weight | genome | Weight of single stranded RNA base | generic | 340 | Dalton | http://www.roche-applied-science.com/PROD_INF/MANUALS/napi_man/pdf/chapter9/page_212-215.pdf | Ausubel et al., 1988 | Itai Yanai | ||||
352 | Weight | genome | Conversion from weight to bp | generic | 978 | Mbp/pgram | Gregory, T.R. (2007). Animal Genome Size Database. http://www.genomesize.com | Dolezel et al., Cytometry 51A: 127-128, 2003 | Ron Milo | ||||
353 | Thermosensitivity | TRP channels | Q10 (24-36°C) of TRPV4 | mouse | 19.1 | Unitless | Watanabe et al., J. Biol. Chem. 2002 | In HEK293 Cell | Daniel Ramot | ||||
354 | Thermosensitivity | TRP channels | TRPV1 Q10 (41�$-1òó50°C) | rat | 27 | Unitless | Liu, Hui, & Qin, Biophys J. 2003 | Single-channel activity in Xenopus laevis oocytes | Daniel Ramot | ||||
355 | Thermosensitivity | Sensory neurons | Q10 (47�$-1òó51°C) of heat activated current in DRG neurons | rat | 17.8 | Unitless | Vyklický et al., J. Physiol 1999 | Cultured neurons | Daniel Ramot | ||||
356 | Thermosensitivity | TRP channels | TRPV3 Q10 | mouse | 6.62 | Unitless | Peier et al., Science 2002 | In CHO cells | Daniel Ramot | ||||
357 | Thermosensitivity | K+ Channels | Q10 (5�$-1òó20°C) of Shaker K+ channel peak amplitude | Drosophila | 1.51 | Unitless | Nobile et al., Exp Brain Res, 1997 | In Xenopus laevis oocytes - cut open oocyte method | Daniel Ramot | ||||
358 | Thermosensitivity | K+ Channels | Q10 (5�$-1òó20°C) of Shaker K+ channel activation time constant | Drosophila | 3.14 | Unitless | Nobile et al., Exp Brain Res, 1997 | In Xenopus laevis oocytes - cut open oocyte method | Daniel Ramot | ||||
359 | Thermosensitivity | K+ Channels | Q10 (5�$-1òó20°C) of Shaker K+ channel inactivation time constant | Drosophila | 7.2 | Unitless | Nobile et al., Exp Brain Res, 1997 | In Xenopus laevis oocytes - cut open oocyte method | Daniel Ramot | ||||
360 | Thermosensitivity | K+ Channels | Q10 (5�$-1òó20°C) of Shaker K+ channel ratio b/w steady-state & peak current | Drosophila | 2.95 | Unitless | Nobile et al., Exp Brain Res, 1997 | In Xenopus laevis oocytes - cut open oocyte method | Daniel Ramot | ||||
361 | Thermosensitivity | TRP channels | TRPV1 Q10 | 20.6 | Unitless | Welch et al., PNAS 2000 | Daniel Ramot | ||||||
362 | Thermosensitivity | TRP channels | TRPV1 Q10 | 25.6 | Unitless | Vlachová et al., J. Neurosci. 2003 | Daniel Ramot | ||||||
363 | Copy numbers | Small Molecule Copy Numbers | Number of Zn ions in YPD | yeast | 8e7 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
364 | Copy numbers | Small Molecule Copy Numbers | Number of Se ions in YPD | yeast | 6e7 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
365 | Copy numbers | Small Molecule Copy Numbers | Number of S ions in YPD | yeast | 5e8 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
366 | Copy numbers | Small Molecule Copy Numbers | Number of P ions in YPD | yeast | 5e9 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
367 | Copy numbers | Small Molecule Copy Numbers | Number of Ni ions in YPD | yeast | 2e7 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
368 | Copy numbers | Small Molecule Copy Numbers | Number of Na ions in YPD | yeast | 2e8 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
369 | Copy numbers | Small Molecule Copy Numbers | Number of Mn ions in YPD | yeast | 5e5 | Eide et al. Genome Biology 2005 | Mike Springer | ||||||
370 | Sizes | Volumes | Nuclear volume (average) | S. cerevisiae | 2.9 | um3 | Jorgensen et al. MBC 2007 | Morphometry | SD 2% glucose medium, wild-type haploid cells | Paul Jorgensen | |||
371 | Sizes | Volumes | Nuclear:cell volume ratio | S. cerevisiae | 0.07 | Unitless | Jorgensen et al. MBC 2007 | SD 2% glucose medium, wild-type haploid cells | Paul Jorgensen | ||||
372 | Sizes | Volumes | Cell volume | S. cerevisiae | 42 | um3 | Jorgensen et al. MBC 2007 | Coulter counter | 17 | SD 2% glucose medium, wild-type haploid cells | Paul Jorgensen | ||
373 | General statistics | Proliferation | Number of cell divisions in an average human lifespan | H. sapiens | 10e17 | Cell divisions | Weinberg, R. The Biology of Cancer 2007 | Paul Jorgensen | |||||
374 | Sizes | Dimensions | Cell diameter | S. cerevisiae | 5 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
375 | Sizes | Volumes | Cell volume | S. cerevisiae | 66 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
376 | Sizes | Dimensions | Cell dimensions | S. pombe | 2 x 7 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
377 | Sizes | Volumes | Cell volume | S. pombe | 22 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
378 | Sizes | Dimensions | Cell diameter | Mammalian cell | 10 - 20 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
379 | Sizes | Volumes | Cell volume | Mammalian cell | 500 - 4000 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
380 | Sizes | Dimensions | Cell dimensions | E. coli | 1 x 3 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
381 | Sizes | Volumes | Cell volume | E. coli | 2 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
382 | Sizes | Organelle size | Mitochonrdia dimensions | Mammalian cell | 1 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
383 | Sizes | Organelle size | Mitochondria volume | Mammalian cell | 0.5 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
384 | Sizes | Organelle size | Nuclear diameter | Mammalian cell | 5 - 10 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
385 | Sizes | Organelle size | Nuclear volume | Mammalian cell | 66 - 500 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
386 | Sizes | Organelle size | Chloroplast dimensions | Plant cell | 1 x 4 | um | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
387 | Sizes | Organelle size | Chloroplast volume | Plant cell | 3 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
388 | Sizes | Virus diameter, head only | Bacteriophase Lambda | 6.6e-5 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | ||||||
389 | Sizes | Virus diameter, head only | Bacteriophase Lambda | 50 | nm | Roskams and Rodgers, LabRef | Paul Jorgensen | ||||||
390 | Sizes | Protein size | Ribosome diameter | ? | 30 | nm | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
391 | Sizes | Protein size | Ribosome volume | ? | 1.4e-5 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
392 | Sizes | Protein size | Globular protein diameter | ? | 5 | nm | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
393 | Sizes | Protein size | Globular protein volume | ? | 6.6e-8 | um3 | Roskams and Rodgers, LabRef | Paul Jorgensen | |||||
394 | Transporters | Rates | Water flow through aquaporin 1 channel | ? | 5*10^8 | molecules/second | Nelson and Cox, "Lehninger - Principles of biochemistry", 3rd ed. p.410 | Ron Milo | |||||
395 | Photosynthesis | Sun | Flux of photons | generic | 4*10^21 | Photons/m^2/sec | Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales. Noy D, Moser CC, Dutton PL. | ||||||
PMID: 16457774 | Intergration | at sea level, based on reference solar irradiance 1.5 air masses, integrated over the whole spectrum | Ron Milo | ||||||||||
396 | Photosynthesis | Sun | Max Photosynthetic photon flux | generic | 2000 | micromol/m^2/sec | Nobel, P. S. "Plant Physiology", 3rd ed. pp.243 | in the range 400-700nm on a horizontal plane | Ron Milo | ||||
397 | Photosynthesis | Sun | Mean Photosynthetic photon flux | generic | 800 | micromol/m^2/sec | Nobel, P. S. "Plant Physiology", 3rd ed. pp.245 | in the range 400-700nm averaged on daytime over the earth's surface on clear days | Ron Milo | ||||
398 | Photosynthesis | concentrations | Chlorophyll concentration | chloroplast | 30 | mol/m^3 | Nobel, P. S. "Plant Physiology", 3rd ed. pp.243 | average | Ron Milo | ||||
399 | Photosynthesis | leaves | Leaf area index | Biosphere | 4.3 | micromol/m^2/sec | Nobel, P. S. "Plant Physiology", 3rd ed. pp.245 | Total area of all leaves divided by the total land area where vegetation occurs | Ron Milo | ||||
400 | Photosynthesis | Cross section | Effective cross section of chlorophyll for useful photons | generic | 0.09 | Angstrom^2 | Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales. Noy D, Moser CC, Dutton PL. | ||||||
PMID: 16457774 | Ron Milo | ||||||||||||
401 | Photosynthesis | Absorption | Maximal absorption rate under sun illumination of chlorophyll pigment | generic | 4 | 1/sec | Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales. Noy D, Moser CC, Dutton PL. | ||||||
PMID: 16457774 | Ron Milo | ||||||||||||
402 | Photosynthesis | Rates | Catalysis rates of photosystem units | generic | 10^2-10^4 | 1/sec | Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales. Noy D, Moser CC, Dutton PL. | ||||||
PMID: 16457774 | Ron Milo | ||||||||||||
403 | Photosynthesis | Rates | Catalysis rates of photosystem units | generic | 200 | 1/sec | Nobel, P. S. "Plant Physiology", 3rd ed. pp.243 | Ron Milo | |||||
404 | Photosynthesis | copy numbers | number of chlorophyll pigments in PSI | Synechococcus elongatus | 96 | unitless | Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.Nature. 2001 Jun 21;411(6840):909-17.PMID: 11418848 | Ron Milo | |||||
405 | Photosynthesis | copy numbers | number of chlorophyll per reaction center | plants | 100-700 | unitless | Nobel, P. S. "Plant Physiology", 3rd ed. pp.245 | depending on illumination level | Ron Milo | ||||
406 | Photosynthesis | copy numbers | number of bacteriochlorophylls per reaction center | bacteria | 40-100 | unitless | Nobel, P. S. "Plant Physiology", 3rd ed. pp.245 | depending on illumination level | Ron Milo | ||||
407 | DNA damage | Rates | number of depurination events | Mammalian cell | 10000 | bases depurinated per cell per day | R. Weinberg, The Biology of Cancer | Paul Jorgensen | |||||
408 | DNA damage | Rates | number of depyrimidination events | Mammalian cell | 500 | bases depyrimidinated per cell per day | R. Weinberg, The Biology of Cancer | Paul Jorgensen | |||||
409 | DNA damage | Rates | number of DNA damage events caused by oxidative damage | H. sapiens cell | 10e3 | bases damaged per cell per day | R. Weinberg, The Biology of Cancer | Paul Jorgensen | |||||
410 | DNA damage | Rates | number of DNA damage events caused by oxidative damage | Rat cell | 10e4 | bases damaged per cell per day | R. Weinberg, The Biology of Cancer | Paul Jorgensen | |||||
411 | Proteins | Diffusion rate | GFP diffusion rate in cytoplasm | E. Coli | 7.7 ± 2.5 | µm^2/s | Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203. | Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203. | FRAP and photoactivation | Ron Milo | |||
412 | Proteins | Diffusion rate | GFP diffusion rate in water | Water | 87 | µm^2/s | Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203. | Swaminathan, R., C. P. Hoang, and A. S. Verkman. 1997. Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophys. J. 72:1900-1907; Terry, B. R., E. K. Matthews, and J. Haseloff. 1995. Molecular characterisation of recombinant green fluorescent protein by fluorescence correlation microscopy. Biochem. Biophys. Res. Commun. 217:21-27 | Ron Milo | ||||
413 | Proteins | Diffusion rate | GFP diffusion rate in cytoplasm | Eukaryotic | 27 | µm^2/s | Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203. | Swaminathan, R., C. P. Hoang, and A. S. Verkman. 1997. Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophys. J. 72:1900-1907 | Ron Milo | ||||
414 | Proteins | Diffusion rate | GFP diffusion rate in mitochondria | Mitochondria | 20-30 | µm^2/s | Elowitz, M.B. et al. (1999) Protein Mobility in the Cytoplasm of E. coli, J. Bacteriol 181, 197-203. | Partikian, A., B. Olveczky, R. Swaminathan, Y. Li, and A. S. Verkman. 1998. Rapid diffusion of green fluorescent protein in the mitochondrial matrix. J. Cell Biol. 140:821-829 | Ron Milo | ||||
415 | Sizes | Dimensions | Cell length at division | S. pombe | 13.5 | um | Das et al. (2007) MBC 18:2090-2101. | Morphometry | 1.3 | Paul Jorgensen | |||
416 | Biosphere | Photosynthesis | Global primary productivity - [carbon] | Biosphere | 10^14 | kg | Nobel, P. S. "Plant Physiology", 3rd ed. pp.219 | Ron Milo | |||||
417 | Biosphere | Atmosphere content | Total CO2 | Atmosphere | 8*10^14 | kg | Nobel, P. S. "Plant Physiology", 3rd ed. pp.220 | Ron Milo | |||||
418 | Biosphere | lakes and oceans | Total CO2 | Biosphere | 400*10^14 | kg | Nobel, P. S. "Plant Physiology", 3rd ed. pp.220 | Ron Milo | |||||
419 | Biosphere | Photosynthesis | Time for O2 replenishment by photosynthesis | Atmosphere | 2000 | years | Nobel, P. S. "Plant Physiology", 3rd ed. pp.220 | Ron Milo | |||||
420 | Copy number | p53 | human | 15 ± 6 x 10^5 | unitless | Ma et al., PNAS (2005) 102:14266 | Measured by ELISA, concentration ranges from 0.06 to 0.5microM depending on cell line | MCF7 breast cancer cell line | Alex Loewer | ||||
421 | DNA | DNA damage | DNA double strand breaks induced by ionizing radiation [DSB per Gray per cell] | human | 36 | unitless | Rothkamm et al., PNAS (2003) 100:5057 | Average number of breaks 3min after radiation as measured by gH2AX staining | MCF7 breast cancer cell line, radiation is gamma- or X-rays | Alex Loewer | |||
422 | Proteins | Diffusion constant | Dextran (40kDa) in Drosophila cytoplasm | Drosophila | 17.6 +/- 1.8 | um^2/s | Gregor et al., 2006, PNAS | Fluorescent dextran injected into Drosophila embryo, confocal imaging, and fitting with 3D diffusion model | (N=20) | Lea Goentoro | |||
423 | DNA | Gene duplication | Gene duplication rate per gene per billion years | Yeast | 0.01 - 0.06 | gene^-1*billion years^-1 | Li-zhi et al. Science 2004 | A very low duplication rate in comparison to other organisms | Ron Milo | ||||
424 | DNA | Mutation rates | Amino acid replacement rate [per site per year] | Generic | 10^-9 | year^-1 | "Principles of population genetics", Hartl and Clark, 3rd. ed. pp. 323 | Average rate among a large number of proteins, very close to the rate found in hemoglobin | Ron Milo | ||||
425 | length | RNA | median length of a yeast RNA molecule [nucleotides] | Yeast | 1474 | unitless | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
426 | Energy cost | RNA | median cost of precursor synthesis per nucleotide [~P] | Yeast | 49.3 | unitless | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | derived from the base composition of yeast-coding regions, in units of phosphate bonds (ATP) | Ron Milo | |||
427 | copy number | RNA | median mRNA abundance | Yeast | 1.2 | unitless | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
428 | degradation | RNA | median mRNA decay constant | Yeast | 5.6*10^-4 | s^-1 | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
429 | length | protein | median length of a yeast protein | Yeast | 385 | aa | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
430 | Energy cost | protein | median cost of precursor synthesis per amino acid [~P] | Yeast | 30.3 | unitless | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
431 | copy number | RNA | median protein abundance | Yeast | 2460 | unitless | Wagner, A., Energy Constraints on the Evolution of Gene Expression, Mol. Biol. Evol. 22(6):1365�$-1òó1374. 2005 | Wang et al. 2002; Arava et al. 2003; Ghaemmaghami et al. 2003; Huh et al. 2003). | Ron Milo | ||||
432 | copy number | polymerase | Available RNAP | E. coli | 30 | nM | A Arkin, J Ross, HH McAdams, Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage {lambda}-Infected Escherichia coli Cells, Genetics, 1998 | MCCLURE, W. R., 1980 Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. USA 77:5634-5638[Abstract/Free Full Text]. | |||||
MCCLURE, W. R., 1983 A biochemical analysis of the effect of RNA polymerase concentration on the in vivo control of RNA chain initiation frequency, pp. 207�$-1òó217 in Biochemistry of Metabolic Processes, Proceedings of the 12th Steenbock Symposium, edited by D. LENNON, F. STRATMAN and R. ZAHLMAN. Elsevier Scientific, New York. | 1nM in a volume the size of e.coli is equivalent to about 1 molecule per cell | Ron Milo | |||||||||||
433 | copy number | ribosomes | Available ribosomes | E. coli | 500 | nM | A Arkin, J Ross, HH McAdams, Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage {lambda}-Infected Escherichia coli Cells, Genetics, 1998 | MCCLURE, W. R., 1980 Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. USA 77:5634-5638[Abstract/Free Full Text]. | |||||
MCCLURE, W. R., 1983 A biochemical analysis of the effect of RNA polymerase concentration on the in vivo control of RNA chain initiation frequency, pp. 207�$-1òó217 in Biochemistry of Metabolic Processes, Proceedings of the 12th Steenbock Symposium, edited by D. LENNON, F. STRATMAN and R. ZAHLMAN. Elsevier Scientific, New York. | 1nM in a volume the size of e.coli is equivalent to about 1 molecule per cell | Ron Milo | |||||||||||
434 | copy number | translation | Average number of proteins per transcript | E. coli | 10 | unitless | A Arkin, J Ross, HH McAdams, Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage {lambda}-Infected Escherichia coli Cells, Genetics, 1998 | KEPES 1963 ; YARCHUK et al. 1992 | Ron Milo | ||||
435 | Rates | translation | Ribosome + RNAn --> Ribosome·RNAn+1 | E. coli | 100 | bp/sec | A Arkin, J Ross, HH McAdams, Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage {lambda}-Infected Escherichia coli Cells, Genetics, 1998 | ADHYA, S. and M. GOTTESMAN, 1982 Promoter occlusion: transcription through a promoter may inhibit its activity. Cell 29:939-944; SORENSEN, M. A. and S. PEDERSEN, 1991 Absolute in vivo translation rates of individual codons in Escherichia coli. J. Mol. Biol. 222:265-280; KENNELL, D. and H. RIEZMAN, 1977 Transcription and translation initiation frequencies of the Escherichia coli lac operon. J. Mol. Biol. 114:1-21 | Sorensen 1991 actually reports a value which is significantly lower | Ron Milo | |||
436 | Biosphere | Osmotic pressure | Osmotic pressure of the ocean | generic | 27 | Atm | http://en.wikipedia.org/wiki/Osmotic_pressure | The genearal equation is: �$-1§À = iMRT where | |||||
i is the van 't Hoff factor | |||||||||||||
M is the molarity | |||||||||||||
R is the gas constant, where R = 0.08206 L · atm · mol-1 · K-1 | |||||||||||||
T is the thermodynamic temperature | Ron Milo | ||||||||||||
437 | Size | Cell size | Diameter of Bacillus subtilis | Bacillus subtilis | 0.87 | um | Weart et al. Cell 130:335-347 (2007) | Paul Jorgensen | |||||
438 | Size | Cell size | Length of Bacillus subtilis in rich media | Bacillus subtilis | 4.7 | um | Weart et al. Cell 130:335-347 (2007) | Paul Jorgensen | |||||
439 | Size | Cell size | Length of Bacillus subtilis in minimal sorbitol medium | Bacillus subtilis | 2.3 | um | Weart et al. Cell 130:335-347 (2007) | Paul Jorgensen | |||||
440 | Concentration | Ion concentration | Intracellular concentration of Na+ in early cleavage stage Xenopus laevis embryos | Xenopus laevis | 21 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
441 | Concentration | Ion concentration | Intracellular concentration of K+ in early cleavage stage Xenopus laevis embryos | Xenopus laevis | 90 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
442 | Concentration | Ion concentration | Intracellular concentration of Cl- in Xenopus laevis eggs | Xenopus laevis | 60 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
443 | Concentration | Ion concentration | Intercellular concentration of Na+ in stage 9 blastula embryos of Xenopus laevis | Xenopus laevis | 91 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
444 | Concentration | Ion concentration | Intercellular concentration of K+ in stage 9 blastula embryos of Xenopus laevis | Xenopus laevis | 4 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
445 | Concentration | Ion concentration | Intercellular concentrationof Cl- in stage 9 blastula embryos of Xenopus laevis | Xenopus laevis | 59 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
446 | Concentration | Ion concentration | Intercellular concentration of Ca2+ in stage 9 blastula embryos of Xenopus laevis | Xenopus laevis | 1.5 | mM | Gillespie J.Physiol. 344:359-377 (1983) | Paul Jorgensen | |||||
447 | Concentration | Nucleotide concentration | Concentration of ATP in Xenopus laevis eggs | Xenopus laevis | 0.6-1 | mM | Woodland and Pestell, Biochem J. 127:597-605 (1972) | Paul Jorgensen | |||||
448 | Concentration | Nucleotide concentration | Concentration of GTP, CTP, and UTP in Xenopus laevis eggs | Xenopus laevis | 0.2-0.6 | mM | Woodland and Pestell, Biochem J. 127:597-605 (1972) | Paul Jorgensen | |||||
449 | Rate | Translation rate | Translation rate of beta-galactosidase in E. coli | E. coli | 13-16 | aa/s | Dalbow and Young, Biochem J. 150:13-20 (1985) | Paul Jorgensen | |||||
450 | DNA | chromosomes | Chromosome number (2n) | Human | 46 | unitless | http://www.genomesize.com/ | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
451 | DNA | chromosomes | Chromosome number (2n) | Mouse | 40 | unitless | http://www.genomesize.com/ | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
452 | DNA | chromosomes | Chromosome number (2n) | Drosophila melanogaster (Fruit fly) | 8 | unitless | http://www.genomesize.com/ | Rasch, E.M., H.J. Barr, and R.W. Rasch (1971). The DNA content of sperm of Drosophila melanogaster. Chromosoma 33: 1-18. | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | |||
453 | DNA | chromosomes | Chromosome number (2n) | Anopheles gambiae | 6 | unitless | http://www.genomesize.com/ | Besansky, N.J. and J.R. Powell (1992). Reassociation kinetics of Anopheles gambiae (Diptera: Culicidae) DNA. Journal of Medical Entomology 29: 125-128. | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | |||
454 | DNA | chromosomes | Chromosome number (2n) | Domestic cat | 38 | unitless | http://www.genomesize.com/ | Vinogradov, A.E. (1998a). Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31: 100-109. | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | |||
455 | DNA | chromosomes | Chromosome number (2n) | rat | 42 | unitless | http://www.genomesize.com/ | Vinogradov, A.E. (1998a). Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31: 100-109. | Brown rat, Rattus norvegicus, common lab rat | Ron Milo | |||
456 | DNA | chromosomes | Chromosome number (2n) | Arabidopsis | 10 | unitless | http://en.wikipedia.org/wiki/Arabidopsis_thaliana | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
457 | DNA | chromosomes | Chromosome number (2n) | c. elegans | 12 | unitless | http://en.wikipedia.org/wiki/Caenorhabditis_elegans | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
458 | DNA | chromosomes | Chromosome number (2n) | gold fish | 104 | unitless | http://en.wikipedia.org/wiki/Chromosome | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
459 | DNA | chromosomes | Chromosome number (2n) | Guinea Pig | 16 | unitless | http://en.wikipedia.org/wiki/Chromosome | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
460 | DNA | chromosomes | Chromosome number (2n) | gorilla | 48 | unitless | http://en.wikipedia.org/wiki/Chromosome | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
461 | DNA | chromosomes | Chromosome number (2n) | chimpanzees | 48 | unitless | http://en.wikipedia.org/wiki/Chromosome | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
462 | DNA | chromosomes | Chromosome number (2n) | Adder's Tongue Fern | 1262 | unitless | http://en.wikipedia.org/wiki/Chromosome | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | ||||
463 | Life history | generation time | c. elegans | 4 | days | http://en.wikipedia.org/wiki/Caenorhabditis_elegans | Notice that this is the 2n value, i.e. counting the sister chromosomes as two separate chromosomes | Ron Milo | |||||
464 | DNA | genes | Number of genes | Arabidopsis | 25498 | unitless | http://en.wikipedia.org/wiki/Arabidopsis_thaliana | Ron Milo | |||||
465 | Life history | longevity | Life span | c. elegans | 2 - 3 | weeks | http://en.wikipedia.org/wiki/Caenorhabditis_elegans | Ron Milo | |||||
466 | RNA | mitochondrial rRNA | Mitochondrial rRNA in egg | X. laevis | 20 | ng | Igor and Dawid, Dev. Biol 27:504-518 (1972) | Paul Jorgensen | |||||
467 | Protein | mitochondrial protein | Mitochondrial protein in egg | X. laevis | 10 | micrograms | Igor and Dawid, Dev. Biol 27:504-518 (1972) | Paul Jorgensen |