Rubisco and Rubisco-like (v4) Ancestral Library

If you use these results in your work, please cite: Hanson-Smith and Johnson, PLoS Comp. Bio., 2016


Overview | Alignments | Sites | Trees | Ancestors | Mutations


Select an Alignment:

Select a Site:

Site 1 in Alignment 'msaprobs'


Similarity to Other Alignments

What percentage of the residues at this site are inferred to be a single site (i.e. homologous) in the alignments produced by other methods? A value of 100% indicates that the existence of site 1 is robust across multiple methods. Values less than 100% indicate that other alignment methods made different homology inferences.

Similarity of Site 1 in 'msaprobs'
to Sites in 'muscle'

What percentage of the residues at this site in msaprobs are inferred to be a single site (i.e. homologous) in the alignments produced by muscle? A value of 100% indicates that the existence of site 1 is reproduced using the muscle method. Values less than 100% indicate that muscle made different homology inferences for the residues at this site.


Species Residue at Site 1
in 'msaprobs'
muscle

The residue for every species at site 1 of the msaprobs alignment can be found in the muscle alignment, but with a possibly different site number.

B.Nicotiana.Plant.tabacco M Site 13
IV.Allochromatium.vinosum M Site 17
B.Physcomitrella.Plant.Moss M Site 13
IV.Bacillus M Site 20
CD.Nitrosococcus.GammaP M Site 12
A.Nitrobacter.AlphaP M Site 20
IV.Symbiodinium L Site 26
B.Nostoc.Cyanob M Site 12
IV.Chlorobium.tepidum M Site 17
A.II.Thiobacillus.BetaP M Site 20
CD.AII.Rhodopse.AlphaP M Site 13
IV.Archaeoglobus.fulgidus M Site 17
B.Synechococcus.Cyanob M Site 16
II.Polaromonas.BetaP M Site 26
A.Acidithiobacillus.GammaP M Site 20
B.Synechocystis.Cyanob M Site 18
IV.Tepidanaerobacter.acetatoxydans M Site 17
A1.Thiomicrospira.GammaP.Hydrothermal.SulfurOx M Site 21
CD.Acidiphilium.AlphaP M Site 5
CD.Odontella.alga M Site 10
II.Thiomicrospira.GammaP M Site 26
A.Hydrogenophilus.BetaP.Thermophilic M Site 19
CD.Paracoccus.AlphaP M Site 10
CD.Nitrobacter.AlphaP M Site 9
IV.Rhodopseudomonas.palustris M Site 17
Species Residue at Site 1
in 'msaprobs'
muscle

The residue for every species at site 1 of the msaprobs alignment can be found in the muscle alignment, but with a possibly different site number.

B.Selaginella.Plant.Fern M Site 13
III1.Methanocaldococcus.Archa M Site 30
CD.Burkholderia.BetaP M Site 1
IV.Octadecabacter.antarcticus M Site 35
A.CDII.Rhodopse.AlphaP.purpleNonsulfur M Site 21
IV.Bordetella.bronchiseptica M Site 34
A.Prochlorococcus.Cyanob M Site 21
II.Rhodoferax.BetaP M Site 26
A.Alkalilimnicola.GammaP M Site 20
B.Trichodesmium.Cyanob M Site 12
CD.Sinorhizobium.AlphaP M Site 11
CD.Pleurochrysis.alga M Site 10
A.Methylococcus.GammaP.Methanotrophic M Site 20
CD.Porphyridium.alga M Site 10
II.ACD.Rhodopse.AlphaP M Site 26
III2.Pyrococcus.Archa.Eu M Site 22
IV.Chlorobaculum.thiosulfatiphilum M Site 17
B.Thermosynechococ.Cyanob M Site 13
III2.Natronomonas.Archa.Eu M Site 30
B.Chlorella.alga M Site 13
A.Halorhodospira.GammaP M Site 20
II.Rhodospirillum.AlphaP M Site 26
B.Ostreococcus.Alga M Site 13
CD.Olisthodiscus.alga M Site 10
II.A.Hydrogenovibr.GammaP M Site 26
Species Residue at Site 1
in 'msaprobs'
muscle

The residue for every species at site 1 of the msaprobs alignment can be found in the muscle alignment, but with a possibly different site number.

II.Dechloromonas.BetaP M Site 26
III2.Methanoculleus.Archa.Eu M Site 27
B.Spinacia.Plant M Site 13
III2.Hyperthermus.Archa.Cren M Site 21
CD.Ectocarpus.alga.brown M Site 10
A1.Allochromatium.GammaP M Site 21
CD.Rubrivivax.BetaP M Site 5
III1.Methanosarcina.Archa M Site 32
III2.Archaeoglobus.Archa.Eu M Site 26
A.II.Rhodobacter.AlphaP M Site 20
B.Euglena.protist M Site 13
A.II.Hydrogenovibr.GammaP.HydrogenOxidizing M Site 20
A.Cupriavidus.BetaP M Site 20
CD.Rhodobacter.AlphaP M Site 12
CD.Emiliania.Diatom.Phytoplankton.Eu M Site 10
II.Magnetospirillum.AlphaP M Site 26
II.A.Thiobacillus.BetaP M Site 26
B.Prochlorothrix.Cyano M Site 18
IV.Variovorax.paradoxus M Site 38
B.Chlamydomonas.Alga M Site 13
II.A.Rhodobacter.AlphaP M Site 26
A2.Thiomicrospira.GammaP.Hydrothermal.SulfurOx M Site 20
CD.Nitrosospira.BetaP M Site 15
CD.Cylindrotheca.alga M Site 10
B.Anabaena.Cyanob M Site 12
Species Residue at Site 1
in 'msaprobs'
muscle

The residue for every species at site 1 of the msaprobs alignment can be found in the muscle alignment, but with a possibly different site number.

B.Gloeobacter.Cyanob M Site 14
A.Synechococcus.Cyanob M Site 21
A2.Allochromatium.GammaP M Site 20
A.Nitrosomonas.BetaP M Site 20
III2.Thermofilum.Archa.Cren M Site 25
III2.Thermococcus.Archa.Eu M Site 21

Generated by PhyloBot at 10:55, February 18th 2020
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