Methods for evolution analysis

FASTA sequences (human NUBP2 and Archae 2PH1) were obtained from GenBank. A Psi-blast search in the nucleotide reducndancy (nr) database was used to find similar sequences. Results from NUBP2 and 2PH1 blast were then compared and analysed. From the NUBP2 blast results, sequences of 33 well-studied organisms* were selected. Sequences were loaded into ClustalX for multiple sequence alignment (msa). The concense phylogenic tree was generated through SeqBoot-->Protdist-->Neighbor-->Consense. Deep evolutionary analysis was conducted on the consense tree.

• Selected organisms (33) across the three domains include:

Archae (6) - A3 (Methanococcus voltae A3), 6A8 (Candidatus Methanoregula boonei 6A8), C.symbiosum (Cenarchaeum symbiosum A), GSS1 (Thermoplasma volcanium GSS1), A. fulgidus (Archaeoglobus fulgidus DSM 4304), uncultured (uncultured methanogenic archaeon RC-I)

Bacteria (7) - Goettinger (Syntrophomonas wolfei subsp. wolfei str. Goettingen), Lettingae (Thermotoga lettingae), ATCC 824 (Clostridium acetobutylicum ATCC 824), MIT 9211 (Prochlorococcus marinus str. MIT 9211), BAV1 (Dehalococcoides sp. BAV1), DSM 4136 (Verrucomicrobium spinosum DSM 4136), DSM 245 (Chlorobium limicola DSM 245)

Eukaryota (20)- Red Rice Japanese / Indian (Oryza sativa), Neurospora (Neurospora crassa OR74A), C.reinhardtii (Chlamydomonas reinhardtii), C.Elegans (Caenorhabditis elegans), Thale cress (Arabidopsis thaliana), Fission yeast (Schizosaccharomyces pombe 972h-), Brewer’s yeast (Saccharomyces cerevisiae), Zebrafish (Danio rerio), Drosophila.pseudo (Drosophila pseudoobscura), Fruit Fly (Drosophila melanogaster), western clawed frog (Xenopus tropicalis), African clawed frog (Xenopus laevis), Chicken (gallus gallus), Mouse (mus mucus), Rat (Rattus norvegicus), Cow (Bos taurus), Chimpanzee (Pan troglodytes), Human (homo sapiens).