Supplementary material for Silverman et al. (2001) Proc. Natl. Acad. Sci. USA 98 (6), 3092–3097. (10.1073/pnas.041613598)
Supplemental Material
A phylogenetic alignment of TIM genes was constructed by using the CLUSTALW algorithm [Thompson, J. D., Higgins, D. G. & Gibson, T .J. (1994) Nucleic Acids Res 22, 4673–4680]. The following 43 SwissProt sequences were aligned to determine a phylogenetic conservation map:
TPIS_YEAST, TPIS_SCHPO, TPIS_EMENI, TPIS_HUMAN, TPIS_MACMU, TPIS_RABIT, TPIS_MOUSE, TPIS_RAT, TPIS_CHICK, TPIS_LATCH, TPIS_DROME, TPIS_CULTA, TPIS_HELVI, TPIS_MAIZE, TPIS_SECCE, TPIS_PETHY, TPIS_ARATH, TPIC_ORYSA, TPIS_CAEEL, TPI_TRYCR, TPIS_TRYBB, TPIS_LEIME, TPI2_GIALA, TPI1_GIALA, TPIS_SCHMA, TPIS_VIBMA, TPIS_STELP, TPIS_PLAFA, TPIS_MORSP, TPIS_GRAVE, TPIS_CORGL, TPIS_COPJA, TPIS_MYCLE, TPIS_MYCHY, TPIS_MYCHR, TPIS_MYCGE, TPIS_MYCFL, TPIS_HAEIN, TPIS_LACLA, TPIS_ECOLI, TPIS_BACSU, TPIS_BACST, and TPIS_BACME.
To generate pKK223f, the f1 origin of replication from the pAED4 plasmid (nucleotides 2,800–3,320) was amplified by using primers containing BamHI and StyI restriction sites, and ligated into the BamHI and StyI sites of pKK223 (Amersham Pharmacia). The in vivo activity of wild-type TIM in this vector is indistinguishable from that in pKK223 (data not shown).