The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum

Additional File 1:

Proteins that share sequence similarities with known or putative transport proteins and/or conserved domains of transport protein families

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Additional File 2:

Proteins that are related to 'hypothetical proteins' from other organisms and have predicted secondary structures that resemble those of characterized transport proteins, but which do not share sequence similarities with known or putative transport proteins and/or conserved domains of transport protein families

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Additional File 3:

Plasmodium-specific proteins that have the (predicted) structural characteristics of a transporter, but which, apart from strong sequence similarities to hypothetical proteins from other Plasmodium species, do not display any similarities to proteins or conserved domains in the current databases

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Additional File 4:

The region over TMDs 1-5 of the alignment is shown. Sequences are separated into clusters of well-related sequences and are grouped as subfamilies of the MFS. P. falciparum sequences are boxed and the protein designators highlighted. For proteins of other organisms, the NCBI accession (gi) number and the known or putative (p) substrate specificity of the transporter are given. In some proteins, one or more of the extramembrane loop regions have been truncated and this is indicated by a solid black line. Residues are shaded as follows: positively charged, blue; negatively charged, red; hydoxyl, orange; amido, grey; proline, green; cysteine, purple; histidine, mid blue; glycine, light blue; tryptophan and tyrosine, olive green; remaining nonpolar, yellow

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Additional File 5:

Both transporter families are distantly related to the MFS. The region over TMDs 2-5 and TMD 8 of the organo anion transporter family alignment is shown. The region over TMDs 3-5 and TMD 10 of the folate-biopterin transporter family alignment is shown. Legend as described for Additional data file 4

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Additional File 6:

(A) Hydropathy plots of two representatives of the novel putative transporter family: the PFI0720w and PFC0530w proteins. The two profiles are very similar and in each, there are 12 clear peaks in hydrophobicity, corresponding to 12 TMDs. A topology of 12 TMDs separated, by an extended extramembrane loop, into two sets of 6 closely spaced TMDs is characteristic of transporters of the MFS. (B) The alignment of the five P. falciparum novel putative transporters. The region over TMDs 2-3 and TMDs 8-9 of the alignment is shown. Members of the MFS family typically possess a conserved amino acid motif between TMDs 2 and 3 and a related but less conserved motif in the corresponding loop in the second half of the protein (between TMDs 8 and 9). The putative novel transport proteins also appear to contain these MFS-specific motifs between TMDs 2 and 3 and, to a lesser extent, between TMDs 8 and 9. For comparison, MFS-specific motifs from a range of known and putative MFS proteins are presented. Legend as described for Additional data file 4

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Additional File 7:

The region over TMDs 1-5, TMD 7 and TMD 10 of the alignment is shown. The sequences are separated into two clusters, one containing plant and insect proteins and the other protozoan, yeast and mammalian proteins. The PFL0420w and PFL1515c proteins appear to be more closely related to the former group of transporters, whereas the MAL6P1.133 is more similar to the latter. Legend as described for Additional data file 4

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Additional File 8:

The region over TMDs 1-3 and TMDs 6-10 of the alignment is shown. The sequences are separated into two clusters, one containing proteins known to transport neurotransmitters, creatine or taurine, and the other proteins known or hypothesized to transport amino acids. The P. falciparum proteins have diverged considerably from the other family members, but are perhaps most similar in sequence to the amino acid transporters. Legend as described for Additional data file 4

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Additional File 9:

The region over TMDs 2-6 of the alignment is shown. The locations of the 'voltage sensor' and 'selectivity sequence' are indicated. Legend as described for Additional data file 4

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Additional File 10:

Additional methods

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