What’s New Nov. 7, 2000
The 46 human carrier genes are being annotated below for intron location, and a map is being made on the sequence alignment showing all the intron locations and their phase (see below). This should be done in the next two days.
What’s New Oct. 31, 2000
33 carriers from Candida albicans have been identified and compared to the S. cerevisiae carriers. See the link below to the Candida carriers.
What’s New Oct. 27, 2000
I have searched for all carriers in Dictyostelium and found 33 genes.23 are full length and 10 are partial. There are also four pseudogene fragments. The sequences, their accession numbers and other identifiers from non Genbank sequences are posted below. I have made an alignment of 32 of these carriers with the yeast sequences and that is also posted below.Trees will follow.
What’s New Oct. 16, 2000
I have searched the human genomic DNA comprehensively for mitochondrial carriers The sequences are posted here: All Human Carriers
An alphabetical list of accession numbers is also posted Accession Number List
S. pombe is carrier deficient compared to Bakers yeast. S. pombe seems tobe missing the succinate fumarate carrier SFC1, the dicarboxylate carrier DIC1The carnitine acylcarnitine carrier CRC1 and 6 other yeast carriersYPR011c, YPR021c, YPR128c, YFR045w, YDR470c, and YGR096w.S. pombe has three carriers that do not have clear orthologs in yeastAL133157, AL034433 and Z56276.
This is a work in progress. Many of these carriers are not completely assembled. There are long runs of mono polymer like QQQQQQQQ or NNNNNNNN.These seem to be in places where they ought to be removed.
Yeast mitochondrial carriers, (5k) are listed here with their chromosome assignment, length and gene name.
Other mitochondrial carriers, (5k) are listed here, with accession numbers and a brief note concerning any known functions they have.
Information on 263 mitochondrial carriers is presented here, including an alignment of the sequences and a list of GenBank accession numbers.
There are 35 of these carriers known in S. cerevisiae, 33 in Candida albicans, 47 carriers in humans, (with many pseudogenes) 44 in Drosophila and 33 in C. elegans Updated 10/31/2000
An Alignment of 263 mitochondrial carriers,(101k) 10/16/2000 Some of these are Expressed Sequence Tags (ESTs) and they contain many frame
shifts. It is not always possible to follow these shifts, so the EST sequences are
approximate. The Emericella nidulans sequence has a frameshift at the end, so the C-terminal is not correct in the original. There are now 47 human carriers in this
alignment, 44 Drosophila carriers, 33 C. elegans and 25 mouse carriers.
An map of intron position in 47 carriers(21k) not finished yet
This is the sequence alignment above with all amino acids changed to dashes.It is much easier to see the intron markers this way. 0= phase 0 intron between Codons. 1 = phase 1 (intron after first nucleotide), 2 = phase 2 (intron after second nucleotide).
These alignments are modular and can be combined in a word processor by pasting the pages together. The alignment positions are the same ineach file. This way all six pairwise species combinations can be made.
The following six PDF files contain phylogenetic trees of all carrier sequences from human, yeast(except YDR470c), C. elegans and Drosophila.The sequence numbers refer to the alignment of 263 carriers. The same numbers are used in the four species alignments above.
- A phylogenetic tree of 34 yeast mitochondrial carriers, and 47 human carriers [PDF}
- A phylogenetic tree of 34 yeast mitochondrial carriers, and 33 C. elegans carriers [PDF}
- A phylogenetic tree of 33 C. elegans mitochondrial carriers, and 47 human carriers [PDF} as an experiment, this tree is drawn backwards for easy comparison to other trees.
- A phylogenetic tree of 44 Drosophila mitochondrial carriers, and 47 human carriers [PDF}
- A phylogenetic tree of 44 Drosophila mitochondrial carriers, and 33 C. elegans carriers [PDF}
- A phylogenetic tree of 44 Drosophila mitochondrial carriers, and 34 yeast carriers [PDF}