Structural Assignments to Mycoplasma genitalium (MG) Proteins SA Teichmann, C Chothia & M Gerstein (1999). "Advances in Structural Genomics," Curr. Opin. Struc. Biol. 9: 390-399.[medline]

This page provides supplementary related to the above paper. In particular, information is given for the different types of structural assignment that have been made to MG proteins.

Types of structural assignments and their files

For a comparison of the results of other 3D fold assigment to MG of many groups, see: data file (help file).

Two primary sets of MG structural assignments used in the paper:

1. For an up-to-date single consistent set of assignments, based on PSI-BLAST sequence comparisons and the SCOP classification of protein domains, see: data file.
2. For a union of many of many of the groups assigments, see data file (help file).
3. High-quality figures showing extent of assignments and top folds, see pdf file.

Standardized assignments of low complexity, transmembrane regions and signal sequences are available from a data directory. In particular:

1. For a page on probable and less probable membrane proteins see: data file.
2. For low complexity assignments, see data file (date file)
3. For signal sequences, see data file (date file).
4. For a concatenation of all masks, see data file (date file).
5. For a general overview describing the process of sequence masking, see help file.

MG sequence regions without structural assignments

After the above assignments are performed, some regions of MG remain unassigned.

• For a fasta file of just the remaining regions that are uncharacterized, see: fasta file.
• For a fasta file of these uncharacterized regions in context of whole genome, see: fasta file (date file).
• These regions have been clustered on the basis of their sequence similarity using PSI-BLAST and GEANFAMMER. For the results, see: data file. (Alternate listing.)

Other Sites and Data files Related to MG Structural Genomics

Groups doing fold assignments: Godzik, Eisenberg, Frishman, Koonin, Bork, Jones, Lengauer, Sali, Levitt, Moult, Sander

TIGR, the organization that sequenced the genome. The original 468 orf file and new 479 orf file. The MG sequence from NCBI via Entrez.

Last updated on 1999.06.28 by Mark.Gerstein@yale.edu