LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles

Table 14 Keywords/Phrases for each Group and Superfamily

Group	SF	Principal Keywords/Phrases
1	4	histone H4, chromosomal protein, nuclear protein, DNA binding
1	6	dsRNA binding, DNA gyrase, breakage, CLP, ATP binding
2	1	break, ATP binding, DNA topoisomerase, protein biosynthesis, topoisomerase, repair
2	3	coiled, coil, nuclear protein, caldesmon, histone H1, chaperone, tropomyosin filament, break, DNA topoisomerase
2	8	DNA topoisomerase, nuclear protein, HMG box, coiled coil
2	9	transcriptional inhibition, glycosyl hydrolase, nuclear protein,
2	10	nuclear protein, DNA binding, transcription regulation, intermediate filament, keratin, chaperone, homeobox, coiled coil, HMG box domain, cytoskeletal
3	2	chaperone, coiled coil, tropomyosin, stress, filament, phosphorylation, caldesmon elongation factor, neurofilament, actin binding, cytoskeleton, rotamase
3	5	coiled coil, histone H1, filament, nuclear protein, neurofilament, flagella, HAMP domain, synuclein, DNA binding, hsp70
6	7	groel protein, nuclear protein, histone H1, chaperonin, DNA binding, HAMP domain, synuclein, transcription regulation
Group	Cluster	Principal Keywords/Phrases
Lea5	299	DNA binding, transcription regulation, nuclear protein, gata, zinc finger, homeobox
Lea14	297	esterase, gapdh, chaperone protein DNA, glycoprotein

For each superfamily, the consensus POPP (Table 13) has been set as a query against a database of POPP vectors representing SwissProt. The protein hits, excluding LEA proteins for each query were submitted to the Protein Annotators' Assistant, which returns a list of keywords and phrases shared by sets of the submitted proteins. A sample of the most prominent are listed against the Group/Class and the corresponding superfamilies/clusters. Rather than being understood as the actual functions which the search hits share with the LEA proteins, matches based on shared biases in peptide composition can indicate shared mechanisms or structural elements.

ISSN: 1471-2105