Protein Domains in Filaggrin

Using the amino acid sequence of filaggrin, I identified protein domains using various programs.

Results using PFAM
25 PFAM-A matches found
Visit the following page to view the domains found: http://pfam.sanger.ac.uk/protein/FILA_HUMAN

 

S_100 S-100/ICaBP type calcium binding domain Domain CL0220 4 47 4 47 1 44 58.0 3.1e-16 n/a 0 #HMM       LEkaietiinvFhqYSgkeGdkdtLsKkELKeLlekELpnflkn
#MATCH     L+++i++iin+F+qYS+k+ ++dtLsKkELKeLlekE+ ++lkn
#PP        789***************************************98
#SEQ       LLENIFAIINLFKQYSKKDKNTDTLSKKELKELLEKEFRQILKN 2

Filaggrin Filaggrin Repeat n/a 258 306 258 306 1 52 52.4 4.2e-14 n/a 2 #HMM       egsRssggerhgaSrhadssrHsgagqgqssgsrtsrrrGSsvSQdsDSeGH
#MATCH     e+sRss+g++   S+++++srH++++q++ ++srt++rrGS+vSQd+DSeGH
#PP        79********...***************************************
#SEQ       ERSRSSDGKS---SSQVNRSRHENTSQVPLQESRTRKRRGSRVSQDRDSEGH

View more domains here.

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A 3D depiction of the filaggrin protein domain.

A 3D depiction of the EF hand protein domain.

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Domains of the filaggrin protein found using InterPro.

 

The protein domains that were found correlate with the functions that we previously associated with the protein filaggrin. The filaggrin domain itself is the keratin intermediate filament binding domain that is produced, which we know helps to hold together the IF matrix which preserves the integrity of the epidermal layer seen strong in non-eczema patients. The fact that there is a calcium binding domain however, remains something that has not been fully researched and an understanding of how calcium affects the protein or is related to it is still unclear.

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The first 3 protein motifs found using MEME:

MOTIF 1
width = 50
sites = 5
llr = 600
E-value = 4.7e-067

gi|60097902|ref|NP_002007.1| 3709 5.38e-54
SAGRSGRSGS FLYQVSTHEQSESAHGRAGPSTGGRQGSRHEQARDSSRHSASQEGQDTIR GHPGSRRGGR gi|60097902|ref|NP_002007.1| 3061 8.79e-53
SGETSGHSGS FLYQVSTHEQSESSHGWTGPSTRGRQGSRHEQAQDSSRHSASQYGQDTIR GHPGSSRGGR gi|60097902|ref|NP_002007.1| 2737 3.88e-52
SGETSGHSGS FLYQVSTHEQSESSHGWTGPSTRGRQGSRHEQAQDSSRHSASQDGQDTIR GHPGSSRGGR gi|60097902|ref|NP_002007.1| 3385 1.29e-49
SGGRSGRSGS FLYQVSTHEQSESAHGRTRTSTGRRQGSHHEQARDSSRHSASQEGQDTIR GHPGSSRRGR gi|60097902|ref|NP_002007.1| 2413 3.55e-49
SAGRSGRSGS FLYQVSTHEQSESAHGRTGTSTGGRQGSHHKQARDSSRHSTSQEGQDTIH GHPGSSSGGR

MOTIF 2
width = 50
sites = 5
llr = 590
E-value = 1.2e-062

gi|60097902|ref|NP_002007.1| 792 1.41e-52
SGERSRRSGS FLYQVSTHKQSESSHGWTGPSTGVRQGSHHEQARDNSRHSASQDGQDTIR GHPGSSRRGR gi|60097902|ref|NP_002007.1| 1764 7.71e-52
SGERSGRSGS FLYQVSTHEQSESAHGRTGPSTGGRQRSRHEQARDSSRHSASQEGQDTIR GHPGSSRGGR gi|60097902|ref|NP_002007.1| 1440 2.08e-50
SGESSGRSRS FLYQVSSHEQSESTHGQTAPSTGGRQGSRHEQARNSSRHSASQDGQDTIR GHPGSSRGGR gi|60097902|ref|NP_002007.1| 1116 8.56e-49
 SGGRSGRSGS FIYQVSTHEQSESAHGRTRTSTGRRQGSHHEQARDSSRHSASQEGQDTIR AHPGSRRGGR gi|60097902|ref|NP_002007.1| 2089 1.11e-48
SGESSGRSGS FLYQVSTHEQSESTHGQSAPSTGGRQGSHYDQAQDSSRHSASQEGQDTIR GHPGPSRGGR.

MOTIF 3
width = 50
sites = 5
llr = 570
E-value = 1.1e-052

gi|60097902|ref|NP_002007.1| 2992 3.51e-51
QQSADSSRHS GIGHGQASSAVRDSGHRGYSGSQASDNEGHSEDSDTQSVSAHGQAGSHQQ SHQESARGRS gi|60097902|ref|NP_002007.1| 2668 3.51e-51
QQSADSSRHS GIGHGQASSAVRDSGHRGYSGSQASDNEGHSEDSDTQSVSAHGQAGSHQQ SHQESARGRS gi|60097902|ref|NP_002007.1| 3640 1.52e-50
QQSADSSRHS GIGHGQASSAVRDSGHRGSSGSQASDSEGHSEDSDTQSVSAHGQAGPHQQ SHQESTRGRS gi|60097902|ref|NP_002007.1| 2344 1.52e-50
QQSADSSRHS GIGHGQASSAVRDSGHRGSSGSQASDSEGHSEDSDTQSVSAHGQAGPHQQ SHQESTRGRS gi|60097902|ref|NP_002007.1| 3316 1.71e-43
QQSADSSRHS GIPRGQASSAVRDSRHWGSSGSQASDSEGHSEESDTQSVSGHGQAGPHQQ SHQESARDRS

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References
1. MEME: http://meme.sdsc.edu/meme/meme-intro.html
2. Uniprot: www.uniprot.org
3. Pfam: http://pfam.sanger.ac.uk
4. InterPro: http://www.ebi.ac.uk/interpro/ISpy?mode=single&ac=P20930

Dalia Saleh
saleh [ @ ] wisc.edu
last updated 2/9/10
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