This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.


Protein Domains

I used SMART and Pfam to determine the domains found in the HLA-DQA1 protein sequence.  Both programs formed similar protein maps and returned similar results, but the Pfam search results provided less information about the cellular roles and involvement in metabolic pathways than the SMART search results. The results obtained from each program and the proteins maps formed are discussed below.


Using the protein sequence for HLA-DQA1, a Pfam search resulted in the protein map below.  The two domains shown are those deemed by the site to be significant.  The green domain shown represents MHC_II_alpha, a class II histocompatibility antigen found near the N-terminus.  Pfam found this domain to begin at position 29 and end at position 110, with an e-value of 3.6e-36.  The red domain represents the Immunoglobulin C-1 set domain (IGc1). Pfam found this IGc1 domain to begin at position 120 and end at position 200, with an e-value of 4.2e-27.  Aside from the 2 significant domains shown, Pfam also found a protein of unidentified function (not shown in image below).  This insignificant protein will not be discussed further here.  All of the significant domain matches obtained from the search sequence were found using Pfam-A under the default settings.  
From Pfam. HLA-DQA1 sequence search results. Retrieved from


SMART found the MHC_II_alpha domain near the N-terminus, beginning at position 30 and ending at position 110 with an e-value of 2.25e-45.  SMART described how this domain functions in cell-cell interaction as a cellular role. SMART also found the IGc1 domain beginning at position 128 and ending at position 199 with an e-value of 2.63e-30.  This domain is described to be involved in a variety of functions: cell-cell recognition, cell surface receptors, muscle structure, and the immune system.  SMART also found an unidentified transmembrane domain beginning at position 218 and ending at position 240, an e-value was not specified. This insignificant protein domain is shown below by the purple rectangle, but will not be discussed further here.  
From SMART. HLA-DQA1 sequence search results. Retrieved from

3D domain structures

The images below show the 3D structures of the two significant domains discussed above in the SMART and Pfam search results, MHC_II alpha and IGc1.
MHC_II alpha domain structure
IGc1 domain structure