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Conserved domains on  [gi|5006695|gb|AAD37615|]
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MHC class II antigen, partial [Rattus fuscipes greyii]

Protein Classification

major histocompatibility complex class II alpha chain( domain architecture ID 10469989)

major histocompatibility complex (MHC) class II alpha chain is expressed on the surface of antigen-presenting cells (APC), where it displays antigens for recognition by helper T cells

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
1-81 3.98e-41

Class II histocompatibility antigen, alpha domain;


:

Pssm-ID: 460019  Cd Length: 81  Bit Score: 129.23  E-value: 3.98e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5006695     1 DHVGSYGINMYQYYESRGQYTLEFDGDEELYVDLDKKETIWRIPEFGQQRSFDPQRGLQEIATAKHNLEILMKRSNSTPA 80
Cdd:pfam00993  1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80


                 .
gi 5006695    81 I 81
Cdd:pfam00993 81 T 81
 
Name Accession Description Interval E-value
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
1-81 3.98e-41

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 129.23  E-value: 3.98e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5006695     1 DHVGSYGINMYQYYESRGQYTLEFDGDEELYVDLDKKETIWRIPEFGQQRSFDPQRGLQEIATAKHNLEILMKRSNSTPA 80
Cdd:pfam00993  1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80


                 .
gi 5006695    81 I 81
Cdd:pfam00993 81 T 81
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
 3-82 7.47e-37

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 118.50  E-value: 7.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5006695      3 VGSYGINMYQ-YYESRGQYTLEFDGDEELYVDLDKKETIWRIPEFGQQRSFDPQRGLQEIATAKHNLEILMKRSNSTPAI 81
Cdd:smart00920  1 VGTYGHIVYCsDYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGALADIAVCKANLDILIKRSNSTPAT 80


                  .
gi 5006695     82 N 82
Cdd:smart00920 81 N 81
 
Name Accession Description Interval E-value
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
1-81 3.98e-41

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 129.23  E-value: 3.98e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5006695     1 DHVGSYGINMYQYYESRGQYTLEFDGDEELYVDLDKKETIWRIPEFGQQRSFDPQRGLQEIATAKHNLEILMKRSNSTPA 80
Cdd:pfam00993  1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80


                 .
gi 5006695    81 I 81
Cdd:pfam00993 81 T 81
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
 3-82 7.47e-37

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 118.50  E-value: 7.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5006695      3 VGSYGINMYQ-YYESRGQYTLEFDGDEELYVDLDKKETIWRIPEFGQQRSFDPQRGLQEIATAKHNLEILMKRSNSTPAI 81
Cdd:smart00920  1 VGTYGHIVYCsDYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGALADIAVCKANLDILIKRSNSTPAT 80


                  .
gi 5006695     82 N 82
Cdd:smart00920 81 N 81
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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