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Conserved domains on  [gi|1370458764|ref|XP_024304119|]
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junctional adhesion molecule-like isoform X3 [Homo sapiens]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 45-103 1.28e-08

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05880:

Pssm-ID: 472250  Cd Length: 116  Bit Score: 51.75  E-value: 1.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1370458764  45 KEEIVFrYYHKlrmsVEYSQSWGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05880    46 REESVF-YYHK----RPYPPPDGRFKGRVVWDGNIMRRDASILIWQLQPTDNGTYTCQV 99
 
Name Accession Description Interval E-value
IgV_EVA1 cd05880
Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are ...
 45-103 1.28e-08

Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development.


Pssm-ID: 409464  Cd Length: 116  Bit Score: 51.75  E-value: 1.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1370458764  45 KEEIVFrYYHKlrmsVEYSQSWGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05880    46 REESVF-YYHK----RPYPPPDGRFKGRVVWDGNIMRRDASILIWQLQPTDNGTYTCQV 99
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-118 1.94e-06

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 45.53  E-value: 1.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370458764  34 RWYcmcFQRSPKE-EIVFRYYHKLRMSveysqswGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSIHLGN-LVFK 111
Cdd:pfam07686  32 YWY---RQPPGKGpTFLIAYYSNGSEE-------GVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGTYTCAVIPSGeGVFG 101


                  ....*..
gi 1370458764 112 KTIVLHV 118
Cdd:pfam07686 102 KGTRLTV 108
IGv smart00406
Immunoglobulin V-Type;
59-103 2.04e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 36.21  E-value: 2.04e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1370458764   59 SVEYSQSWghFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:smart00406  39 GSSYYQES--YKGRFTISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
 
Name Accession Description Interval E-value
IgV_EVA1 cd05880
Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are ...
 45-103 1.28e-08

Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development.


Pssm-ID: 409464  Cd Length: 116  Bit Score: 51.75  E-value: 1.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1370458764  45 KEEIVFrYYHKlrmsVEYSQSWGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05880    46 REESVF-YYHK----RPYPPPDGRFKGRVVWDGNIMRRDASILIWQLQPTDNGTYTCQV 99
IgV_P0-like cd05715
Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here ...
 47-103 5.59e-07

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.


Pssm-ID: 409380  Cd Length: 117  Bit Score: 47.42  E-value: 5.59e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1370458764  47 EIVFRYYHKLRMsveYSQSWGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05715    47 TESMFHYSKGKP---YILKVGRFKDRVSWAGNPSKKDASIVISNLQFSDNGTYTCDV 100
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-118 1.94e-06

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 45.53  E-value: 1.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370458764  34 RWYcmcFQRSPKE-EIVFRYYHKLRMSveysqswGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSIHLGN-LVFK 111
Cdd:pfam07686  32 YWY---RQPPGKGpTFLIAYYSNGSEE-------GVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGTYTCAVIPSGeGVFG 101


                  ....*..
gi 1370458764 112 KTIVLHV 118
Cdd:pfam07686 102 KGTRLTV 108
IgV_P0 cd05879
Immunoglobulin (Ig)-like domain of protein zero (P0); The members here are composed of the ...
 62-103 3.99e-04

Immunoglobulin (Ig)-like domain of protein zero (P0); The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin.


Pssm-ID: 409463  Cd Length: 117  Bit Score: 39.09  E-value: 3.99e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370458764  62 YSQSWGHFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05879    59 YIDNVGPFKERIEWVGNPSRKDGSIVIHNLDYTDNGTFTCDV 100
IGv smart00406
Immunoglobulin V-Type;
59-103 2.04e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 36.21  E-value: 2.04e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1370458764   59 SVEYSQSWghFQNRVNLVGDIFRNDGSIMLQGVRESDGGNYTCSI 103
Cdd:smart00406  39 GSSYYQES--YKGRFTISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 62-103 5.89e-03

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 35.89  E-value: 5.89e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1370458764  62 YSQSWG-HFQN----RVNLVGDIFR-NDGSIMLQGVRESDGGNYTCSI 103
Cdd:cd05718    50 FHPQYGpSVPNpyaeRVEFLAARLGlRNATLRIRNLRVEDEGNYICEF 97
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 64-118 6.16e-03

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 35.17  E-value: 6.16e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1370458764   64 QSWGHFQNRVNLVGDifRNDGSIMLQGVRESDGGNYTCSIHLGNLVFKKTIVLHV 118
Cdd:smart00410  33 GKLLAESGRFSVSRS--GSTSTLTISNVTPEDSGTYTCAATNSSGSASSGTTLTV 85
IgV_MOG_like cd05713
Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here ...
 34-119 6.31e-03

Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here are composed of the immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the CNS on the outermost lamellae of the myelin sheath, and on the surface of oligodendrocytes, and may participate in the completion, compaction, and/or maintenance of myelin. This group also includes butyrophilin (BTN). BTN is the most abundant protein in bovine milk-fat globule membrane (MFGM).


Pssm-ID: 409378  Cd Length: 114  Bit Score: 35.63  E-value: 6.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370458764  34 RWYcmcfqRSPKEEIVFRYyhklRMSVE-YSQSWGHFQNRVNLVGDiFRNDGSIMLQ--GVRESDGGNYTCSIHLGNLVF 110
Cdd:cd05713    36 RWF-----RSQFSPVVHLY----RDGQDqEEEQMPEYRGRTELLKD-AIAEGSVALRihNVRPSDEGQYTCFFRSGSFYE 105


                  ....*....
gi 1370458764 111 KKTIVLHVS 119
Cdd:cd05713   106 EATLELKVA 114
IgV_HHLA2 cd16091
Immunoglobulin Variable (IgV) domain in HERV-H LTR-associating 2 (HHLA2); The members here are ...
 49-101 6.74e-03

Immunoglobulin Variable (IgV) domain in HERV-H LTR-associating 2 (HHLA2); The members here are composed of the immunoglobulin variable (IgV) region in HERV-H LTR-associating 2 (HHLA2; also known as B7-H7/B7 homolog 7). HHLA2 is a member of the B7 family of immune regulatory proteins. Mature human HHLA2 consists of an extracellular domain (ECD) with three immunoglobulin-like domains, a transmembrane segment, and a cytoplasmic domain. HHLA2 is widely expressed in human cancers including non-small cell lung carcinoma (NSCLS), triple negative breast cancer (TNBC), and melanoma, but has limited expression on normal tissues. Interestingly, unlike other members of B7 family, HHLA2 is not expressed in mice or rats. HHLA2 functions as a T cell coinhibitory molecules as it inhibits the proliferation of activated CD4(+) and CD8(+) T cells and their cytokine production. Furthermore, HHLA2 is constitutively expressed on the surface of human monocytes and is induced on B cells after stimulation, however it is not inducible on T cells.


Pssm-ID: 409512  Cd Length: 107  Bit Score: 35.44  E-value: 6.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1370458764  49 VFRYYHKlrmSVEYSQSWGHFQNRVNLVGDIFRN-DGSIMLQGVRESDGGNYTC 101
Cdd:cd16091    40 VHSYYYG---KDQLESQDQRYRNRTSLFKDQISNgNASLLLRRVQLQDEGRYKC 90
 
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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