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Conserved domains on  [gi|564390084|ref|XP_006253545|]
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tumor necrosis factor ligand superfamily member 13B isoform X3 [Rattus norvegicus]

Protein Classification

TNF domain-containing protein( domain architecture ID 10075925)

TNF domain-containing protein similar to Homo sapiens lymphotoxin-alpha, which acts as cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 143-271 2.49e-21

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


:

Pssm-ID: 238108  Cd Length: 137  Bit Score: 87.02  E-value: 2.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084 143 FQGPEETGTYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIHVfgdeLSL 215
Cdd:cd00184    5 LIGTNSSSGGTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSY----PEP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564390084 216 VTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 271
Cdd:cd00184   80 ILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 143-271 2.49e-21

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


Pssm-ID: 238108  Cd Length: 137  Bit Score: 87.02  E-value: 2.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084 143 FQGPEETGTYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIHVfgdeLSL 215
Cdd:cd00184    5 LIGTNSSSGGTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSY----PEP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564390084 216 VTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 271
Cdd:cd00184   80 ILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
147-273 1.41e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 51.93  E-value: 1.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084  147 EETGTYTFVPWLLSFKrgnaleekENKIVVRQTGYFFIYSQVLY------TDPIFaMGHVIQRKKIHVFGDelslVTLFR 220
Cdd:pfam00229   4 ESDRGGAFLLNGVTYS--------NGELVVPQAGLYYVYSQVYFrgegcpSGSVP-LTHYLYKFSSSYPGP----VLLLK 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 564390084  221 CIQNmPKTLPNN-----SCYSAGIAKLEEGDEIQLAIPRENAQISRNGDDTFFGALKL 273
Cdd:pfam00229  71 GAES-PCSSENPeywyqSIYLGGLFELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 165-273 7.29e-08

Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.


Pssm-ID: 214557  Cd Length: 125  Bit Score: 50.04  E-value: 7.29e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084   165 NALEEKENKIVVRQTGYFFIYSQVLYTDPIFAMGHVIQRKKIHVFG----DELSLVTLFRCIqNMPKTLP-NNSCYSAGI 239
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564390084   240 AKLEEGDEIQLAIpRENAQISRNGDDTFFGALKL 273
Cdd:smart00207  93 FPLTAGDRLSVNV-TEPSLVDLAPGATFFGAFLV 125
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 143-271 2.49e-21

Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.


Pssm-ID: 238108  Cd Length: 137  Bit Score: 87.02  E-value: 2.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084 143 FQGPEETGTYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIHVfgdeLSL 215
Cdd:cd00184    5 LIGTNSSSGGTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDSY----PEP 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564390084 216 VTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 271
Cdd:cd00184   80 ILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
147-273 1.41e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 51.93  E-value: 1.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084  147 EETGTYTFVPWLLSFKrgnaleekENKIVVRQTGYFFIYSQVLY------TDPIFaMGHVIQRKKIHVFGDelslVTLFR 220
Cdd:pfam00229   4 ESDRGGAFLLNGVTYS--------NGELVVPQAGLYYVYSQVYFrgegcpSGSVP-LTHYLYKFSSSYPGP----VLLLK 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 564390084  221 CIQNmPKTLPNN-----SCYSAGIAKLEEGDEIQLAIPRENAQISRNGDDTFFGALKL 273
Cdd:pfam00229  71 GAES-PCSSENPeywyqSIYLGGLFELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 165-273 7.29e-08

Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.


Pssm-ID: 214557  Cd Length: 125  Bit Score: 50.04  E-value: 7.29e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390084   165 NALEEKENKIVVRQTGYFFIYSQVLYTDPIFAMGHVIQRKKIHVFG----DELSLVTLFRCIqNMPKTLP-NNSCYSAGI 239
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564390084   240 AKLEEGDEIQLAIpRENAQISRNGDDTFFGALKL 273
Cdd:smart00207  93 FPLTAGDRLSVNV-TEPSLVDLAPGATFFGAFLV 125
 
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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