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Conserved domains on  [gi|564390078|ref|XP_006253542|]
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tumor necrosis factor ligand superfamily member 13B isoform X1 [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 ...
 186-322 4.29e-22

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: 90.10  E-value: 4.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078 186 CLQLIADSNTPTirkgtYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIH 258
Cdd:cd00184    2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDS 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564390078 259 VfgdeLSLVTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 322
Cdd:cd00184   76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
 
Name Accession Description Interval E-value
TNF cd00184
Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT ...
 186-322 4.29e-22

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: 90.10  E-value: 4.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078 186 CLQLIADSNTPTirkgtYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIH 258
Cdd:cd00184    2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDS 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564390078 259 VfgdeLSLVTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 322
Cdd:cd00184   76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
211-324 3.51e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 51.16  E-value: 3.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078  211 SFKRGNaLEEKENKIVVRQTGYFFIYSQVLY------TDPIFaMGHVIQRKKIHVFGDelslVTLFRCIQNmPKTLPNN- 283
Cdd:pfam00229  10 AFLLNG-VTYSNGELVVPQAGLYYVYSQVYFrgegcpSGSVP-LTHYLYKFSSSYPGP----VLLLKGAES-PCSSENPe 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 564390078  284 ----SCYSAGIAKLEEGDEIQLAIPRENAQISRNGDDTFFGALKL 324
Cdd:pfam00229  83 ywyqSIYLGGLFELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 216-324 9.59e-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: 9.59e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078   216 NALEEKENKIVVRQTGYFFIYSQVLYTDPIFAMGHVIQRKKIHVFG----DELSLVTLFRCIqNMPKTLP-NNSCYSAGI 290
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564390078   291 AKLEEGDEIQLAIpRENAQISRNGDDTFFGALKL 324
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 ...
 186-322 4.29e-22

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: 90.10  E-value: 4.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078 186 CLQLIADSNTPTirkgtYTFVPWL----LSFKRgNALEEKENKIVVRQTGYFFIYSQVLY---TDPIFAMGHVIQRKKIH 258
Cdd:cd00184    2 AAHLIGTNSSSG-----GTGLSWEsddgRAFLS-GGLELQNGELVVPQDGLYYIYSQVYFrgqCCSTLSVSHVLQLRTDS 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564390078 259 VfgdeLSLVTLFRCIQNMPKTLP---NNSCYSAGIAKLEEGDEIQLAIPReNAQISRNGDDTFFGAL 322
Cdd:cd00184   76 Y----PEPILLLKGIRSVCSSVSegwYNSVYLGGLFQLRAGDRLSVNVSA-PALLDLSQGTTFFGAF 137
TNF pfam00229
TNF(Tumour Necrosis Factor) family;
211-324 3.51e-08

TNF(Tumour Necrosis Factor) family;


Pssm-ID: 425540  Cd Length: 127  Bit Score: 51.16  E-value: 3.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078  211 SFKRGNaLEEKENKIVVRQTGYFFIYSQVLY------TDPIFaMGHVIQRKKIHVFGDelslVTLFRCIQNmPKTLPNN- 283
Cdd:pfam00229  10 AFLLNG-VTYSNGELVVPQAGLYYVYSQVYFrgegcpSGSVP-LTHYLYKFSSSYPGP----VLLLKGAES-PCSSENPe 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 564390078  284 ----SCYSAGIAKLEEGDEIQLAIPRENAQISRNGDDTFFGALKL 324
Cdd:pfam00229  83 ywyqSIYLGGLFELRAGDRLSVNVSNPSLVDLSAPGKTYFGAFLL 127
TNF smart00207
Tumour necrosis factor family; Family of cytokines that form homotrimeric or heterotrimeric ...
 216-324 9.59e-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: 9.59e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564390078   216 NALEEKENKIVVRQTGYFFIYSQVLYTDPIFAMGHVIQRKKIHVFG----DELSLVTLFRCIqNMPKTLP-NNSCYSAGI 290
Cdd:smart00207  14 SGMELQNGELVVPRDGLYYIYSQVYFRGQGCNGKSVELSLSLHLRKpsypLPLLLLEAARSS-CWSASSAwKDSVYLGGL 92

                           90       100       110
                   ....*....|....*....|....*....|....
gi 564390078   291 AKLEEGDEIQLAIpRENAQISRNGDDTFFGALKL 324
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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