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Conserved domains on  [gi|119331218|ref|NP_001073261|]
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protein yippee-like 5 [Bos taurus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RLR_C_like super family cl13152
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ...
14-107 1.46e-08

C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains; Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. RLRs and Cereblon contain a common conserved zinc binding site in their C-terminal domains.


The actual alignment was detected with superfamily member pfam03226:

Pssm-ID: 448830  Cd Length: 99  Bit Score: 48.47  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119331218   14 LFSCANCDTILTNRSELISTrftGATGRAFLFNKVvnlqysevqDRVMLTGRHMVRD-----------VSCKNCNSKLGW 82
Cdd:pfam03226   2 VFQCKRCNTILGDSLALVSS---GRELNTIVLKKV---------TRNVVVGKELVTSesgfddctyspLFCAGCGAVLGR 69
                          90       100
                  ....*....|....*....|....*
gi 119331218   83 IYEfATEDSQRYKEGRVILERALVR 107
Cdd:pfam03226  70 KYR-STPEELDYKRGLFCLETDAIS 93
 
Name Accession Description Interval E-value
Yippee-Mis18 pfam03226
Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both ...
14-107 1.46e-08

Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.


Pssm-ID: 427204  Cd Length: 99  Bit Score: 48.47  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119331218   14 LFSCANCDTILTNRSELISTrftGATGRAFLFNKVvnlqysevqDRVMLTGRHMVRD-----------VSCKNCNSKLGW 82
Cdd:pfam03226   2 VFQCKRCNTILGDSLALVSS---GRELNTIVLKKV---------TRNVVVGKELVTSesgfddctyspLFCAGCGAVLGR 69
                          90       100
                  ....*....|....*....|....*
gi 119331218   83 IYEfATEDSQRYKEGRVILERALVR 107
Cdd:pfam03226  70 KYR-STPEELDYKRGLFCLETDAIS 93
 
Name Accession Description Interval E-value
Yippee-Mis18 pfam03226
Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both ...
14-107 1.46e-08

Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.


Pssm-ID: 427204  Cd Length: 99  Bit Score: 48.47  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119331218   14 LFSCANCDTILTNRSELISTrftGATGRAFLFNKVvnlqysevqDRVMLTGRHMVRD-----------VSCKNCNSKLGW 82
Cdd:pfam03226   2 VFQCKRCNTILGDSLALVSS---GRELNTIVLKKV---------TRNVVVGKELVTSesgfddctyspLFCAGCGAVLGR 69
                          90       100
                  ....*....|....*....|....*
gi 119331218   83 IYEfATEDSQRYKEGRVILERALVR 107
Cdd:pfam03226  70 KYR-STPEELDYKRGLFCLETDAIS 93
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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