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Conserved domains on  [gi|334186327|ref|NP_001190662|]
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RNI-like superfamily protein [Arabidopsis thaliana]

Protein Classification

F-box/LRR-repeat protein( domain architecture ID 1903223)

F-box/LRR-repeat protein functions as the substrate-recognition component of a SCF (Skp1-Cullin-F-box protein) ubiquitin-protein ligase that is involved in ubiquitin-dependent degradation

CATH:  1.20.1280.50
Gene Ontology:  GO:0019005|GO:0005515|GO:0006511|GO:0016567
PubMed:  31898225|11178263|14747988|7583641|11751054|10581972
SCOP:  4001927

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
F-box_SF super family cl45894
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 117-159 1.31e-04

F-box domain superfamily; This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures.


The actual alignment was detected with superfamily member cd22139:

Pssm-ID: 459239  Cd Length: 45  Bit Score: 39.53  E-value: 1.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 334186327 117 WPLLP-ELTIKVFSMLDTKSLMQASACCTMFNKCAMDRVCYSHI 159
Cdd:cd22139    1 WLCLPdELWLHIFSFLSPKDLCQVALVCRRFNRLASDESLWKQI 44
AMN1 super family cl39120
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
 210-328 4.91e-04

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


The actual alignment was detected with superfamily member cd09293:

Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 41.93  E-value: 4.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186327 210 PLTFNHGFTGGHLRSLHLYHLRMIDCGSLSPVLSACLNL--TDLKIVGLISgsrDNPLEQLGLltrNCRLIEHLFIEIYG 287
Cdd:cd09293   42 DPPLDQLSNCNKLKKLILPGSKLIDDEGLIALAQSCPNLqvLDLRACENIT---DSGIVALAT---NCPKLQTINLGRHR 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 334186327 288 AAGLITDSSLLEFAANCPNLSSISLLGFLLNDAILQKLIKG 328
Cdd:cd09293  116 NGHLITDVSLSALGKNCTFLQTVGFAGCDVTDKGVWELASG 156
 
Name Accession Description Interval E-value
F-box_unchar cd22139
F-box domain found in uncharacterized F-box protein group similar to F-box only protein 3 ...
 117-159 1.31e-04

F-box domain found in uncharacterized F-box protein group similar to F-box only protein 3 (FBXO3); This subfamily corresponds to a group of uncharacterized F-box proteins which show sequence similarity to F-box only protein 3 (FBXO3). FBXO3, also called FBX3, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, that mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. It also promotes ubiquitylation and transcriptional activity of AIRE (autoimmune regulator). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438911  Cd Length: 45  Bit Score: 39.53  E-value: 1.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 334186327 117 WPLLP-ELTIKVFSMLDTKSLMQASACCTMFNKCAMDRVCYSHI 159
Cdd:cd22139    1 WLCLPdELWLHIFSFLSPKDLCQVALVCRRFNRLASDESLWKQI 44
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
 210-328 4.91e-04

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 41.93  E-value: 4.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186327 210 PLTFNHGFTGGHLRSLHLYHLRMIDCGSLSPVLSACLNL--TDLKIVGLISgsrDNPLEQLGLltrNCRLIEHLFIEIYG 287
Cdd:cd09293   42 DPPLDQLSNCNKLKKLILPGSKLIDDEGLIALAQSCPNLqvLDLRACENIT---DSGIVALAT---NCPKLQTINLGRHR 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 334186327 288 AAGLITDSSLLEFAANCPNLSSISLLGFLLNDAILQKLIKG 328
Cdd:cd09293  116 NGHLITDVSLSALGKNCTFLQTVGFAGCDVTDKGVWELASG 156
 
Name Accession Description Interval E-value
F-box_unchar cd22139
F-box domain found in uncharacterized F-box protein group similar to F-box only protein 3 ...
 117-159 1.31e-04

F-box domain found in uncharacterized F-box protein group similar to F-box only protein 3 (FBXO3); This subfamily corresponds to a group of uncharacterized F-box proteins which show sequence similarity to F-box only protein 3 (FBXO3). FBXO3, also called FBX3, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, that mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. It also promotes ubiquitylation and transcriptional activity of AIRE (autoimmune regulator). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.


Pssm-ID: 438911  Cd Length: 45  Bit Score: 39.53  E-value: 1.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 334186327 117 WPLLP-ELTIKVFSMLDTKSLMQASACCTMFNKCAMDRVCYSHI 159
Cdd:cd22139    1 WLCLPdELWLHIFSFLSPKDLCQVALVCRRFNRLASDESLWKQI 44
AMN1 cd09293
Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in ...
 210-328 4.91e-04

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.


Pssm-ID: 187754 [Multi-domain]  Cd Length: 226  Bit Score: 41.93  E-value: 4.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334186327 210 PLTFNHGFTGGHLRSLHLYHLRMIDCGSLSPVLSACLNL--TDLKIVGLISgsrDNPLEQLGLltrNCRLIEHLFIEIYG 287
Cdd:cd09293   42 DPPLDQLSNCNKLKKLILPGSKLIDDEGLIALAQSCPNLqvLDLRACENIT---DSGIVALAT---NCPKLQTINLGRHR 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 334186327 288 AAGLITDSSLLEFAANCPNLSSISLLGFLLNDAILQKLIKG 328
Cdd:cd09293  116 NGHLITDVSLSALGKNCTFLQTVGFAGCDVTDKGVWELASG 156
 
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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