NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1063713997|ref|NP_001327583|]
View 

Protein with RNI-like/FBD-like domain [Arabidopsis thaliana]

Protein Classification

F-box/FBD/LRR-repeat protein( domain architecture ID 18135498)

F-box/FBD/LRR-repeat protein may be a component of an SCF (Skp1-Cullin-F-box protein) ubiquitin-protein ligase that is involved in ubiquitin-dependent degradation

CATH:  1.20.1280.50|3.80.10.10
Gene Ontology:  GO:0006511|GO:0019005|GO:0005515|GO:0016567
PubMed:  31898225|11178263|11751054|14747988|10581972|7583641
SCOP:  4001927|4003523

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
366-443 1.21e-15

domain in FBox and BRCT domain containing plant proteins;


:

Pssm-ID: 214730  Cd Length: 72  Bit Score: 71.41  E-value: 1.21e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997  366 CLLFNLETFIWKGCKRIgEDEKEVAKYILRNTNRLKRATFTREIYEENnsqdmfENLEMVEELESVVRASKSCKLVFE 443
Cdd:smart00579   2 CLLSSLEVLEIKGYRGT-EEEKELVKYFLENAPCLKKLTISVETSDDE------EKLEILKELLSLPRASSSCQVQFL 72
F-box_SF super family cl45894
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 23-58 2.89e-07

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 cd22160:

Pssm-ID: 459239  Cd Length: 36  Bit Score: 46.51  E-value: 2.89e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063713997  23 ISELPEALLLQILSLLPTKKVVAMSVLSKRWRSLWK 58
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 162-186 5.09e-06

Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model.


:

Pssm-ID: 336782  Cd Length: 26  Bit Score: 42.76  E-value: 5.09e-06
                          10        20
                  ....*....|....*....|....*
gi 1063713997 162 SLRTLHLDGVEYTDDESVVNLLSGC 186
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGC 25
LRR super family cl34836
Leucine-rich repeat (LRR) protein [Transcription];
114-170 6.02e-03

Leucine-rich repeat (LRR) protein [Transcription];


The actual alignment was detected with superfamily member COG4886:

Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 38.76  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997 114 HIRELVLYVNGFQEsftFPLSLCNCESLETLTLGHNVLIDVPSPVF-LKSLRTLHLDG 170
Cdd:COG4886   183 NLKELDLSNNQITD---LPEPLGNLTNLEELDLSGNQLTDLPEPLAnLTNLETLDLSN 237
 
Name Accession Description Interval E-value
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
366-443 1.21e-15

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 71.41  E-value: 1.21e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997  366 CLLFNLETFIWKGCKRIgEDEKEVAKYILRNTNRLKRATFTREIYEENnsqdmfENLEMVEELESVVRASKSCKLVFE 443
Cdd:smart00579   2 CLLSSLEVLEIKGYRGT-EEEKELVKYFLENAPCLKKLTISVETSDDE------EKLEILKELLSLPRASSSCQVQFL 72
FBD pfam08387
FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it ...
 360-405 3.65e-11

FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it is repeated in two family members. Its precise function is unknown, but it is thought to be associated with nuclear processes. In fact, several family members are annotated as being similar to transcription factors.


Pssm-ID: 462458  Cd Length: 45  Bit Score: 57.73  E-value: 3.65e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063713997 360 PKNIPGCLLFNLETFIWKGCKRIgEDEKEVAKYILRNTNRLKRATF 405
Cdd:pfam08387   1 PSSVPECLLSSLETVEWRGYRGE-EEEKEFAKYILENARVLKKATI 45
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 23-58 2.89e-07

F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) and similar proteins; AtARP13 and AtARP25 belong to the largest subfamily of plant F-box proteins, F-box/LRR-repeat protein (FBLs). It contains tandem leucine-rich repeats (LRRs). Like other F-box proteins, they may be components of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. 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: 438931  Cd Length: 36  Bit Score: 46.51  E-value: 2.89e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063713997  23 ISELPEALLLQILSLLPTKKVVAMSVLSKRWRSLWK 58
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 162-186 5.09e-06

Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model.


Pssm-ID: 336782  Cd Length: 26  Bit Score: 42.76  E-value: 5.09e-06
                          10        20
                  ....*....|....*....|....*
gi 1063713997 162 SLRTLHLDGVEYTDDESVVNLLSGC 186
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGC 25
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
114-170 6.02e-03

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 38.76  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997 114 HIRELVLYVNGFQEsftFPLSLCNCESLETLTLGHNVLIDVPSPVF-LKSLRTLHLDG 170
Cdd:COG4886   183 NLKELDLSNNQITD---LPEPLGNLTNLEELDLSGNQLTDLPEPLAnLTNLETLDLSN 237
 
Name Accession Description Interval E-value
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
366-443 1.21e-15

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 71.41  E-value: 1.21e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997  366 CLLFNLETFIWKGCKRIgEDEKEVAKYILRNTNRLKRATFTREIYEENnsqdmfENLEMVEELESVVRASKSCKLVFE 443
Cdd:smart00579   2 CLLSSLEVLEIKGYRGT-EEEKELVKYFLENAPCLKKLTISVETSDDE------EKLEILKELLSLPRASSSCQVQFL 72
FBD pfam08387
FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it ...
 360-405 3.65e-11

FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it is repeated in two family members. Its precise function is unknown, but it is thought to be associated with nuclear processes. In fact, several family members are annotated as being similar to transcription factors.


Pssm-ID: 462458  Cd Length: 45  Bit Score: 57.73  E-value: 3.65e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063713997 360 PKNIPGCLLFNLETFIWKGCKRIgEDEKEVAKYILRNTNRLKRATF 405
Cdd:pfam08387   1 PSSVPECLLSSLETVEWRGYRGE-EEEKEFAKYILENARVLKKATI 45
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 23-58 2.89e-07

F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) and similar proteins; AtARP13 and AtARP25 belong to the largest subfamily of plant F-box proteins, F-box/LRR-repeat protein (FBLs). It contains tandem leucine-rich repeats (LRRs). Like other F-box proteins, they may be components of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. 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: 438931  Cd Length: 36  Bit Score: 46.51  E-value: 2.89e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063713997  23 ISELPEALLLQILSLLPTKKVVAMSVLSKRWRSLWK 58
Cdd:cd22160     1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 162-186 5.09e-06

Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model.


Pssm-ID: 336782  Cd Length: 26  Bit Score: 42.76  E-value: 5.09e-06
                          10        20
                  ....*....|....*....|....*
gi 1063713997 162 SLRTLHLDGVEYTDDESVVNLLSGC 186
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGC 25
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
114-170 6.02e-03

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 38.76  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063713997 114 HIRELVLYVNGFQEsftFPLSLCNCESLETLTLGHNVLIDVPSPVF-LKSLRTLHLDG 170
Cdd:COG4886   183 NLKELDLSNNQITD---LPEPLGNLTNLEELDLSGNQLTDLPEPLAnLTNLETLDLSN 237
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH