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Conserved domains on  [gi|42569822|ref|NP_181623|]
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F-box and associated interaction domains-containing protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
F_box_assoc_1 super family cl44343
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 166-411 3.05e-42

F-box protein interaction domain; This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.


The actual alignment was detected with superfamily member TIGR01640:

Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 149.05  E-value: 3.05e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   166 VRGLLCFSVREKACIYNPTTRQRLTLPAIKSDIiaLKDERKdiRYYIGHDPVNDQYKLVCtigISSAFFTNLKSEHWVFV 245
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRR--SNKESD--TYFLGYDPIEKQYKVLC---FSDRSGNRNQSEHQVYT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   246 LEaGGSWRKVRTleSYHPHAPSTVGQFINGsVVYYMAWLDMDT--CAVVSFDITSEELTTIIVtleagdvaLPAGR---- 319
Cdd:TIGR01640  77 LG-SNSWRTIEC--SPPHHPLKSRGVCING-VLYYLAYTLKTNpdYFIVSFDVSSERFKEFIP--------LPCGNsdsv 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   320 MKAGLIQYHGEIAVFDHTHLKEKFlvDLWVLKDAGMKKWSKKRLVLQPCQKHLVhDDIELVvkGTTQDGKVILAPVNmCS 399
Cdd:TIGR01640 145 DYLSLINYKGKLAVLKQKKDTNNF--DLWVLNDAGKQEWSKLFTVPIPPLPDLV-DDNFLS--GFTDKGEIVLCCED-EN 218

                         250
                  ....*....|..
gi 42569822   400 QLYILCYDMGSN 411
Cdd:TIGR01640 219 PFYIFYYNVGEN 230
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 68-105 1.02e-10

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. 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: 438928  Cd Length: 39  Bit Score: 56.32  E-value: 1.02e-10
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 42569822  68 EIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLISCRYF 105
Cdd:cd22157   2 SLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 17-56 5.61e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member smart00652:

Pssm-ID: 471952  Cd Length: 83  Bit Score: 38.77  E-value: 5.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 42569822     17 EECQSVPQVVSLRDSDQLQIMDEKGDNSLALLPAKLPMRM 56
Cdd:smart00652   3 EDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKV 42
 
Name Accession Description Interval E-value
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 166-411 3.05e-42

F-box protein interaction domain; This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.


Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 149.05  E-value: 3.05e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   166 VRGLLCFSVREKACIYNPTTRQRLTLPAIKSDIiaLKDERKdiRYYIGHDPVNDQYKLVCtigISSAFFTNLKSEHWVFV 245
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRR--SNKESD--TYFLGYDPIEKQYKVLC---FSDRSGNRNQSEHQVYT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   246 LEaGGSWRKVRTleSYHPHAPSTVGQFINGsVVYYMAWLDMDT--CAVVSFDITSEELTTIIVtleagdvaLPAGR---- 319
Cdd:TIGR01640  77 LG-SNSWRTIEC--SPPHHPLKSRGVCING-VLYYLAYTLKTNpdYFIVSFDVSSERFKEFIP--------LPCGNsdsv 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   320 MKAGLIQYHGEIAVFDHTHLKEKFlvDLWVLKDAGMKKWSKKRLVLQPCQKHLVhDDIELVvkGTTQDGKVILAPVNmCS 399
Cdd:TIGR01640 145 DYLSLINYKGKLAVLKQKKDTNNF--DLWVLNDAGKQEWSKLFTVPIPPLPDLV-DDNFLS--GFTDKGEIVLCCED-EN 218

                         250
                  ....*....|..
gi 42569822   400 QLYILCYDMGSN 411
Cdd:TIGR01640 219 PFYIFYYNVGEN 230
FBA_3 pfam08268
F-box associated domain;
270-403 1.74e-36

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 130.49  E-value: 1.74e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   270 GQFINGsVVYYMAWL-DMDTCAVVSFDITSEELTTIIVTLEagdvalPAGRMKAGLIQYHGEIAVFDHTHLKEkflVDLW 348
Cdd:pfam08268   1 GICING-VLYYGAWTsDNSKSVIVSFDVRSEKFDFIKLPVP------LANDLSSTLINYKGKLAVVSHTSDGG---IELW 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 42569822   349 VLKDAGMKKWSKKRLVLQPCQKHLVhDDIELVVKGTTQDGKVILA-PVNMCSQLYI 403
Cdd:pfam08268  71 VLEDAEKHEWSKKIFVLPPSHEHLV-DNTDLSVVGTTRTGEIILVlPSTLSKPFYV 125
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 68-105 1.02e-10

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. 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: 438928  Cd Length: 39  Bit Score: 56.32  E-value: 1.02e-10
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 42569822  68 EIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLISCRYF 105
Cdd:cd22157   2 SLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 67-101 3.85e-05

F-box domain; This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). 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: 425796  Cd Length: 43  Bit Score: 40.60  E-value: 3.85e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42569822    67 CEIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLIS 101
Cdd:pfam00646   2 LDLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVD 36
FBOX smart00256
A Receptor for Ubiquitination Targets;
69-101 5.91e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 40.11  E-value: 5.91e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 42569822     69 IPPDLLMEIVMRLPAKSMVRFKCISKQWSSLIS 101
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLID 33
eIF1a smart00652
eukaryotic translation initiation factor 1A;
17-56 5.61e-04

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 38.77  E-value: 5.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 42569822     17 EECQSVPQVVSLRDSDQLQIMDEKGDNSLALLPAKLPMRM 56
Cdd:smart00652   3 EDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKV 42
 
Name Accession Description Interval E-value
F_box_assoc_1 TIGR01640
F-box protein interaction domain; This model describes a large family of plant domains, with ...
 166-411 3.05e-42

F-box protein interaction domain; This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.


Pssm-ID: 273726 [Multi-domain]  Cd Length: 230  Bit Score: 149.05  E-value: 3.05e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   166 VRGLLCFSVREKACIYNPTTRQRLTLPAIKSDIiaLKDERKdiRYYIGHDPVNDQYKLVCtigISSAFFTNLKSEHWVFV 245
Cdd:TIGR01640   4 CDGLICFSYGKRLVVWNPSTGQSRWLPTPKSRR--SNKESD--TYFLGYDPIEKQYKVLC---FSDRSGNRNQSEHQVYT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   246 LEaGGSWRKVRTleSYHPHAPSTVGQFINGsVVYYMAWLDMDT--CAVVSFDITSEELTTIIVtleagdvaLPAGR---- 319
Cdd:TIGR01640  77 LG-SNSWRTIEC--SPPHHPLKSRGVCING-VLYYLAYTLKTNpdYFIVSFDVSSERFKEFIP--------LPCGNsdsv 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   320 MKAGLIQYHGEIAVFDHTHLKEKFlvDLWVLKDAGMKKWSKKRLVLQPCQKHLVhDDIELVvkGTTQDGKVILAPVNmCS 399
Cdd:TIGR01640 145 DYLSLINYKGKLAVLKQKKDTNNF--DLWVLNDAGKQEWSKLFTVPIPPLPDLV-DDNFLS--GFTDKGEIVLCCED-EN 218

                         250
                  ....*....|..
gi 42569822   400 QLYILCYDMGSN 411
Cdd:TIGR01640 219 PFYIFYYNVGEN 230
FBA_3 pfam08268
F-box associated domain;
270-403 1.74e-36

F-box associated domain;


Pssm-ID: 285468  Cd Length: 125  Bit Score: 130.49  E-value: 1.74e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42569822   270 GQFINGsVVYYMAWL-DMDTCAVVSFDITSEELTTIIVTLEagdvalPAGRMKAGLIQYHGEIAVFDHTHLKEkflVDLW 348
Cdd:pfam08268   1 GICING-VLYYGAWTsDNSKSVIVSFDVRSEKFDFIKLPVP------LANDLSSTLINYKGKLAVVSHTSDGG---IELW 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 42569822   349 VLKDAGMKKWSKKRLVLQPCQKHLVhDDIELVVKGTTQDGKVILA-PVNMCSQLYI 403
Cdd:pfam08268  71 VLEDAEKHEWSKKIFVLPPSHEHLV-DNTDLSVVGTTRTGEIILVlPSTLSKPFYV 125
F-box_AtFBW1-like cd22157
F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) ...
 68-105 1.02e-10

F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins; AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. 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: 438928  Cd Length: 39  Bit Score: 56.32  E-value: 1.02e-10
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 42569822  68 EIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLISCRYF 105
Cdd:cd22157   2 SLPDDLVEEILSRLPAKSLLRFRCVCKQWNSLISSPSF 39
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 67-101 3.85e-05

F-box domain; This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). 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: 425796  Cd Length: 43  Bit Score: 40.60  E-value: 3.85e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 42569822    67 CEIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLIS 101
Cdd:pfam00646   2 LDLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVD 36
FBOX smart00256
A Receptor for Ubiquitination Targets;
69-101 5.91e-05

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 40.11  E-value: 5.91e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 42569822     69 IPPDLLMEIVMRLPAKSMVRFKCISKQWSSLIS 101
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLID 33
F-box_AtGID2-like cd22151
F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, ...
 69-99 3.57e-04

F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins; AtGID2, also called protein SLEEPY 1, is an essential component of the SCF-type E3 ligase complex, SCF(GID2), a complex that positively regulates the gibberellin signaling pathway. Upon gibberellin treatment, the SCF(GID2) complex mediates the ubiquitination and subsequent degradation of DELLA proteins (GAI, RGA and RGL2), some repressors of the gibberellin pathway, leading to the activation of the pathway. 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: 438922  Cd Length: 44  Bit Score: 38.07  E-value: 3.57e-04
                        10        20        30
                ....*....|....*....|....*....|.
gi 42569822  69 IPPDLLMEIVMRLPAKSMVRFKCISKQWSSL 99
Cdd:cd22151   3 LPDDLLQEIFKRLDPKSLARAACVCRRWRAA 33
eIF1a smart00652
eukaryotic translation initiation factor 1A;
17-56 5.61e-04

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 38.77  E-value: 5.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 42569822     17 EECQSVPQVVSLRDSDQLQIMDEKGDNSLALLPAKLPMRM 56
Cdd:smart00652   3 EDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKV 42
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 68-101 4.61e-03

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.


Pssm-ID: 438852  Cd Length: 35  Bit Score: 34.73  E-value: 4.61e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 42569822  68 EIPPDLLMEIVMRLPAKSMVRFKCISKQWSSLIS 101
Cdd:cd09917   2 DLPDEILLKILSYLDPRDLLRLSLVCKRWRELAS 35
 
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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