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Conserved domains on  [gi|147812093|emb|CAN74740|]
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hypothetical protein VITISV_040899 [Vitis vinifera]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
481-544 3.15e-17

RNase H-like domain found in reverse transcriptase;


:

Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 77.15  E-value: 3.15e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093  481 EVANKAFEEIKSKMVNPSILRLPNFEKVVEVACDASHMGIGVVLSQDG-----HLVAFFSDKLNGAKKK 544
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERN 71
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 12-47 1.60e-16

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: 73.09  E-value: 1.60e-16
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 147812093  12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLWA 47
Cdd:cd22160    1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
387-455 1.30e-12

domain in FBox and BRCT domain containing plant proteins;


:

Pssm-ID: 214730  Cd Length: 72  Bit Score: 63.32  E-value: 1.30e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093   387 CLVLHLKEIEIRRIVGEDYELEAVEYLLKNAEVLQQMTIDCHESYMDQEFCVCKKLLGLPRGSRSCFVV 455
Cdd:smart00579   2 CLLSSLEVLEIKGYRGTEEEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQ 70
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 164-189 3.91e-07

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: 46.22  E-value: 3.91e-07
                          10        20
                  ....*....|....*....|....*.
gi 147812093  164 SLKALHLKSVEYSDDDSIQKLLSGCP 189
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGCP 26
 
Name Accession Description Interval E-value
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
481-544 3.15e-17

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 77.15  E-value: 3.15e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093  481 EVANKAFEEIKSKMVNPSILRLPNFEKVVEVACDASHMGIGVVLSQDG-----HLVAFFSDKLNGAKKK 544
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERN 71
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 12-47 1.60e-16

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: 73.09  E-value: 1.60e-16
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 147812093  12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLWA 47
Cdd:cd22160    1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
387-455 1.30e-12

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 63.32  E-value: 1.30e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093   387 CLVLHLKEIEIRRIVGEDYELEAVEYLLKNAEVLQQMTIDCHESYMDQEFCVCKKLLGLPRGSRSCFVV 455
Cdd:smart00579   2 CLLSSLEVLEIKGYRGTEEEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQ 70
FBD pfam08387
FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it ...
 381-425 5.28e-09

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: 51.95  E-value: 5.28e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 147812093  381 PLQVPACLVLHLKEIEIRRIVGEDYELEAVEYLLKNAEVLQQMTI 425
Cdd:pfam08387   1 PSSVPECLLSSLETVEWRGYRGEEEEKEFAKYILENARVLKKATI 45
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 164-189 3.91e-07

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: 46.22  E-value: 3.91e-07
                          10        20
                  ....*....|....*....|....*.
gi 147812093  164 SLKALHLKSVEYSDDDSIQKLLSGCP 189
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGCP 26
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 12-52 6.15e-07

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: 45.99  E-value: 6.15e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 147812093   12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLWASVPIL 52
Cdd:pfam00646   1 LLDLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKLW 41
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 510-544 9.38e-06

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 45.18  E-value: 9.38e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 147812093 510 EVACDASHMGIGVVLSQD-----GHLVAFFSDKLNGAKKK 544
Cdd:cd09274    1 ILETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERN 40
FBOX smart00256
A Receptor for Ubiquitination Targets;
15-51 2.16e-04

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 38.96  E-value: 2.16e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 147812093    15 LPDELLCHILSFLPTKFAVGTSILSKRWRYLWASVPI 51
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDF 37
 
Name Accession Description Interval E-value
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
481-544 3.15e-17

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 77.15  E-value: 3.15e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093  481 EVANKAFEEIKSKMVNPSILRLPNFEKVVEVACDASHMGIGVVLSQDG-----HLVAFFSDKLNGAKKK 544
Cdd:pfam17919   3 EECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERN 71
F-box_AtFBL13-like cd22160
F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) ...
 12-47 1.60e-16

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: 73.09  E-value: 1.60e-16
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 147812093  12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLWA 47
Cdd:cd22160    1 ISDLPDELLCHILSFLPTKDAVKTSVLSKRWRHLWR 36
FBD smart00579
domain in FBox and BRCT domain containing plant proteins;
387-455 1.30e-12

domain in FBox and BRCT domain containing plant proteins;


Pssm-ID: 214730  Cd Length: 72  Bit Score: 63.32  E-value: 1.30e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147812093   387 CLVLHLKEIEIRRIVGEDYELEAVEYLLKNAEVLQQMTIDCHESYMDQEFCVCKKLLGLPRGSRSCFVV 455
Cdd:smart00579   2 CLLSSLEVLEIKGYRGTEEEKELVKYFLENAPCLKKLTISVETSDDEEKLEILKELLSLPRASSSCQVQ 70
FBD pfam08387
FBD; This region is found in F-box (pfam00646) and other domain containing plant proteins; it ...
 381-425 5.28e-09

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: 51.95  E-value: 5.28e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 147812093  381 PLQVPACLVLHLKEIEIRRIVGEDYELEAVEYLLKNAEVLQQMTI 425
Cdd:pfam08387   1 PSSVPECLLSSLETVEWRGYRGEEEEKEFAKYILENARVLKKATI 45
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 504-560 2.15e-07

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 49.43  E-value: 2.15e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 147812093  504 NFEKVVEVACDASHMGIGVVLSQDG-----HLVAFFSDKLNGAKKKNTPH--MILNSMWWCKKL 560
Cdd:pfam17917   1 DPSKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTekELLAIVWALKKF 64
LRR_2 pfam07723
Leucine Rich Repeat; This Pfam entry includes some LRRs that fail to be detected with the ...
 164-189 3.91e-07

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: 46.22  E-value: 3.91e-07
                          10        20
                  ....*....|....*....|....*.
gi 147812093  164 SLKALHLKSVEYSDDDSIQKLLSGCP 189
Cdd:pfam07723   1 SLKTLHLDSVVFSDEDSLEKLLSGCP 26
F-box pfam00646
F-box domain; This domain is approximately 50 amino acids long, and is usually found in the ...
 12-52 6.15e-07

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: 45.99  E-value: 6.15e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 147812093   12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLWASVPIL 52
Cdd:pfam00646   1 LLDLPDDLLLEILSRLDPKDLLRLSLVSKRWRSLVDSLKLW 41
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 510-544 9.38e-06

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 45.18  E-value: 9.38e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 147812093 510 EVACDASHMGIGVVLSQD-----GHLVAFFSDKLNGAKKK 544
Cdd:cd09274    1 ILETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERN 40
FBOX smart00256
A Receptor for Ubiquitination Targets;
15-51 2.16e-04

A Receptor for Ubiquitination Targets;


Pssm-ID: 197608  Cd Length: 41  Bit Score: 38.96  E-value: 2.16e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 147812093    15 LPDELLCHILSFLPTKFAVGTSILSKRWRYLWASVPI 51
Cdd:smart00256   1 LPDEILEEILSKLDPKDLLRLRKVSRKWRSLIDSHDF 37
F-box-like pfam12937
F-box-like; This is an F-box-like family.
 12-59 8.90e-04

F-box-like; This is an F-box-like family.


Pssm-ID: 463757 [Multi-domain]  Cd Length: 45  Bit Score: 37.46  E-value: 8.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 147812093   12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYLwAsvpildFDDELW 59
Cdd:pfam12937   1 LSSLPDEILLQIFSYLDPKDLLRLALVCRRWREL-A------SDDSLW 41
F-box_SF cd09917
F-box domain superfamily; This short domain is commonly found at the N-terminus of various ...
 13-45 4.11e-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: 35.11  E-value: 4.11e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 147812093  13 SNLPDELLCHILSFLPTKFAVGTSILSKRWRYL 45
Cdd:cd09917    1 SDLPDEILLKILSYLDPRDLLRLSLVCKRWREL 33
F-box_FBXL12 cd22123
F-box domain found in F-box/LRR-repeat protein 12 (FBXL12) and similar proteins; FBXL12, also ...
 12-45 7.65e-03

F-box domain found in F-box/LRR-repeat protein 12 (FBXL12) and similar proteins; FBXL12, also called F-box and leucine-rich repeat protein 12, or F-box protein FBL12, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It mediates the polyubiquitination and proteasomal degradation of calcium/calmodulin dependent protein kinase I (CAMK1) leading to disruption of cyclin D1/CDK4 complex assembly, which results in G1 cell cycle arrest in lung epithelia. It regulates T-cell differentiation in a cell-autonomous manner. 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: 438895  Cd Length: 42  Bit Score: 34.63  E-value: 7.65e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 147812093  12 ISNLPDELLCHILSFLPTKFAVGTSILSKRWRYL 45
Cdd:cd22123    1 LDQLPENVLLEILSYLPVRDLLRISRVCKRWRRL 34
 
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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