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Conserved domains on  [gi|2099372365|ref|NP_001012905|]
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NF-kappa-B-repressing factor [Gallus gallus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XTBD pfam11952
XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an ...
 15-99 4.97e-30

XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an XRN2-binding module. XRN2 is an essential exoribonuclease in eukaryotes that processes and degrades a number of different substrates. XTBD is found on a number of different proteins to link them to XRN, such as PAXT-1.


:

Pssm-ID: 463409  Cd Length: 85  Bit Score: 113.53  E-value: 4.97e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365  15 EQWRQYSESERHWAVRRRFILRHLHSYPgaaIDQLLALSVLWSNHVFMGCRYGSQVMEKVLKMAEGIdigeMQTFELVPS 94
Cdd:pfam11952   2 EAYRGEWESDEHWELRREFIERHKDDFP---EDRLLSLAQVFANMEFLGCRYPQEVMEKVAELAEGI----AAEVREAPK 74


                  ....*
gi 2099372365  95 KKLKR 99
Cdd:pfam11952  75 FKLTR 79
R3H_NRF cd02640
R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB ...
 681-740 8.97e-29

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


:

Pssm-ID: 100069  Cd Length: 60  Bit Score: 109.02  E-value: 8.97e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365 681 KRDIEQIIRNYAHSESHVDLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02640     1 KNDYRQIIQNYAHSDDIRDMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 528-589 7.57e-07

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member cd19875:

Pssm-ID: 444671  Cd Length: 67  Bit Score: 46.88  E-value: 7.57e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099372365 528 NPVCTLNDTAQFNKMTVEYVFER---MTGMRWKCKVLLENEFIAEAVG-VKKSVKHEAAEEAVKIL 589
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEFVDVSvgpDHCPGFTASATIDGIVFASATGtSKKEAKRAAAKLALKKL 67
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 627-670 3.80e-05

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


:

Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 41.38  E-value: 3.80e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2099372365  627 IKEDNIGNQILRKMGWTGGGLG-KDGEGIREPISVKEQFKREGLG 670
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLgKNEQGIVEPISAEIKKDRKGLG 45
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 426-487 6.49e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member smart00358:

Pssm-ID: 444671 [Multi-domain]  Cd Length: 67  Bit Score: 35.70  E-value: 6.49e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365  426 AIGILNNSASYNKMSVEYKY----DYMPNRMWRCRVYLQDHCLAEGYGT-KKTSKHTAADEALKILQ 487
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELvkeeGPDHAPRFTVTVKVGGKRTGEGEGSsKKEAKQRAAEAALRSLK 67
 
Name Accession Description Interval E-value
XTBD pfam11952
XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an ...
 15-99 4.97e-30

XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an XRN2-binding module. XRN2 is an essential exoribonuclease in eukaryotes that processes and degrades a number of different substrates. XTBD is found on a number of different proteins to link them to XRN, such as PAXT-1.


Pssm-ID: 463409  Cd Length: 85  Bit Score: 113.53  E-value: 4.97e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365  15 EQWRQYSESERHWAVRRRFILRHLHSYPgaaIDQLLALSVLWSNHVFMGCRYGSQVMEKVLKMAEGIdigeMQTFELVPS 94
Cdd:pfam11952   2 EAYRGEWESDEHWELRREFIERHKDDFP---EDRLLSLAQVFANMEFLGCRYPQEVMEKVAELAEGI----AAEVREAPK 74


                  ....*
gi 2099372365  95 KKLKR 99
Cdd:pfam11952  75 FKLTR 79
R3H_NRF cd02640
R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB ...
 681-740 8.97e-29

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100069  Cd Length: 60  Bit Score: 109.02  E-value: 8.97e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365 681 KRDIEQIIRNYAHSESHVDLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02640     1 KNDYRQIIQNYAHSDDIRDMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
662-741 5.52e-11

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 59.24  E-value: 5.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365  662 EQFKREGLGLDVERvNKIAKRDIEQIIRNYAH-SESHVDLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:smart00393   1 ADFLPVTLDALSYR-PRRREELIELELEIARFvKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISK 78


                   .
gi 2099372365  741 K 741
Cdd:smart00393  79 K 79
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 682-740 1.28e-10

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 57.50  E-value: 1.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099372365 682 RDIEQIIRNYAHSESHVdLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:pfam01424   4 EQLAEKLAEFVKDTGKS-LELPP-MSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
Jag COG1847
Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General ...
 710-742 4.71e-07

Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only];


Pssm-ID: 441452 [Multi-domain]  Cd Length: 143  Bit Score: 49.72  E-value: 4.71e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2099372365 710 ERKQIHQIAQKY-GLKSKSHGQGRDRYLVVSRKR 742
Cdd:COG1847   110 ERRIIHDALADDpGVETESEGEEPYRRVVISPKR 143
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 528-589 7.57e-07

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 46.88  E-value: 7.57e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099372365 528 NPVCTLNDTAQFNKMTVEYVFER---MTGMRWKCKVLLENEFIAEAVG-VKKSVKHEAAEEAVKIL 589
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEFVDVSvgpDHCPGFTASATIDGIVFASATGtSKKEAKRAAAKLALKKL 67
DSRM smart00358
Double-stranded RNA binding motif;
529-590 5.78e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 5.78e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365  529 PVCTLNDTAQFNKMTVEYVFERMTGM----RWKCKVLLENEFIAEAVGV-KKSVKHEAAEEAVKILK 590
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPdhapRFTVTVKVGGKRTGEGEGSsKKEAKQRAAEAALRSLK 67
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 627-670 3.80e-05

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 41.38  E-value: 3.80e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2099372365  627 IKEDNIGNQILRKMGWTGGGLG-KDGEGIREPISVKEQFKREGLG 670
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLgKNEQGIVEPISAEIKKDRKGLG 45
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 630-672 4.81e-03

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 35.56  E-value: 4.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2099372365 630 DNIGNQILRKMGWTGGGLG-KDGEGIREPISVKEQFKREGLGLD 672
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLgKNEQGIAEPIEAKIKKDRRGLGAE 45
DSRM smart00358
Double-stranded RNA binding motif;
426-487 6.49e-03

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 35.70  E-value: 6.49e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365  426 AIGILNNSASYNKMSVEYKY----DYMPNRMWRCRVYLQDHCLAEGYGT-KKTSKHTAADEALKILQ 487
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELvkeeGPDHAPRFTVTVKVGGKRTGEGEGSsKKEAKQRAAEAALRSLK 67
 
Name Accession Description Interval E-value
XTBD pfam11952
XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an ...
 15-99 4.97e-30

XRN-Two Binding Domain, XTBD; XTBD is a family of eukaryotic proteins that act as an XRN2-binding module. XRN2 is an essential exoribonuclease in eukaryotes that processes and degrades a number of different substrates. XTBD is found on a number of different proteins to link them to XRN, such as PAXT-1.


Pssm-ID: 463409  Cd Length: 85  Bit Score: 113.53  E-value: 4.97e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365  15 EQWRQYSESERHWAVRRRFILRHLHSYPgaaIDQLLALSVLWSNHVFMGCRYGSQVMEKVLKMAEGIdigeMQTFELVPS 94
Cdd:pfam11952   2 EAYRGEWESDEHWELRREFIERHKDDFP---EDRLLSLAQVFANMEFLGCRYPQEVMEKVAELAEGI----AAEVREAPK 74


                  ....*
gi 2099372365  95 KKLKR 99
Cdd:pfam11952  75 FKLTR 79
R3H_NRF cd02640
R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB ...
 681-740 8.97e-29

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100069  Cd Length: 60  Bit Score: 109.02  E-value: 8.97e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365 681 KRDIEQIIRNYAHSESHVDLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02640     1 KNDYRQIIQNYAHSDDIRDMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 681-740 3.42e-13

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 64.56  E-value: 3.42e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365 681 KRDIEQIIRNYAHSESHVDLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02325     1 REEREEELEAFAKDAAGKSLELPP-MNSYERKLIHDLAEYYGLKSESEGEGPNRRVVITK 59
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
662-741 5.52e-11

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 59.24  E-value: 5.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365  662 EQFKREGLGLDVERvNKIAKRDIEQIIRNYAH-SESHVDLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:smart00393   1 ADFLPVTLDALSYR-PRRREELIELELEIARFvKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISK 78


                   .
gi 2099372365  741 K 741
Cdd:smart00393  79 K 79
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 682-740 1.28e-10

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 57.50  E-value: 1.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099372365 682 RDIEQIIRNYAHSESHVdLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:pfam01424   4 EQLAEKLAEFVKDTGKS-LELPP-MSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
R3H_DEXH_helicase cd06007
R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may ...
 683-740 3.09e-09

R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100077  Cd Length: 59  Bit Score: 53.47  E-value: 3.09e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099372365 683 DIEQIIRNYAHSESHVdLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd06007     3 AINKALEDFRASDNEE-YEFPSSLTNHERAVIHRLCRKLGLKSKSKGKGSNRRLSVYK 59
R3H_G-patch cd02646
R3H domain of a group of fungal and plant proteins with unknown function, who also contain a ...
 683-740 4.55e-07

R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100075  Cd Length: 58  Bit Score: 47.18  E-value: 4.55e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099372365 683 DIEQIIRNYAHSESHVdLTFSTeLTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02646     3 DIKDEIEAFLLDSRDS-LSFPP-MDKHGRKTIHKLANCYNLKSKSRGKGKKRFVTVTK 58
Jag COG1847
Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General ...
 710-742 4.71e-07

Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only];


Pssm-ID: 441452 [Multi-domain]  Cd Length: 143  Bit Score: 49.72  E-value: 4.71e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2099372365 710 ERKQIHQIAQKY-GLKSKSHGQGRDRYLVVSRKR 742
Cdd:COG1847   110 ERRIIHDALADDpGVETESEGEEPYRRVVISPKR 143
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 681-740 5.40e-07

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100070  Cd Length: 60  Bit Score: 47.35  E-value: 5.40e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099372365 681 KRDIEQIIRNYAHSESHVDLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVVSR 740
Cdd:cd02641     1 VKHLKAMVKAFMKDPKATELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 528-589 7.57e-07

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 46.88  E-value: 7.57e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099372365 528 NPVCTLNDTAQFNKMTVEYVFER---MTGMRWKCKVLLENEFIAEAVG-VKKSVKHEAAEEAVKIL 589
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEFVDVSvgpDHCPGFTASATIDGIVFASATGtSKKEAKRAAAKLALKKL 67
R3H_jag cd02644
R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with ...
 706-741 2.38e-06

R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100073  Cd Length: 67  Bit Score: 45.54  E-value: 2.38e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2099372365 706 LTNDERKQIHQIAQKY-GLKSKSHGQGRDRYLVVSRK 741
Cdd:cd02644    31 MNAYERRIIHDALANDeDVETESEGEGPYRRVVISPK 67
DSRM smart00358
Double-stranded RNA binding motif;
529-590 5.78e-06

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 44.56  E-value: 5.78e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365  529 PVCTLNDTAQFNKMTVEYVFERMTGM----RWKCKVLLENEFIAEAVGV-KKSVKHEAAEEAVKILK 590
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELVKEEGPdhapRFTVTVKVGGKRTGEGEGSsKKEAKQRAAEAALRSLK 67
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 627-670 3.80e-05

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 41.38  E-value: 3.80e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2099372365  627 IKEDNIGNQILRKMGWTGGGLG-KDGEGIREPISVKEQFKREGLG 670
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLgKNEQGIVEPISAEIKKDRKGLG 45
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 528-589 1.93e-03

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 37.54  E-value: 1.93e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365 528 NPVCTLNDTAQFNKMTVEYVFERMTGM----RWKCKVLLEN-EFIAEAVGVKKSVKHEAAEEAVKIL 589
Cdd:cd19913     2 NPVSGLMEYAQFLGQTCEFLLLEQSGPshdpRFKFQAVIDGrRFPPAEASSKKVAKKDAAAIALKIL 68
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 528-585 2.53e-03

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 36.86  E-value: 2.53e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099372365 528 NPVCTLNDTAQFNKMTVEYVFERMTG------MRWKCKVLLENEFIAEAVGVKKsVKHEAAEEA 585
Cdd:cd19857     1 TPMCLLNELARFNKIRPQYTLVDEEGpahkktFTVKLTLGDEEEYEASGSSIKK-AQHAAAEKA 63
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 630-672 4.81e-03

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 35.56  E-value: 4.81e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2099372365 630 DNIGNQILRKMGWTGGGLG-KDGEGIREPISVKEQFKREGLGLD 672
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLgKNEQGIAEPIEAKIKKDRRGLGAE 45
DSRM smart00358
Double-stranded RNA binding motif;
426-487 6.49e-03

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 35.70  E-value: 6.49e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099372365  426 AIGILNNSASYNKMSVEYKY----DYMPNRMWRCRVYLQDHCLAEGYGT-KKTSKHTAADEALKILQ 487
Cdd:smart00358   1 PKSLLQELAQKRKLPPEYELvkeeGPDHAPRFTVTVKVGGKRTGEGEGSsKKEAKQRAAEAALRSLK 67
R3H_RRM cd02639
R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) ...
 699-738 9.35e-03

R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100068  Cd Length: 60  Bit Score: 35.35  E-value: 9.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2099372365 699 DLTFSTELTNDERKQIHQIAQKYGLKSKSHGQGRDRYLVV 738
Cdd:cd02639    19 ELAFPSSLSPAERRIVHLLASRLGLNHVSDGTGERRQVQI 58
 
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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