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Conserved domains on  [gi|1497483253|gb|RMB98362|]
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hypothetical protein DUI87_25268 [Hirundo rustica rustica]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH_I_FMR1_rpt1 cd22506
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 99-175 5.47e-49

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411934  Cd Length: 77  Bit Score: 165.14  E-value: 5.47e-49
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22506     1 KDTFHKIKLDVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 77
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 257-376 1.84e-42

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


:

Pssm-ID: 411940 [Multi-domain]  Cd Length: 78  Bit Score: 147.41  E-value: 1.84e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEElsihtsvspvndisktgtacaascvscvmp 336
Cdd:cd22512     1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1497483253 337 gaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22512    51 ------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 194-256 2.90e-42

second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411937  Cd Length: 63  Bit Score: 146.70  E-value: 2.90e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253 194 RFHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22509     1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 6.93e-37

first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410542  Cd Length: 55  Bit Score: 131.59  E-value: 6.93e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPPAGY 55
Cdd:cd20471     1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 372-442 9.08e-30

Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.


:

Pssm-ID: 463501  Cd Length: 129  Bit Score: 114.16  E-value: 9.08e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1497483253 372 HLNYLKEVDQLRLERLQIDEQLRQIGATSRPPPNRT-DKDKGYMTDDGPGLGRGS----RPYRNRGHSRRGPGYAS 442
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTS 76
Tudor_SF super family cl02573
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 66-102 7.90e-18

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


The actual alignment was detected with superfamily member cd20476:

Pssm-ID: 470623  Cd Length: 68  Bit Score: 78.18  E-value: 7.90e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1497483253  66 EFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 102
Cdd:cd20476    32 DFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68
 
Name Accession Description Interval E-value
KH_I_FMR1_rpt1 cd22506
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 99-175 5.47e-49

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411934  Cd Length: 77  Bit Score: 165.14  E-value: 5.47e-49
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22506     1 KDTFHKIKLDVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 77
KH_9 pfam17904
FMRP KH0 domain; This entry corresponds to the KH0 domain from the FMRP protein. This is a ...
 99-183 4.02e-45

FMRP KH0 domain; This entry corresponds to the KH0 domain from the FMRP protein. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein. KH0 does not have the canonical G-X-X-G motif between helices A and B. It has been suggested that this domain may be involved in RNA binding.


Pssm-ID: 436130  Cd Length: 85  Bit Score: 154.94  E-value: 4.02e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLILRN 178
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80


                  ....*
gi 1497483253 179 EEASK 183
Cdd:pfam17904  81 EEAAK 85
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 257-376 1.84e-42

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411940 [Multi-domain]  Cd Length: 78  Bit Score: 147.41  E-value: 1.84e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEElsihtsvspvndisktgtacaascvscvmp 336
Cdd:cd22512     1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1497483253 337 gaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22512    51 ------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 194-256 2.90e-42

second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411937  Cd Length: 63  Bit Score: 146.70  E-value: 2.90e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253 194 RFHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22509     1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 6.93e-37

first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410542  Cd Length: 55  Bit Score: 131.59  E-value: 6.93e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPPAGY 55
Cdd:cd20471     1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
Tudor_FRX1 pfam18336
Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in ...
 4-52 1.77e-31

Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in Fragile X mental retardation syndrome-related protein 1 (Fxr1). The Tud1 domain forms a canonical Tudor barrel. It is usually found in tandem with Agenet domain pfam05641.


Pssm-ID: 408142  Cd Length: 49  Bit Score: 116.03  E-value: 1.77e-31
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1497483253   4 LVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 372-442 9.08e-30

Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.


Pssm-ID: 463501  Cd Length: 129  Bit Score: 114.16  E-value: 9.08e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1497483253 372 HLNYLKEVDQLRLERLQIDEQLRQIGATSRPPPNRT-DKDKGYMTDDGPGLGRGS----RPYRNRGHSRRGPGYAS 442
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTS 76
Tudor_Agenet_FXR2_rpt2 cd20476
second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 66-102 7.90e-18

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410547  Cd Length: 68  Bit Score: 78.18  E-value: 7.90e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1497483253  66 EFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 102
Cdd:cd20476    32 DFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 262-318 1.85e-06

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 45.74  E-value: 1.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEaENDKNIPQEELSIHTSVSPVND 318
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETG-AKIQIP-PSESEGNERIVTITGTPEAVEA 58
KH smart00322
K homology RNA-binding domain;
259-302 2.85e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 44.98  E-value: 2.85e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1497483253  259 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENDKNI 302
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVkIDIPGPGSEERVV 48
KH smart00322
K homology RNA-binding domain;
197-256 1.47e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 40.36  E-value: 1.47e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253  197 EQFVVREDLMGLAIGTHGANIQQARKVPGVTaIDLDEDTC---TFHIYGEDQDaVKKARSYLE 256
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVK-IDIPGPGSeerVVEITGPPEN-VEKAAELIL 65
PRK13764 PRK13764
ATPase; Provisional
 261-306 7.25e-04

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 42.52  E-value: 7.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1497483253 261 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENDKNIPQEE 306
Cdd:PRK13764  484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIdIDVRPLDEEPGEEAEEG 530
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 197-256 9.01e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 35.33  E-value: 9.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253 197 EQFVVREDLMGLAIGTHGANIQQARKVPGVTaIDL-----DEDTCTFHIYGeDQDAVKKARSYLE 256
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAK-IQIppsesEGNERIVTITG-TPEAVEAAKALIE 64
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 199-285 9.15e-03

NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.


Pssm-ID: 273892  Cd Length: 141  Bit Score: 37.00  E-value: 9.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 199 FVVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDEDTCTFhIYGEDQDAVKKARSYLEFAED---VIQVPRNLVGKVI 273
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 1497483253 274 GKNGKLIQEIVD 285
Cdd:TIGR01952 116 GKGGKNIERAKE 127
 
Name Accession Description Interval E-value
KH_I_FMR1_rpt1 cd22506
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 99-175 5.47e-49

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411934  Cd Length: 77  Bit Score: 165.14  E-value: 5.47e-49
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22506     1 KDTFHKIKLDVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 77
KH_9 pfam17904
FMRP KH0 domain; This entry corresponds to the KH0 domain from the FMRP protein. This is a ...
 99-183 4.02e-45

FMRP KH0 domain; This entry corresponds to the KH0 domain from the FMRP protein. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein. KH0 does not have the canonical G-X-X-G motif between helices A and B. It has been suggested that this domain may be involved in RNA binding.


Pssm-ID: 436130  Cd Length: 85  Bit Score: 154.94  E-value: 4.02e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLILRN 178
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80


                  ....*
gi 1497483253 179 EEASK 183
Cdd:pfam17904  81 EEAAK 85
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 257-376 1.84e-42

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411940 [Multi-domain]  Cd Length: 78  Bit Score: 147.41  E-value: 1.84e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEElsihtsvspvndisktgtacaascvscvmp 336
Cdd:cd22512     1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1497483253 337 gaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22512    51 ------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 194-256 2.90e-42

second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411937  Cd Length: 63  Bit Score: 146.70  E-value: 2.90e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253 194 RFHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22509     1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 6.93e-37

first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410542  Cd Length: 55  Bit Score: 131.59  E-value: 6.93e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPPAGY 55
Cdd:cd20471     1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
KH_I_FMR1_FXR_rpt1 cd22425
first type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 99-175 6.37e-36

first type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411853  Cd Length: 77  Bit Score: 129.27  E-value: 6.37e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22425     1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77
KH_I_FXR1_rpt2 cd22507
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 195-256 4.58e-35

second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411935  Cd Length: 63  Bit Score: 126.66  E-value: 4.58e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1497483253 195 FHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22507     2 FHEEFTVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESAEAVKKARSYLE 63
KH_I_FXR2_rpt2 cd22508
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 195-256 2.65e-34

second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411936  Cd Length: 63  Bit Score: 124.41  E-value: 2.65e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1497483253 195 FHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22508     2 FQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELDEETCTFRIYGETPEAVKQARSYLE 63
KH_I_FXR2_rpt3 cd22511
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 257-376 6.25e-33

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411939 [Multi-domain]  Cd Length: 78  Bit Score: 121.25  E-value: 6.25e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEElsihtsvspvndisktgtacaascvscvmp 336
Cdd:cd22511     1 FSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREE------------------------------ 50

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1497483253 337 gaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22511    51 ------------GMVPFIFVGTKENISNAQALLEYHLSYL 78
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 195-256 8.43e-33

second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411854 [Multi-domain]  Cd Length: 63  Bit Score: 120.33  E-value: 8.43e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1497483253 195 FHEQFVVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd22426     2 FIEEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIDVDEEDGTFRIYGETPEAVEKARALLE 63
KH_I_FXR1_rpt3 cd22510
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 257-376 3.45e-32

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411938 [Multi-domain]  Cd Length: 78  Bit Score: 118.92  E-value: 3.45e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEElsihtsvspvndisktgtacaascvscvmp 336
Cdd:cd22510     1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPRED------------------------------ 50

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1497483253 337 gaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22510    51 ------------GMVPFVFVGTKESIGNVQVLLEYHIAYL 78
Tudor_Agenet_FXR2_rpt1 cd20473
first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 4-57 5.82e-32

first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410544  Cd Length: 55  Bit Score: 117.79  E-value: 5.82e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1497483253   4 LVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPPAGYNK 57
Cdd:cd20473     2 LAVEVRGSNGAFYKGFIKDVHEDSVTIFFENNWQPERQIPFGDVRLPPPADYHK 55
Tudor_FRX1 pfam18336
Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in ...
 4-52 1.77e-31

Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in Fragile X mental retardation syndrome-related protein 1 (Fxr1). The Tud1 domain forms a canonical Tudor barrel. It is usually found in tandem with Agenet domain pfam05641.


Pssm-ID: 408142  Cd Length: 49  Bit Score: 116.03  E-value: 1.77e-31
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1497483253   4 LVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49
KH_I_FMR1_FXR_rpt3 cd22427
third type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 257-376 6.93e-31

third type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411855 [Multi-domain]  Cd Length: 79  Bit Score: 115.40  E-value: 6.93e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAEN-DKNIPQEElsihtsvspvndisktgtacaascvscvm 335
Cdd:cd22427     1 FAEEIFQVPRDLVGKVIGKNGRVIQEIVDKSGVVRVKIEGDNeDGPRPREE----------------------------- 51

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1497483253 336 pgaiqtpeirlkqGMVPFVFVGTKDSITNATVLLDYHLNYL 376
Cdd:cd22427    52 -------------GLVPFIFVGTREAIANAKLLLEYHLAHL 79
Tudor_Agenet_FXR1_rpt1 cd20472
first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 3-57 1.42e-30

first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410543  Cd Length: 55  Bit Score: 113.95  E-value: 1.42e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253   3 ELVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPPAGYNK 57
Cdd:cd20472     1 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 55
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 372-442 9.08e-30

Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.


Pssm-ID: 463501  Cd Length: 129  Bit Score: 114.16  E-value: 9.08e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1497483253 372 HLNYLKEVDQLRLERLQIDEQLRQIGATSRPPPNRT-DKDKGYMTDDGPGLGRGS----RPYRNRGHSRRGPGYAS 442
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTS 76
KH_I_FXR2_rpt1 cd22505
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 99-175 5.40e-28

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411933  Cd Length: 77  Bit Score: 107.26  E-value: 5.40e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22505     1 KNSFFKVTIAVPEDLKEACSNENVHKEFKKAIGANCIFFNTSNNELIILSTNESTVKRASLLSDMHFRSIRTKLMLM 77
Tudor_Agenet_FMRP-like_rpt1 cd20402
first Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; ...
 3-52 6.28e-28

first Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1), and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410473  Cd Length: 50  Bit Score: 106.17  E-value: 6.28e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1497483253   3 ELVVEVRGSNGAFYKAFVKDVHEDSITVSFENNWQPERQIPFHDVRFPPP 52
Cdd:cd20402     1 DLAVEVRGPNGAYYKAFVKDVHEDEVTVAFENDWQPERKVPFSDVRLPPP 50
KH_I_FXR1_rpt1 cd22504
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 99-175 3.00e-26

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411932  Cd Length: 77  Bit Score: 102.26  E-value: 3.00e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253  99 KDTFHKIKLAVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENHQLIILSINDVTTKRANMLIDMHFRSLRTKLSLI 175
Cdd:cd22504     1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77
Tudor_Agenet_FXR2_rpt2 cd20476
second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 66-102 7.90e-18

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410547  Cd Length: 68  Bit Score: 78.18  E-value: 7.90e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1497483253  66 EFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 102
Cdd:cd20476    32 DFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68
Tudor_Agenet_FMR1_rpt2 cd20474
second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 58-96 9.45e-18

second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410545  Cd Length: 63  Bit Score: 77.77  E-value: 9.45e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253  58 DINESDEVE------------------------FYVIEYAACDATYNEIVTIERLRSVNPNKP 96
Cdd:cd20474     1 DINESDEVEvysranekepccwwlakvrmikgeFYVIEYAACDATYNEIVTIERLRSVNPNKP 63
Tudor_Agenet_FXR1_rpt2 cd20475
second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 66-102 2.71e-17

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410546  Cd Length: 66  Bit Score: 76.23  E-value: 2.71e-17
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1497483253  66 EFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 102
Cdd:cd20475    30 EFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 262-318 1.85e-06

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 45.74  E-value: 1.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEaENDKNIPQEELSIHTSVSPVND 318
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETG-AKIQIP-PSESEGNERIVTITGTPEAVEA 58
KH smart00322
K homology RNA-binding domain;
259-302 2.85e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 44.98  E-value: 2.85e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1497483253  259 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENDKNI 302
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVkIDIPGPGSEERVV 48
Tudor_Agenet_FMRP-like_rpt2 cd20403
second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) ...
 66-89 5.44e-06

second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1) and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410474  Cd Length: 50  Bit Score: 43.85  E-value: 5.44e-06
                          10        20
                  ....*....|....*....|....
gi 1497483253  66 EFYVIEYAACDATYNEIVTIERLR 89
Cdd:cd20403    26 EFYVVEFPGFDETYTEIVELERLR 49
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 192-256 3.63e-05

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 42.08  E-value: 3.63e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253 192 ASRFHeQFVVREDLMGLAIGTHGANIQQARKVPGVTaIDLDEDtCTFHIYGEDQDAVKKARSYLE 256
Cdd:cd02393     2 APRIT-TIKIPPDKIGDVIGPGGKTIRAIIEETGAK-IDIEDD-GTVTIFATDKESAEAAKAMIE 63
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 260-301 6.97e-05

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 41.13  E-value: 6.97e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1497483253 260 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKN 301
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETG-ARIQIPKEGEGS 41
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 261-307 1.29e-04

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411874 [Multi-domain]  Cd Length: 86  Bit Score: 40.85  E-value: 1.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1497483253 261 VIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKNIPQEEL 307
Cdd:cd22446    10 TISVPSSVRGAIIGSRGKNLKSIQDKTG-TKIQIPKRNEEGNYDEDD 55
KH smart00322
K homology RNA-binding domain;
197-256 1.47e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 40.36  E-value: 1.47e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1497483253  197 EQFVVREDLMGLAIGTHGANIQQARKVPGVTaIDLDEDTC---TFHIYGEDQDaVKKARSYLE 256
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVK-IDIPGPGSeerVVEITGPPEN-VEKAAELIL 65
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 262-295 1.54e-04

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 40.15  E-value: 1.54e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIE 295
Cdd:cd02393     8 IKIPPDKIGDVIGPGGKTIRAIIEETG-AKIDIE 40
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 261-289 2.06e-04

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.


Pssm-ID: 411823 [Multi-domain]  Cd Length: 68  Bit Score: 39.81  E-value: 2.06e-04
                          10        20
                  ....*....|....*....|....*....
gi 1497483253 261 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV 289
Cdd:cd22395     3 EFEVPSELVGRLIGKQGRNVKQLKQKSGA 31
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 262-311 2.52e-04

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 39.53  E-value: 2.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSG-VVRVRIEAENDKNipqEELSIHT 311
Cdd:cd22403     4 IRVPSSMVGRIIGKGGQNVRELQRLTGaIIKLPRDQTPDEG---DEVPVEI 51
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 257-301 3.62e-04

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 39.09  E-value: 3.62e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1497483253 257 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKN 301
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESG-VSIRIPDDEANS 44
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 262-301 4.23e-04

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411867 [Multi-domain]  Cd Length: 68  Bit Score: 39.14  E-value: 4.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVrVRIEAENDKN 301
Cdd:cd22439     6 ITIPNDLIGCIIGKGGTKINEIRQLSGAT-IKIANSEDGS 44
PRK13764 PRK13764
ATPase; Provisional
 261-306 7.25e-04

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 42.52  E-value: 7.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1497483253 261 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENDKNIPQEE 306
Cdd:PRK13764  484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIdIDVRPLDEEPGEEAEEG 530
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 262-294 1.09e-03

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 37.94  E-value: 1.09e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRI 294
Cdd:cd09031     5 LEVPENLVGAILGKGGKTLVEIQELTG-ARIQI 36
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 262-307 2.05e-03

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 37.40  E-value: 2.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKNIPQEEL 307
Cdd:cd22447     8 VPIPASTRARIIGKKGANLKQIREKTG-VRIDIPPRDADAAPADED 52
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 262-308 2.06e-03

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411914  Cd Length: 70  Bit Score: 37.24  E-value: 2.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENDKNIPQEELS 308
Cdd:cd22486     7 VSVPRFAVGIVIGRNGEMIKKIQNDAG---VRIQFKPDDGISPERVA 50
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 260-298 2.67e-03

second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411854 [Multi-domain]  Cd Length: 63  Bit Score: 36.74  E-value: 2.67e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1497483253 260 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAEN 298
Cdd:cd22426     4 EEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIDVDEED 42
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 264-335 5.93e-03

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 35.66  E-value: 5.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1497483253 264 VPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKNIPQEELSIhtsvspvndiskTGTACAASCVSCVM 335
Cdd:cd22437     5 VPNSSCGLIIGKGGSTIKELREDSN-ANIKISPKDQLLPGSSERIV------------TITGSFDQVVKAVA 63
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 262-305 6.30e-03

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 35.70  E-value: 6.30e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENDKNIPQE 305
Cdd:cd22398     4 VPVPRFAVGVVIGKGGEMIKKIQNETG---ARVQFKPDDGNSPD 44
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 262-317 6.55e-03

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 35.77  E-value: 6.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1497483253 262 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAEnDKNIPQEELSIHTSVSPVN 317
Cdd:cd22428     9 MKVPREAVGLIIGRQGATIKQIQKETG-ARIDFKDE-GSGGELPERVLLIQGNPVQ 62
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 197-256 9.01e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 35.33  E-value: 9.01e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1497483253 197 EQFVVREDLMGLAIGTHGANIQQARKVPGVTaIDL-----DEDTCTFHIYGeDQDAVKKARSYLE 256
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAK-IQIppsesEGNERIVTITG-TPEAVEAAKALIE 64
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 199-285 9.15e-03

NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.


Pssm-ID: 273892  Cd Length: 141  Bit Score: 37.00  E-value: 9.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1497483253 199 FVVREDLMGLAIGTHGANIQQARKVPG--VTAIDLDEDTCTFhIYGEDQDAVKKARSYLEFAED---VIQVPRNLVGKVI 273
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 1497483253 274 GKNGKLIQEIVD 285
Cdd:TIGR01952 116 GKGGKNIERAKE 127
 
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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