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Conserved domains on  [gi|30794228|ref|NP_434691|]
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fragile X messenger ribonucleoprotein 1 isoform 2 [Rattus norvegicus]

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 ...
 123-199 1.83e-50

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: 168.22  E-value: 1.83e-50
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
Cdd:cd22506   1 KDTFHKIKLDVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 77
Tudor_Agenet_FMR1_rpt2 cd20474
second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 58-120 1.16e-44

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: 152.11  E-value: 1.16e-44
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228  58 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 120
Cdd:cd20474   1 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 63
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 218-280 1.24e-41

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: 144.00  E-value: 1.24e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228 218 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd22509   1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 398-491 8.73e-41

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: 144.21  E-value: 8.73e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   398 HLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRT-DKEKGYVTDDGQGMGRGS----RPYRNRGHGRRGPGYTS---- 468
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTSgygt 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 30794228   469 ----------ESDHRDELSDWSLAPTEEERESF 491
Cdd:pfam12235  81 nselsnasetESERRDELSDWSLAGTERERGPR 113
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 281-402 2.74e-40

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: 140.86  E-value: 2.74e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22512   1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqrGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22512  51 --------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 3.61e-36

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: 128.89  E-value: 3.61e-36
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
Cdd:cd20471   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
FXMR_C2 super family cl24613
Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly ...
 516-581 1.47e-23

Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly conserved region at the very C-terminus of Fragile X-related proteins FMR1. The family is found in association with pfam05641, pfam00013, PF16096.


The actual alignment was detected with superfamily member pfam16098:

Pssm-ID: 465020  Cd Length: 86  Bit Score: 94.60  E-value: 1.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   516 FKGNDDHSRTDNRPRNPRETKGRTTDGSLQ-------------------STSSEGSRLRTGKDRNQKKEKPDSVDGLQPL 576
Cdd:pfam16098   2 FKGNDDMQWSDSRPRNSRDPKPRPQEDSLQirvdsnnersvhtktlqnsSGDSGGSRQRPGKDRGQKKEKQDGQDGPQVL 81


                  ....*
gi 30794228   577 VNGVP 581
Cdd:pfam16098  82 VNGVS 86
 
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 ...
 123-199 1.83e-50

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: 168.22  E-value: 1.83e-50
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
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 ...
 123-207 9.19e-46

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: 156.10  E-value: 9.19e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLILRN 202
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80


                  ....*
gi 30794228   203 EEASK 207
Cdd:pfam17904  81 EEAAK 85
Tudor_Agenet_FMR1_rpt2 cd20474
second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 58-120 1.16e-44

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: 152.11  E-value: 1.16e-44
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228  58 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 120
Cdd:cd20474   1 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 63
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 218-280 1.24e-41

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: 144.00  E-value: 1.24e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228 218 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd22509   1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 398-491 8.73e-41

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: 144.21  E-value: 8.73e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   398 HLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRT-DKEKGYVTDDGQGMGRGS----RPYRNRGHGRRGPGYTS---- 468
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTSgygt 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 30794228   469 ----------ESDHRDELSDWSLAPTEEERESF 491
Cdd:pfam12235  81 nselsnasetESERRDELSDWSLAGTERERGPR 113
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 281-402 2.74e-40

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: 140.86  E-value: 2.74e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22512   1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqrGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22512  51 --------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 3.61e-36

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: 128.89  E-value: 3.61e-36
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 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 2.04e-30

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: 112.95  E-value: 2.04e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30794228     4 LVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49
FXMR_C2 pfam16098
Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly ...
 516-581 1.47e-23

Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly conserved region at the very C-terminus of Fragile X-related proteins FMR1. The family is found in association with pfam05641, pfam00013, PF16096.


Pssm-ID: 465020  Cd Length: 86  Bit Score: 94.60  E-value: 1.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   516 FKGNDDHSRTDNRPRNPRETKGRTTDGSLQ-------------------STSSEGSRLRTGKDRNQKKEKPDSVDGLQPL 576
Cdd:pfam16098   2 FKGNDDMQWSDSRPRNSRDPKPRPQEDSLQirvdsnnersvhtktlqnsSGDSGGSRQRPGKDRGQKKEKQDGQDGPQVL 81


                  ....*
gi 30794228   577 VNGVP 581
Cdd:pfam16098  82 VNGVS 86
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 286-331 1.27e-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: 1.27e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30794228   286 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENEKSVPQEEE 331
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETG---AKIQIPPSESEGNERI 46
KH smart00322
K homology RNA-binding domain;
283-326 2.39e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.36  E-value: 2.39e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 30794228    283 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKSV 326
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVkIDIPGPGSEERVV 48
KH smart00322
K homology RNA-binding domain;
221-280 5.25e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 41.51  E-value: 5.25e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228    221 EQFIVREDLMGLAIGTHGANIQQARKVPGVTaIDLDEDTC---TFHIYGEDQDaVKKARSFLE 280
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVK-IDIPGPGSeerVVEITGPPEN-VEKAAELIL 65
Agenet pfam05641
Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the ...
 63-117 5.96e-05

Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins.


Pssm-ID: 461700  Cd Length: 61  Bit Score: 41.15  E-value: 5.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30794228    63 DEVEVYSRANEKEpCCWWLAKV-RMIKGEFYVIEYAACD-----ATYNEIVTIERLRSVNP 117
Cdd:pfam05641   2 DKVEVLSDEEGFR-GAWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61
PRK13764 PRK13764
ATPase; Provisional
 285-331 1.47e-04

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 44.83  E-value: 1.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 30794228  285 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKSVPQEEE 331
Cdd:PRK13764 484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIdIDVRPLDEEPGEEAEEGE 531
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 221-280 6.09e-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: 6.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   221 EQFIVREDLMGLAIGTHGANIQQARKVPGVTaIDL-----DEDTCTFHIYGeDQDAVKKARSFLE 280
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAK-IQIppsesEGNERIVTITG-TPEAVEAAKALIE 64
 
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 ...
 123-199 1.83e-50

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: 168.22  E-value: 1.83e-50
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
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 ...
 123-207 9.19e-46

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: 156.10  E-value: 9.19e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLILRN 202
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80


                  ....*
gi 30794228   203 EEASK 207
Cdd:pfam17904  81 EEAAK 85
Tudor_Agenet_FMR1_rpt2 cd20474
second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 58-120 1.16e-44

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: 152.11  E-value: 1.16e-44
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228  58 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 120
Cdd:cd20474   1 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 63
KH_I_FMR1_rpt2 cd22509
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 218-280 1.24e-41

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: 144.00  E-value: 1.24e-41
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228 218 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd22509   1 RFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63
FXMRP1_C_core pfam12235
Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is ...
 398-491 8.73e-41

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: 144.21  E-value: 8.73e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   398 HLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRT-DKEKGYVTDDGQGMGRGS----RPYRNRGHGRRGPGYTS---- 468
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRpPKEKGYTTDNGESASSGSlhgsRSYGGRGRGRRGGGYTSgygt 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 30794228   469 ----------ESDHRDELSDWSLAPTEEERESF 491
Cdd:pfam12235  81 nselsnasetESERRDELSDWSLAGTERERGPR 113
KH_I_FMR1_rpt3 cd22512
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein ...
 281-402 2.74e-40

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: 140.86  E-value: 2.74e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22512   1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEE------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqrGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22512  51 --------------GMVPFVFVGTKDSITNATVLLDYHLNYL 78
Tudor_Agenet_FXR2_rpt2 cd20476
second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 59-126 5.19e-40

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: 139.81  E-value: 5.19e-40
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30794228  59 INESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 126
Cdd:cd20476   1 ITEGDEVEVYSRANEQEPCGWWLARVRMMKGDFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68
Tudor_Agenet_FXR1_rpt2 cd20475
second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 61-126 1.96e-39

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: 138.24  E-value: 1.96e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30794228  61 ESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTF 126
Cdd:cd20475   1 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66
KH_I_FMR1_FXR_rpt1 cd22425
first type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 123-199 1.83e-37

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: 133.12  E-value: 1.83e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
Cdd:cd22425   1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77
Tudor_Agenet_FMR1_rpt1 cd20471
first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar ...
 1-55 3.61e-36

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: 128.89  E-value: 3.61e-36
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
Cdd:cd20471   1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGY 55
KH_I_FXR1_rpt2 cd22507
second type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 219-280 1.04e-33

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: 122.42  E-value: 1.04e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30794228 219 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
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 ...
 219-280 1.06e-33

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: 122.48  E-value: 1.06e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30794228 219 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd22508   2 FQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELDEETCTFRIYGETPEAVKQARSYLE 63
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 219-280 5.49e-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: 5.49e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30794228 219 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd22426   2 FIEEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIDVDEEDGTFRIYGETPEAVEKARALLE 63
KH_I_FMR1_FXR_rpt3 cd22427
third type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 281-402 2.66e-32

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: 118.87  E-value: 2.66e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22427   1 FAEEIFQVPRDLVGKVIGKNGRVIQEIVDKSGVVRVKIEGDNEDGPRPRE------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqRGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22427  51 -------------EGLVPFIFVGTREAIANAKLLLEYHLAHL 79
Tudor_Agenet_FXR2_rpt1 cd20473
first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 4-57 1.06e-31

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: 116.63  E-value: 1.06e-31
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30794228   4 LVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGYNK 57
Cdd:cd20473   2 LAVEVRGSNGAFYKGFIKDVHEDSVTIFFENNWQPERQIPFGDVRLPPPADYHK 55
KH_I_FXR1_rpt3 cd22510
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 281-402 4.82e-31

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: 115.45  E-value: 4.82e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22510   1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPRED------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqrGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22510  51 --------------GMVPFVFVGTKESIGNVQVLLEYHIAYL 78
KH_I_FXR2_rpt3 cd22511
third type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 281-402 1.12e-30

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: 114.32  E-value: 1.12e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKSVPQEEenlppsslpsnnsrvgsnsseekkhldtke 360
Cdd:cd22511   1 FSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREE------------------------------ 50

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 30794228 361 nthfsqpnstkvqrGMVPFVFVGTKDSIANATVLLDYHLNYL 402
Cdd:cd22511  51 --------------GMVPFIFVGTKENISNAQALLEYHLSYL 78
Tudor_FRX1 pfam18336
Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in ...
 4-52 2.04e-30

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: 112.95  E-value: 2.04e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30794228     4 LVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49
Tudor_Agenet_FXR1_rpt1 cd20472
first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein ...
 3-57 1.71e-28

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: 107.79  E-value: 1.71e-28
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   3 ELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPPVGYNK 57
Cdd:cd20472   1 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 55
KH_I_FXR1_rpt1 cd22504
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 123-199 4.13e-27

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: 104.57  E-value: 4.13e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77
Tudor_Agenet_FMRP-like_rpt1 cd20402
first Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; ...
 3-52 6.93e-27

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: 103.08  E-value: 6.93e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30794228   3 ELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPERQIPFHDVRFPPP 52
Cdd:cd20402   1 DLAVEVRGPNGAYYKAFVKDVHEDEVTVAFENDWQPERKVPFSDVRLPPP 50
KH_I_FXR2_rpt1 cd22505
first type I K homology (KH) RNA-binding domain found in fragile X mental retardation ...
 123-199 6.91e-26

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: 101.09  E-value: 6.91e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30794228 123 KDTFHKIKLEVPEDLRQMCAKESAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 199
Cdd:cd22505   1 KNSFFKVTIAVPEDLKEACSNENVHKEFKKAIGANCIFFNTSNNELIILSTNESTVKRASLLSDMHFRSIRTKLMLM 77
FXMR_C2 pfam16098
Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly ...
 516-581 1.47e-23

Fragile X-related mental retardation protein C-terminal region 2; FXMR_C2 is a small highly conserved region at the very C-terminus of Fragile X-related proteins FMR1. The family is found in association with pfam05641, pfam00013, PF16096.


Pssm-ID: 465020  Cd Length: 86  Bit Score: 94.60  E-value: 1.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30794228   516 FKGNDDHSRTDNRPRNPRETKGRTTDGSLQ-------------------STSSEGSRLRTGKDRNQKKEKPDSVDGLQPL 576
Cdd:pfam16098   2 FKGNDDMQWSDSRPRNSRDPKPRPQEDSLQirvdsnnersvhtktlqnsSGDSGGSRQRPGKDRGQKKEKQDGQDGPQVL 81


                  ....*
gi 30794228   577 VNGVP 581
Cdd:pfam16098  82 VNGVS 86
Tudor_Agenet_FMRP-like_rpt2 cd20403
second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) ...
 61-113 5.84e-20

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: 83.14  E-value: 5.84e-20
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30794228  61 ESDEVEVYSRAnekePCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLR 113
Cdd:cd20403   1 EGDEVEVYSRA----PDGWWEGVVKMVKGEFYVVEFPGFDETYTEIVELERLR 49
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 286-331 1.27e-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: 1.27e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30794228   286 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENEKSVPQEEE 331
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETG---AKIQIPPSESEGNERI 46
KH smart00322
K homology RNA-binding domain;
283-326 2.39e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.36  E-value: 2.39e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 30794228    283 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKSV 326
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVkIDIPGPGSEERVV 48
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 284-329 1.71e-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: 42.67  E-value: 1.71e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30794228 284 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENEKSVPQE 329
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETG-ARIQIPKEGEGSGERV 45
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 286-326 2.93e-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: 2.93e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGVV-------RVRIEAENEKSV 326
Cdd:cd02393   8 IKIPPDKIGDVIGPGGKTIRAIIEETGAKidieddgTVTIFATDKESA 55
KH smart00322
K homology RNA-binding domain;
221-280 5.25e-05

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 41.51  E-value: 5.25e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30794228    221 EQFIVREDLMGLAIGTHGANIQQARKVPGVTaIDLDEDTC---TFHIYGEDQDaVKKARSFLE 280
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVK-IDIPGPGSeerVVEITGPPEN-VEKAAELIL 65
Agenet pfam05641
Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the ...
 63-117 5.96e-05

Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins.


Pssm-ID: 461700  Cd Length: 61  Bit Score: 41.15  E-value: 5.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30794228    63 DEVEVYSRANEKEpCCWWLAKV-RMIKGEFYVIEYAACD-----ATYNEIVTIERLRSVNP 117
Cdd:pfam05641   2 DKVEVLSDEEGFR-GAWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 228-280 6.88e-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: 41.31  E-value: 6.88e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30794228 228 DLMGLAIGTHGANIQQARKVPGVTaIDLDEDtCTFHIYGEDQDAVKKARSFLE 280
Cdd:cd02393  13 DKIGDVIGPGGKTIRAIIEETGAK-IDIEDD-GTVTIFATDKESAEAAKAMIE 63
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 285-313 8.35e-05

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: 40.97  E-value: 8.35e-05
                        10        20
                ....*....|....*....|....*....
gi 30794228 285 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV 313
Cdd:cd22395   3 EFEVPSELVGRLIGKQGRNVKQLKQKSGA 31
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 286-326 1.19e-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: 40.29  E-value: 1.19e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVrVRI----EAENEKSV 326
Cdd:cd22439   6 ITIPNDLIGCIIGKGGTKINEIRQLSGAT-IKIanseDGSTERSV 49
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 281-325 1.28e-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: 40.25  E-value: 1.28e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 30794228 281 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENEKS 325
Cdd:cd02394   1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESG-VSIRIPDDEANS 44
PRK13764 PRK13764
ATPase; Provisional
 285-331 1.47e-04

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 44.83  E-value: 1.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 30794228  285 VIQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKSVPQEEE 331
Cdd:PRK13764 484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIdIDVRPLDEEPGEEAEEGE 531
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 286-334 2.61e-04

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: 39.71  E-value: 2.61e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRI---EAENEKSVPQEEENLP 334
Cdd:cd22447   8 VPIPASTRARIIGKKGANLKQIREKTG-VRIDIpprDADAAPADEDDDTMVE 58
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 286-331 3.32e-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: 39.15  E-value: 3.32e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVrvrIEAENEKSVPQEEE 331
Cdd:cd22403   4 IRVPSSMVGRIIGKGGQNVRELQRLTGAI---IKLPRDQTPDEGDE 46
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 285-332 3.81e-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: 39.70  E-value: 3.81e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30794228 285 VIQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENEKSVPQEEEN 332
Cdd:cd22446  10 TISVPSSVRGAIIGSRGKNLKSIQDKTG-TKIQIPKRNEEGNYDEDDD 56
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 286-318 6.17e-04

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: 38.33  E-value: 6.17e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRI 318
Cdd:cd09031   5 LEVPENLVGAILGKGGKTLVEIQELTG-ARIQI 36
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 288-331 1.46e-03

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 37.60  E-value: 1.46e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 30794228 288 VPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKSVPQEEE 331
Cdd:cd22460   6 VASSQAGSLIGKGGAIIKQIREESGAsVRILPEEELPPCASPDDR 50
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 284-326 1.97e-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: 1.97e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30794228 284 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRV---------RIEAENEKSV 326
Cdd:cd22426   4 EEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIdvdeedgtfRIYGETPEAV 55
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 221-280 6.09e-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: 6.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30794228   221 EQFIVREDLMGLAIGTHGANIQQARKVPGVTaIDL-----DEDTCTFHIYGeDQDAVKKARSFLE 280
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAK-IQIppsesEGNERIVTITG-TPEAVEAAKALIE 64
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 286-313 6.31e-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: 6.31e-03
                        10        20
                ....*....|....*....|....*...
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGV 313
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGA 31
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 286-331 6.36e-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: 6.36e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30794228 286 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENEKSVPQEEE 331
Cdd:cd22428   9 MKVPREAVGLIIGRQGATIKQIQKETG---ARIDFKDEGSGGELPE 51
 
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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