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Conserved domains on  [gi|291084699|ref|NP_001014060|]
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tudor and KH domain-containing protein [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tudor_TDRD2 cd20412
Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, ...
 328-420 1.60e-54

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. 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: 410483  Cd Length: 95  Bit Score: 179.03  E-value: 1.60e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 328 SRSLQLDKLVSEMTQHYENS--LPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEenRHTLLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 291084699 406 RSDFLSLPFQAIECS 420
Cdd:cd20412   81 RSDFLSLPFQAIECS 95
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 124-205 1.15e-42

second 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 second one.


:

Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 147.10  E-value: 1.15e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKR 203
Cdd:cd22429    1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEEEEFRQR 80


                 ..
gi 291084699 204 IA 205
Cdd:cd22429   81 LA 82
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 49-119 4.94e-34

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: 123.60  E-value: 4.94e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22428    1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEAIHQII 74
 
Name Accession Description Interval E-value
Tudor_TDRD2 cd20412
Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, ...
 328-420 1.60e-54

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. 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: 410483  Cd Length: 95  Bit Score: 179.03  E-value: 1.60e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 328 SRSLQLDKLVSEMTQHYENS--LPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEenRHTLLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 291084699 406 RSDFLSLPFQAIECS 420
Cdd:cd20412   81 RSDFLSLPFQAIECS 95
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 124-205 1.15e-42

second 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 second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 147.10  E-value: 1.15e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKR 203
Cdd:cd22429    1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEEEEFRQR 80


                 ..
gi 291084699 204 IA 205
Cdd:cd22429   81 LA 82
TUDOR pfam00567
Tudor domain;
306-422 2.04e-35

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 128.63  E-value: 2.04e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  306 EYLEVYVSASEHPNHFWIQIIgSRSLQLDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLD 385
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPK-SDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVE 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 291084699  386 LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:pfam00567  80 VLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLA 116
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 49-119 4.94e-34

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: 123.60  E-value: 4.94e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22428    1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEAIHQII 74
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 54-117 5.43e-17

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: 75.40  E-value: 5.43e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699   54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIpPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 127-192 1.13e-16

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: 74.24  E-value: 1.13e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILE 192
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEG--NERIVTITGTPEAVEAAKALIEE 65
KH smart00322
K homology RNA-binding domain;
51-119 4.78e-15

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 70.02  E-value: 4.78e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699    51 DDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-EERVVEITGPPENVEKAAELILEIL 68
KH smart00322
K homology RNA-binding domain;
123-194 1.36e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 62.70  E-value: 1.36e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699   123 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE----ERVVEITGPPENVEKAAELILEIL 68
Krr1 COG1094
rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and ...
 56-158 7.68e-11

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440711 [Multi-domain]  Cd Length: 177  Bit Score: 60.99  E-value: 7.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDerVLLISGF-PVQVCKAKAAIHQI-----------LTENT 123
Cdd:COG1094    3 YVKIPKDRIGVLIGKGGETKKEIEEKTGVKLDIDSET-GE--VTIEPGEdPLAALKARDIVKAIgrgfspekalrLLDDD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 291084699 124 PVFEQLSVPQ---------RSVGRIIGRGGETIRSICKASGAKI 158
Cdd:COG1094   80 YMLEVIDLPDvgkspnaldRIKGRIIGREGRTRRIIEELTGVDI 123
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 119-199 6.75e-07

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 52.36  E-value: 6.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 119 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKItcDKESEGTlllsrlIKISGTQKE-VAAAKHLILEKVSED 197
Cdd:PRK11824 548 LSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKI--DIEDDGT------VKIAATDGEaAEAAKERIEGITAEP 619


                 ..
gi 291084699 198 EE 199
Cdd:PRK11824 620 EV 621
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 54-158 9.23e-07

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 49.10  E-value: 9.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEdvgDERVLLISGF---PVQVCKAKAAIHQI-----------L 119
Cdd:PRK13763   4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDgedPLAVLKARDIVKAIgrgfspekalrL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 291084699 120 TENTPVFEQLSVP---------QRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:PRK13763  81 LDDDYVLEVIDLSdygdspnalRRIKGRIIGEGGKTRRIIEELTGVDI 128
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 355-409 6.58e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 43.42  E-value: 6.58e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 291084699   355 HVGDIVAAPLsTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 409
Cdd:smart00333   4 KVGDKVAARW-EDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 115-150 1.83e-03

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


Pssm-ID: 441442  Cd Length: 76  Bit Score: 37.34  E-value: 1.83e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 291084699 115 IHQILTENTPVFEqLSVPQRSVGRIIGRGGETIRSI 150
Cdd:COG1837   21 VTEEEGERTVVLE-LRVAPEDLGKVIGKQGRTAKAI 55
 
Name Accession Description Interval E-value
Tudor_TDRD2 cd20412
Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, ...
 328-420 1.60e-54

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. 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: 410483  Cd Length: 95  Bit Score: 179.03  E-value: 1.60e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 328 SRSLQLDKLVSEMTQHYENS--LPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEenRHTLLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 291084699 406 RSDFLSLPFQAIECS 420
Cdd:cd20412   81 RSDFLSLPFQAIECS 95
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 124-205 1.15e-42

second 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 second one.


Pssm-ID: 411857 [Multi-domain]  Cd Length: 82  Bit Score: 147.10  E-value: 1.15e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKR 203
Cdd:cd22429    1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEEEEFRQR 80


                 ..
gi 291084699 204 IA 205
Cdd:cd22429   81 LA 82
TUDOR pfam00567
Tudor domain;
306-422 2.04e-35

Tudor domain;


Pssm-ID: 425754 [Multi-domain]  Cd Length: 117  Bit Score: 128.63  E-value: 2.04e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  306 EYLEVYVSASEHPNHFWIQIIgSRSLQLDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLD 385
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPK-SDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVE 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 291084699  386 LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:pfam00567  80 VLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLA 116
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 49-119 4.94e-34

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: 123.60  E-value: 4.94e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22428    1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEAIHQII 74
Tudor_AKAP1 cd20407
Tudor domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; ...
 354-426 9.27e-20

Tudor domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. It contains a C-terminal Tudor domain. 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: 410478  Cd Length: 76  Bit Score: 83.41  E-value: 9.27e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 354 VHVGDIVAAPlsTNGSWYRARVLGTLENGNL-DLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20407    5 IEVGVICAAP--VMNAWYRAQVVGVFEETDEvEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 54-117 5.43e-17

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: 75.40  E-value: 5.43e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699   54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIpPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 127-192 1.13e-16

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: 74.24  E-value: 1.13e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILE 192
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEG--NERIVTITGTPEAVEAAKALIEE 65
Tudor_TDRD6_rpt7 cd20426
seventh Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 308-422 2.42e-16

seventh Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the seventh 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: 410497  Cd Length: 140  Bit Score: 76.00  E-value: 2.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 308 LEVYVSASEHPNHFWIQIIGSRSLQLDKLVSEMTQH---YENSLPEdltVHVGDIVAAPLSTNGSWYRARVLGTLENgNL 384
Cdd:cd20426    1 IEAYATAVDSPEYFWCQFATEKIQCLAVKVQEAGEQvadRGNFIPS---IYVGDPCIVKYSEDNHWYRALVTKINDN-LV 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 291084699 385 DLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:cd20426   77 SVRFVDYGNEEDVVREQVRALPSELLKIPVQAFPCCLS 114
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 55-115 6.24e-16

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: 72.33  E-value: 6.24e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD-ERVLLISGFPVQVCKAKAAI 115
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSgERVVTITGTPEAVEKAKELI 62
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 127-191 8.36e-16

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: 71.95  E-value: 8.36e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLIL 191
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGS--GERVVTITGTPEAVEKAKELIE 63
KH smart00322
K homology RNA-binding domain;
51-119 4.78e-15

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 70.02  E-value: 4.78e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699    51 DDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-EERVVEITGPPENVEKAAELILEIL 68
Tudor_TDRD1_rpt1 cd20408
first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 310-426 1.14e-14

first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This 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: 410479  Cd Length: 130  Bit Score: 70.86  E-value: 1.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 310 VYVSASEHPNHFWIQIIGSRSLQ-LDKLVSEMTQHYENSLPEDLTV-HVGDIVAAPLSTNGSWYRARVlgtlENGNLD-- 385
Cdd:cd20408    1 GTVTEFKNPGEFYIQIYTLEVLEsLVKLTSQLKKTYASVNNHKEYIpEVGEVCVAKYSEDQNWYRALV----QTVDVQqk 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 291084699 386 ---LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20408   77 kagVFYIDYGNEETVPLNRIQPLKKDIELFPPCAIKCCLANVKP 120
Tudor_TDRD15_rpt4 cd20439
fourth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 308-421 4.72e-14

fourth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the fourth 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: 410510  Cd Length: 125  Bit Score: 69.06  E-value: 4.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 308 LEVYVSASEHPNHFWIQIIgSRSLQLDKLVSEMTQHYENSlpEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLY 387
Cdd:cd20439   12 VDVKCSYVNSPGDFWCQLQ-TKSSELKSLMKQIQSYYLIH--NDPYKHGQIACVAKYSKDGKWYRAAVLKQVSAKEVDVI 88

                         90       100       110
                 ....*....|....*....|....*....|....
gi 291084699 388 FVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 421
Cdd:cd20439   89 FVDYGNQERVLISDLRAIKPQFLLLEGQAFRCSL 122
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
 55-119 8.57e-14

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; 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. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 66.12  E-value: 8.57e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22462    1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVlKPDSATGERIVLISGTPDQARHAQNLIEAFI 66
Tudor_TDRD4_rpt2 cd20415
second Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 367-426 9.30e-14

second Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This 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: 410486  Cd Length: 96  Bit Score: 67.07  E-value: 9.30e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 367 NGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20415   37 DGAWYRARIIGLPGHREVEVKYVDFGNTATVTIKHVRKIKDDFLSLPEKARECRLAFIEP 96
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 53-118 1.28e-13

first 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 first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 65.74  E-value: 1.28e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQI 118
Cdd:cd22396    1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGlPERPCTLTGTPDAIETAKRLIDQI 67
Tudor_dTUD-like cd20379
Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar ...
 356-405 2.88e-13

Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar proteins; dTUD is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation. It contains 11 Tudor domains. The family also includes mitochondrial A-kinase anchor protein 1 (AKAP1) and Tudor domain-containing proteins (TDRDs). AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), or dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), or protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. TDRDs have diverse biological functions and may contain one or more copies of the Tudor domain. 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: 410450  Cd Length: 50  Bit Score: 64.07  E-value: 2.88e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 291084699 356 VGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20379    1 VGDLCAAKYEEDGKWYRARVLEVLSNDKVEVFFVDYGNTETVPLSDLRPL 50
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 127-190 3.60e-13

first 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 first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 64.58  E-value: 3.60e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22396    3 EEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGG--LPERPCTLTGTPDAIETAKRLI 64
Tudor_TDRD5 cd20419
Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins; TDRD5 is ...
 311-421 6.15e-13

Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins; TDRD5 is an RNA-binding protein directly associated with piRNA precursors. It is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis. TDRD5 participates in the repression of transposable elements and prevents their mobilization, which is essential for germline integrity. TDRD5 contains three LOTUS domains and one Tudor domain. 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: 410490  Cd Length: 118  Bit Score: 65.55  E-value: 6.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 311 YVSASEHPNHFWIQIIGS-RSLQLDKLVSEMTQHYENS-------LPEDLtVHVGDIVAAPLSTNGSWYRARVLGTLENG 382
Cdd:cd20419    1 FVEYIESPSQFYVRFYSKdTSEMLEDMMIEMRRCYSNEhvseryvMPEAF-IQPGQVCCVRIPEDVWWYRVIIHQVLNKQ 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 291084699 383 NLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 421
Cdd:cd20419   80 EVEVFYPDFGDIGTVQKSRLRFLKCCYSKLPAQAIPASL 118
Tudor_TDRD12_rpt2 cd20435
second Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; ...
 317-426 1.26e-12

second Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the second/C-terminal 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: 410506  Cd Length: 134  Bit Score: 64.96  E-value: 1.26e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 317 HPNHFWIQIIG----------SRSLQLDKLVSEMTQHY---ENSLPEDlTVHVGDIVAApLSTNGSWYRARVLGTLENG- 382
Cdd:cd20435    1 DATHYSARILEhrssdgevtkSMSSTYLKLSMKLNMYYsdpSNRILHG-KVKVGDLCAV-EDENNLYHRVKVLEITEKDd 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 291084699 383 -----NLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20435   79 ktkprEVLVKFIDEGRVETVVVSQLLELPEELKSLPPQAVEVFLCNVKP 127
KH smart00322
K homology RNA-binding domain;
123-194 1.36e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 62.70  E-value: 1.36e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699   123 TPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSE----ERVVEITGPPENVEKAAELILEIL 68
Tudor_TDRD6_rpt4 cd20423
fourth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 362-428 1.76e-11

fourth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fourth 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: 410494  Cd Length: 80  Bit Score: 60.19  E-value: 1.76e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 362 APLSTNGSWYRARVLGTLEN-GNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLAR-IAPSG 428
Cdd:cd20423   11 AKYSEDGKWCRALIDNVYEPvEMVEVTYVDYGNKELVSLKNLRSISEEFLKLKAQAFRCSLYNlIQPSG 79
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 131-192 1.89e-11

first 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 first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 59.59  E-value: 1.89e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDKeSEGTLLLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22400    6 VPSEFVGAIIGKGGATIRQITQQTGARIDIHR-KENAGAAEKAITIYGTPEGCSSACKQILE 66
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 124-195 1.93e-11

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: 59.51  E-value: 1.93e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLILEKVS 195
Cdd:cd02394    1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEAN----SDEIRIEGSPEGVKKAKAEILELVD 68
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 125-192 2.44e-11

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: 59.66  E-value: 2.44e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 125 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22428    5 IEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELPERVLLIQGNPVQAQRAEEAIHQ 72
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 128-196 3.50e-11

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 59.26  E-value: 3.50e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22434    5 QVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGS--EDRIITITGTQDQIQNAQYLLQNSVKQ 71
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 127-193 7.13e-11

fourth 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 fourth one.


Pssm-ID: 411827 [Multi-domain]  Cd Length: 67  Bit Score: 58.00  E-value: 7.13e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEgTLLLSRLIKISGTQKEVAAAKHLILEK 193
Cdd:cd22399    2 VTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPP-PNPNEKLFIIRGNPQQIEHAKQLIREK 67
Krr1 COG1094
rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and ...
 56-158 7.68e-11

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440711 [Multi-domain]  Cd Length: 177  Bit Score: 60.99  E-value: 7.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDerVLLISGF-PVQVCKAKAAIHQI-----------LTENT 123
Cdd:COG1094    3 YVKIPKDRIGVLIGKGGETKKEIEEKTGVKLDIDSET-GE--VTIEPGEdPLAALKARDIVKAIgrgfspekalrLLDDD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 291084699 124 PVFEQLSVPQ---------RSVGRIIGRGGETIRSICKASGAKI 158
Cdd:COG1094   80 YMLEVIDLPDvgkspnaldRIKGRIIGREGRTRRIIEELTGVDI 123
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 128-194 8.08e-11

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: 58.00  E-value: 8.08e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCD-KESEGTLLLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22437    2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISpKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69
Tudor_TDRD15_rpt2 cd20437
second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 309-422 2.34e-10

second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This 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: 410508  Cd Length: 120  Bit Score: 58.20  E-value: 2.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 309 EVYVSASEHPNHFWIQIIgSRSLQLDKLVSEMTQHYE------NSLPEDLtvhvgDIVAAPLSTNGSWYRARVLGTLENG 382
Cdd:cd20437    6 KVKITAAVSPSKFYCQLL-SWEPELSKLTTQMTLHYEsvskelNPSCENF-----GLLCAAKGKDGQWHRGFLQQLLPPS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 291084699 383 NLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:cd20437   80 QVKVWFIDYGNSEAVSSHSVLKLPPDFFSLPLMSFPCSLS 119
Tudor_TDRD1_rpt4 cd20411
fourth Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 318-422 2.55e-10

fourth Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the fourth 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: 410482  Cd Length: 116  Bit Score: 57.84  E-value: 2.55e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 318 PNHFWIQIIGSRSLQ--LDKLVSEMTQhYENSLPEDLTVH--VGDIVAAPLSTNGSWYRARVLGTLENGNLDLYfVDFGD 393
Cdd:cd20411    9 PDLFYALPKTGQVNVekLKALMTELAE-YCSKQSVPQQFRprIGDACCARFTGDKNWYRAVVLETSDSEVKVLY-ADYGN 86

                         90       100
                 ....*....|....*....|....*....
gi 291084699 394 NGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:cd20411   87 TETLPLSRILPITKSHLELPFQIIRCSLA 115
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 122-198 3.85e-10

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: 55.95  E-value: 3.85e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 122 NTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKItcDKESEGTlllsrlIKISGTQKE-VAAAKHLILEKVSEDE 198
Cdd:cd02393    1 YAPRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKI--DIEDDGT------VTIFATDKEsAEAAKAMIEDIVAEPE 70
KH-I_Vigilin_rpt10 cd22413
tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 54-116 3.86e-10

tenth 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 tenth one.


Pssm-ID: 411841 [Multi-domain]  Cd Length: 66  Bit Score: 55.73  E-value: 3.86e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLISGFPVQVCKAKAAIH 116
Cdd:cd22413    4 TVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQELITIIGTKEAVEKAKEELE 66
Tudor_TDRD7_rpt1 cd20427
first Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; ...
 334-426 7.03e-10

first Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. 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: 410498  Cd Length: 98  Bit Score: 56.28  E-value: 7.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 334 DKLVSEMTQHYENS--LPEDLTVHVGDIVAAPlSTNGSWYRARVLGTLENgNLDLYFVDFGDNGDCPLKDLRALRSDFLS 411
Cdd:cd20427    1 EQMEDEMKEFYSKSstAMCLRSPSVGQLVAVK-AEEDAWLRAQVIEVEED-KVKVYYVDHGFSEVVERSKLFKLNKQFYS 78

                         90
                 ....*....|....*
gi 291084699 412 LPFQAIECSLARIAP 426
Cdd:cd20427   79 LPFQATKCKLAGLEP 93
Tudor_TDRD6_rpt3 cd20422
third Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 307-441 8.20e-10

third Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the third 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: 410493  Cd Length: 135  Bit Score: 57.14  E-value: 8.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 307 YLEVYVSASEHPNHFWIQIiGSRSLQLDKLVSEMTQHYENSLPED---LTVHVGDIVAAPLSTNGsWYRARVLGTLENGn 383
Cdd:cd20422    1 FYDAQVEFVKDPSEFWIRL-GEHAVPFSKLMRSMTAFYSQASKLDgvvLKPQPGQLCCAKWKEDR-YYRAIVTAVKGKM- 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 384 LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGEEWEEEALDEFDR 441
Cdd:cd20422   78 VEVFLVDRGNTEMVDWYDVKKLLPQFRELPALALKCCLADICPLGERWSPEAISAFKR 135
Tudor_TDRD6_rpt6 cd20425
sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 309-421 1.06e-09

sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the sixth 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: 410496  Cd Length: 115  Bit Score: 56.31  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 309 EVYVSASEHPNHFWIQIIgsrslQLDKLVSEMTQHYENS--LPEDL---TVHVGDIVAAPLSTNGSWYRARVLGTLENGN 383
Cdd:cd20425    3 EVYVSHVNSPSDFYVQLA-----QDEDELSMISEKLNASkaNDEEVeceSLQLGDLICAEYPEDGLWYRAVVKEKIPNNL 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 291084699 384 LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 421
Cdd:cd20425   78 VSVQFIDYGNTSVVQPSKIHRLPKELLSIPALSIHCFL 115
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 128-194 1.63e-09

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: 54.12  E-value: 1.63e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd09031    4 ELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEfvpGT--RNRKVTITGTPAAVQAAQYLIEQRI 71
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 55-119 2.08e-09

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: 53.76  E-value: 2.08e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV----GDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22437    1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQllpgSSERIVTITGSFDQVVKAVALILEKL 69
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 54-115 2.46e-09

eighth 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 eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 53.36  E-value: 2.46e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDErVLLISGFPVQVCKAKAAI 115
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSD-VITITGKKEDVEKARERI 61
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 131-194 2.56e-09

second 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 second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 53.78  E-value: 2.56e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22436    7 VPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLQERVVTVTGEPEANRKAVSLILQKI 70
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 127-194 2.96e-09

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 53.47  E-value: 2.96e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22454    6 IEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGS--PNREVQITGSPDNVAAAKRLIEDTI 71
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 55-119 3.50e-09

first 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 first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 53.05  E-value: 3.50e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVD-TEDVGD-ERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22400    2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHrKENAGAaEKAITIYGTPEGCSSACKQILEIM 68
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 54-119 5.90e-09

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: 52.65  E-value: 5.90e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22398    1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDgNSPDRICVITGPPDQVQHAARMIQELI 67
Tudor_TDRD1_rpt3 cd20410
third Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 356-410 6.15e-09

third Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the third 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: 410481 [Multi-domain]  Cd Length: 59  Bit Score: 52.34  E-value: 6.15e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 356 VGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL 410
Cdd:cd20410    5 VGEPCCAFFSGDGNWYRAMVKEILPGGAVKVHFVDYGNVEEVTLDKLRKITSTFL 59
Tudor_TDRD15_rpt3 cd20438
third Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 311-426 7.78e-09

third Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the third 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: 410509  Cd Length: 141  Bit Score: 54.40  E-value: 7.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 311 YVSASEHPNHFWIQIIGSRSlQLDKLVSEMTQHYENSLPEDLTVHV---GDIVAAPLSTNGSWYRArVLGTLENGNLDLY 387
Cdd:cd20438   10 FVEYVLNPSNFWIRTDEYNN-EFQALMKNIADIYNLCGNDEELLKKpepGLLCCARYSKDRHYYRA-VITEVLDLKVSVY 87

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 291084699 388 FVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20438   88 FLDFGNTDTVPFYDVKTLLPEFSELPALAMCCSLAHVFP 126
Tudor_TDRD11 cd20433
Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, ...
 332-409 8.73e-09

Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene. It contains multiple Staphylococcal nuclease (SN) domains and a C-terminal Tudor domain. 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: 410504 [Multi-domain]  Cd Length: 84  Bit Score: 52.69  E-value: 8.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 332 QLDKLVSEMTQHYENS--LPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 409
Cdd:cd20433    4 QLEKLMEKLRFEIASNppLPGSYTPRKGDLCAAKFVEDGEWYRAKVEKVEGDKKVHVLYIDYGNREVLPSTRLAALPPAF 83
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
 128-194 9.44e-09

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; 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. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.


Pssm-ID: 411890 [Multi-domain]  Cd Length: 66  Bit Score: 51.87  E-value: 9.44e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22462    2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSAT--GERIVLISGTPDQARHAQNLIEAFI 66
Tudor_TDRD15_rpt6 cd20441
sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 318-424 1.02e-08

sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the sixth 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: 410512  Cd Length: 108  Bit Score: 53.21  E-value: 1.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 318 PNHFWIQIIGSRSLQLdKLVSEMTQHYENS-LPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGD 396
Cdd:cd20441    2 PSRFFIQLSEDEKVIL-QLAEELNETSEKSrENAAVKLKVGDLVAAEYDEDLALYRAVITAVLPGKSFKVEFIDYGNTAV 80

                         90       100
                 ....*....|....*....|....*...
gi 291084699 397 CPLKDLRALRSDFLSLPFQAIECSLARI 424
Cdd:cd20441   81 VDKSNIYTLQEKFLSLPRLSIPCSLSGV 108
Tudor_TDRD7_rpt3 cd20429
third Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; ...
 332-417 1.06e-08

third Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the third 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: 410500  Cd Length: 91  Bit Score: 52.49  E-value: 1.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 332 QLDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNgsWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLS 411
Cdd:cd20429    8 KLEVLMEEMILYYNKTEERPVAIEKNKVYAAKIENN--WYRVLVKGILTNGLVSVYELDYGKHELVSIRKVQPLIEKFRQ 85


                 ....*.
gi 291084699 412 LPFQAI 417
Cdd:cd20429   86 LPFQAI 91
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 52-120 1.43e-08

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 51.49  E-value: 1.43e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  52 DIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV--GDERVLLISGFPVQVckaKAAIHQILT 120
Cdd:cd22433    1 DCELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCprSTDRVVQIGGKPDKV---VECIREILE 68
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 56-120 1.82e-08

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: 51.03  E-value: 1.82e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVlLISGFPVQVCKAKAAIHQILT 120
Cdd:cd02394    5 TIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEI-RIEGSPEGVKKAKAEILELVD 68
Tudor_AtTudor1-like cd20443
Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor ...
 321-426 1.83e-08

Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor 2 (AtTudor2), and similar proteins; The family includes AtTudor1 (also called Tudor-SN protein 1) and AtTudor2 (also called Tudor-SN protein 2 or 100 kDa coactivator-like protein). They are cytoprotective ribonucleases (RNases) required for resistance to abiotic stresses, acting as positive regulators of mRNA decapping during stress. Members of this family contain one Tudor domain. 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: 410514 [Multi-domain]  Cd Length: 117  Bit Score: 52.85  E-value: 1.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 321 FWIQIIGSRSL-----QLDKLVSEmtqhyENSLPED-LTVHVGDIVAAPLSTNGSWYRARVLGTLENGN------LDLYF 388
Cdd:cd20443    4 FYVQVVSDQRLssiqqQLEGLSLK-----DKANPPGgFNPKKGELVLAQFSADNSWNRAMVVNAPRQGTqspkdeYEVFY 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 291084699 389 VDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20443   79 IDYGNQETVPLSALRPLDPSVSSAPGLAQLCSLAHIKV 116
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 54-117 2.18e-08

second 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 second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 51.08  E-value: 2.18e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV---DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22436    2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQIsqkPESINLQERVVTVTGEPEANRKAVSLILQ 68
Tudor_TDRD6_rpt5 cd20424
fifth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 309-421 2.76e-08

fifth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fifth 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: 410495  Cd Length: 126  Bit Score: 52.51  E-value: 2.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 309 EVYVSASEHPNHFWIQIigSRSLQ-LDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLsTNGSWYRARVLGTLENgnLDLY 387
Cdd:cd20424   15 EVYITYVNDPWTFYCQL--ARNAGvLDQLASAISRLSSEIRKLELSVNPGTLCLAKY-SDQHWYRGIIITNKNS--TEVF 89

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 291084699 388 FVDFGDNGDCPLKDLRALRSD---FLSLPFQAIECSL 421
Cdd:cd20424   90 FVDYGNTEKVEKEDMLPIPSDayeLLLLPMQAIKCSL 126
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 55-121 3.06e-08

first 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 first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 50.33  E-value: 3.06e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22438    1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSC-PERIVTVTGTTDAVFKAFELICRKLEE 66
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
 56-121 4.47e-08

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 50.29  E-value: 4.47e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22404    4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKgEQGDRRITIKGSADATRQAAQLINALIKD 70
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 55-119 8.58e-08

second 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 second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 49.16  E-value: 8.58e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGAR---IDVDTEDVGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22397    2 IEIMIPGNKVGLIIGKGGETIKQLQERAGVKmvmIQDGPQPTGQDKPLRITGDPQKVQRAKELVMELI 69
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 133-197 9.61e-08

first 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 first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 9.61e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 133 QRSVGRIIGRGGETIRSICKASGAKITCdkeSEGTlLLSRLIKISGTQKEVAAAKHLILEKVSED 197
Cdd:cd22438    7 GKEVGSIIGKKGETIKKFREESGARINI---SDGS-CPERIVTVTGTTDAVFKAFELICRKLEED 67
Tudor_TDRD15_rpt5 cd20440
fifth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 309-421 9.86e-08

fifth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the fifth 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: 410511  Cd Length: 127  Bit Score: 50.92  E-value: 9.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 309 EVYVSASEHPNHFWIQIiGSRSLQLDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYF 388
Cdd:cd20440   13 EVYITHVYSPAKFYCQL-DRNTEILEALMEKIAEISKLFNSQILDNCKTRLCLAKYFEDGQWYRALAHPVESSSHLSVYF 91

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 291084699 389 VDFGDNGDCPLKDLRAL---RSDFLSLPFQAIECSL 421
Cdd:cd20440   92 VDYGNKQIVEKNEVLPIpdtAVDLLLTPMQAIKCCL 127
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 131-194 1.12e-07

first 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 first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 49.07  E-value: 1.12e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22435    8 VPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDfypGT--TERVCLIQGEVEAVNAVLDFILEKI 72
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 54-117 1.39e-07

fourth 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 fourth one.


Pssm-ID: 411827 [Multi-domain]  Cd Length: 67  Bit Score: 48.76  E-value: 1.39e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVD--TEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22399    1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDrnPPPNPNEKLFIIRGNPQQIEHAKQLIRE 66
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 56-117 1.56e-07

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.


Pssm-ID: 411886 [Multi-domain]  Cd Length: 65  Bit Score: 48.60  E-value: 1.56e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22458    4 EIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNSSQQTIHLSGTDKQIALAISSIEE 65
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 53-118 1.63e-07

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: 48.95  E-value: 1.63e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED------VGDERVLL---ISGFPVQVCKAKAAIHQI 118
Cdd:cd22447    4 QNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDadaapaDEDDDTMVevtITGDEFNVQHAKQRIEEI 78
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 136-196 1.75e-07

second 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 second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 48.38  E-value: 1.75e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699 136 VGRIIGRGGETIRSICKASGAKITCDKESEGTLL-LSRLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22401   11 CGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYnPERTITIKGSLEAMSEAESLISEKLRE 72
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 57-111 1.94e-07

third 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 third one.


Pssm-ID: 411830 [Multi-domain]  Cd Length: 66  Bit Score: 48.02  E-value: 1.94e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  57 MRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD--ERVLLISGFPVQVCKA 111
Cdd:cd22402    5 LYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDapERKVTITGPPEAQWKA 61
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 128-190 2.86e-07

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; 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 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.


Pssm-ID: 411891 [Multi-domain]  Cd Length: 71  Bit Score: 47.81  E-value: 2.86e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22463    5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQKILRISGTEEQLKRAQSLV 67
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 56-117 3.26e-07

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: 47.61  E-value: 3.26e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22439    5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIaNSEDGSTERSVTITGTPEAVSLAQYLINA 67
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 128-194 3.94e-07

third 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 third one.


Pssm-ID: 411942 [Multi-domain]  Cd Length: 71  Bit Score: 47.42  E-value: 3.94e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES---EGTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22514    4 TIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGdfvSGT--RNRKVTITGPQDAVQMAQYLLEQKL 71
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 128-190 4.59e-07

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: 47.22  E-value: 4.59e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22439    5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGS--TERSVTITGTPEAVSLAQYLI 65
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 129-195 6.15e-07

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: 47.41  E-value: 6.15e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE----GTLLLSRL--IKISGTQKEVAAAKHLILEKVS 195
Cdd:cd22447    8 VPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDAdaapADEDDDTMveVTITGDEFNVQHAKQRIEEIIS 80
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 54-111 6.64e-07

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: 46.75  E-value: 6.64e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  54 EIEmrVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDE-RVLLISGFPVQVCKA 111
Cdd:cd22395    3 EFE--VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNfQICSIEGTQQQIDKA 59
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 127-196 6.71e-07

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411906 [Multi-domain]  Cd Length: 75  Bit Score: 46.94  E-value: 6.71e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLiLEKVSE 196
Cdd:cd22478    6 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG--LPERSCMLTGTPESVQSAKRL-LDQIVE 72
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 119-199 6.75e-07

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 52.36  E-value: 6.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 119 LTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKItcDKESEGTlllsrlIKISGTQKE-VAAAKHLILEKVSED 197
Cdd:PRK11824 548 LSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKI--DIEDDGT------VKIAATDGEaAEAAKERIEGITAEP 619


                 ..
gi 291084699 198 EE 199
Cdd:PRK11824 620 EV 621
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 128-197 8.06e-07

second 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 second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 46.92  E-value: 8.06e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLIlEKVSED 197
Cdd:cd22406    8 TVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDN----SDEIKITGTKEGIEKARHEI-QLISDE 72
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 131-193 8.07e-07

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: 46.36  E-value: 8.07e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKIT-----CDKEsegtlllSRLIKISGTQKEVAAAKHLILEK 193
Cdd:cd22395    6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYikphpYTQN-------FQICSIEGTQQQIDKALKLIRKK 66
Tudor_TDRD4_rpt5 cd20418
fifth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; ...
 367-448 8.42e-07

fifth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the fifth 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: 410489  Cd Length: 105  Bit Score: 47.79  E-value: 8.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 367 NGSWYRARVLGTLENGNLDLY--FVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGEEWeeealdEFDRLTH 444
Cdd:cd20418   16 DGKWYRAKLLSILEFNPVKILvrHVDYGSTAALPTSRLRQIPAELMQYPCQAIKVKLAGFKPPLNDS------ETERIPY 89


                 ....
gi 291084699 445 CADW 448
Cdd:cd20418   90 CPEW 93
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 125-195 8.53e-07

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411907 [Multi-domain]  Cd Length: 71  Bit Score: 46.47  E-value: 8.53e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699 125 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLILEKVS 195
Cdd:cd22479    1 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG--LPERSVSLTGSPEAVQKAKMMLDDIVS 69
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 56-116 9.06e-07

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411950 [Multi-domain]  Cd Length: 75  Bit Score: 46.64  E-value: 9.06e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD-ERVLLISGFPVQVCKAKAAIH 116
Cdd:cd22522   12 ELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSsERQITITGSPANISLAQYLIN 73
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 59-119 9.17e-07

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: 46.46  E-value: 9.17e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  59 VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV------GDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVRILPEEElppcasPDDRVVQISGEAQAVKKALELVSSRL 72
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 54-158 9.23e-07

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 49.10  E-value: 9.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEdvgDERVLLISGF---PVQVCKAKAAIHQI-----------L 119
Cdd:PRK13763   4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---TGEVIIEPTDgedPLAVLKARDIVKAIgrgfspekalrL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 291084699 120 TENTPVFEQLSVP---------QRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:PRK13763  81 LDDDYVLEVIDLSdygdspnalRRIKGRIIGEGGKTRRIIEELTGVDI 128
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 55-121 1.10e-06

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: 46.32  E-value: 1.10e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDtedvgDERVLLISGFPVQVC-KAKAAIHQILTE 121
Cdd:cd02393    6 TTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE-----DDGTVTIFATDKESAeAAKAMIEDIVAE 68
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 131-192 1.11e-06

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: 46.10  E-value: 1.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCdKESEGTlLLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22398    6 VPRFAVGVVIGKGGEMIKKIQNETGARVQF-KPDDGN-SPDRICVITGPPDQVQHAARMIQE 65
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 56-103 1.27e-06

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: 45.69  E-value: 1.27e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV---DTEDVGDERVLLISG 103
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLprdQTPDEGDEVPVEIIG 53
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
 129-196 1.34e-06

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411832 [Multi-domain]  Cd Length: 71  Bit Score: 46.05  E-value: 1.34e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLlsRLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22404    5 VTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGD--RRITIKGSADATRQAAQLINALIKD 70
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 124-194 1.39e-06

first 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 first one.


Pssm-ID: 411941 [Multi-domain]  Cd Length: 73  Bit Score: 45.89  E-value: 1.39e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22513    1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQEffpGT--TDRVLLVSGSLNEVLTALNLILEKL 72
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 119-190 1.70e-06

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411950 [Multi-domain]  Cd Length: 75  Bit Score: 45.87  E-value: 1.70e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 119 LTENTPV-FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22522    2 LDASPPAsTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGS--SERQITITGSPANISLAQYLI 72
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 55-115 1.78e-06

fourth 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 fourth one.


Pssm-ID: 411877 [Multi-domain]  Cd Length: 70  Bit Score: 45.72  E-value: 1.78e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDteDVGDERVLLISGFPVQVCKAKAAI 115
Cdd:cd22449    6 VKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFE--DKTGEGNVEIKGSKKNVEEAKKRI 64
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 127-190 2.00e-06

first 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 first one.


Pssm-ID: 411908 [Multi-domain]  Cd Length: 71  Bit Score: 45.66  E-value: 2.00e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22480    3 EEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGG--MPERPCVLTGTPESIEQAKRLL 64
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 128-186 2.65e-06

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 44.98  E-value: 2.65e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKEsegTLLLS--RLIKISGTQKEVAAA 186
Cdd:cd22456    3 RLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKE---FLPLSteRILEVQGTPDAIHNA 60
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 127-192 2.72e-06

second 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 second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 44.93  E-value: 2.72e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22397    2 IEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQDKPLRITGDPQKVQRAKELVME 67
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 55-121 2.98e-06

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains 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 third one.


Pssm-ID: 411926 [Multi-domain]  Cd Length: 78  Bit Score: 45.45  E-value: 2.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD--ERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22498    7 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDakLRMVIITGPPEAQFKAQGRIYGKLKE 75
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 54-121 3.01e-06

fourteenth 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 fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 44.89  E-value: 3.01e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22417    2 TLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDDEITITGYEKNAEAAKDAILKIVQE 69
KH-I_MEX3_rpt2 cd22424
second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding ...
 50-115 3.04e-06

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.


Pssm-ID: 411852 [Multi-domain]  Cd Length: 72  Bit Score: 45.02  E-value: 3.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  50 EDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgdERVLLISGFPVQVCKAKAAI 115
Cdd:cd22424    1 PGQTTIQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRDK--EPVFEVTGMPENVERAREEI 64
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 53-119 3.47e-06

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; 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 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.


Pssm-ID: 411891 [Multi-domain]  Cd Length: 71  Bit Score: 44.73  E-value: 3.47e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARI----DVDTEDvGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22463    2 SKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVaivqDRYPLE-ETQKILRISGTEEQLKRAQSLVEGLI 71
Tudor_TDRD1_rpt2 cd20409
second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 332-410 3.60e-06

second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This 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: 410480  Cd Length: 82  Bit Score: 45.14  E-value: 3.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 332 QLDKLVSEMTQHYENSLPE-DLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL 410
Cdd:cd20409    3 QLAELQESLSAYCKVAPASsDFSPAVGEVCCAQFTEDNQWYRASVLAYSSEDSVLVGYIDFGNSEEVALSRLRPIPPSLL 82
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 59-116 3.72e-06

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411885 [Multi-domain]  Cd Length: 64  Bit Score: 44.37  E-value: 3.72e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  59 VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTE--DVGDERVLLISGFPVQVCKAKAAIH 116
Cdd:cd22457    5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAphDETGERMFTITGTPEANDRALRLLY 64
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 53-118 3.73e-06

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 44.61  E-value: 3.73e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQI 118
Cdd:cd22454    4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGsPNREVQITGSPDNVAAAKRLIEDT 70
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 55-121 3.80e-06

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 44.59  E-value: 3.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  55 IEMR--VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22455    1 LTLRalVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGvHDRVLTVSGPLEGVAKAFGLIARTLNE 70
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 128-186 4.58e-06

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.


Pssm-ID: 411886 [Multi-domain]  Cd Length: 65  Bit Score: 44.36  E-value: 4.58e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTlllSRLIKISGTQKEVAAA 186
Cdd:cd22458    4 EIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNSS---QQTIHLSGTDKQIALA 59
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 128-158 4.87e-06

first 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 KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 44.14  E-value: 4.87e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:cd22459    5 RLLCPVSKAGSVIGKGGEIIKQLRQETGARI 35
Tudor_TDRD6_rpt2 cd20421
second Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; ...
 302-421 4.91e-06

second Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This 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: 410492  Cd Length: 130  Bit Score: 46.26  E-value: 4.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 302 FHADEYLEVYVSASEHPNHFWIQIiGSRSLQLDKLVSEMTQHYEN---SLPEDLTVHVGDIVAAPlSTNGSWYRARVLGT 378
Cdd:cd20421    7 LQVGVTETVVVTEVTDPHRIFCQL-RSLSQELKRLSESMHQYYEGrvgSGYETRPEKLGSPCAAR-GSDGRWYRAVLQQV 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 291084699 379 LENGNL-DLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 421
Cdd:cd20421   85 FSANRVvEVLHVDYGRKEVVSVSNLRYLAPEYFRMPVVTYPCAL 128
Tudor_TDRD12_rpt1 cd20434
first Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; ...
 316-426 5.06e-06

first Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the first/N-terminal 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: 410505  Cd Length: 164  Bit Score: 46.65  E-value: 5.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 316 EHPNHFWIQIIGSRSLQLD------KLVSEMTQHYeNSLPEDL------TVHVGDIVAAPLSTNGSWYRARVLGTLENGN 383
Cdd:cd20434    7 EDPGCFWGRILKGSGDLVVnpeeyeNLQDEMNQFY-HKGYKDVeeikpsTLEEGQVCVVFCEELKCWCRAVVESLMSSAD 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 291084699 384 LDL---YFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20434   86 DYLaecFLVDYAKYIPVKSKDIRVALEAFMKLPYRAKKFRLYGIKP 131
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 127-191 6.19e-06

eighth 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 eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 43.73  E-value: 6.19e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLIL 191
Cdd:cd22411    2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSD----SDVITITGKKEDVEKARERIL 62
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 55-121 6.46e-06

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains 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 third one.


Pssm-ID: 411925  Cd Length: 77  Bit Score: 44.31  E-value: 6.46e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD--ERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22497    5 VYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPDvsERMVIITGPPEAQFKAQGRIFGKLKE 73
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 355-409 6.58e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 43.42  E-value: 6.58e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 291084699   355 HVGDIVAAPLsTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 409
Cdd:smart00333   4 KVGDKVAARW-EDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 55-112 6.81e-06

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 44.23  E-value: 6.81e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAK 112
Cdd:cd22434    4 TQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGsEDRIITITGTQDQIQNAQ 62
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 55-121 7.05e-06

sixth 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 sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 43.98  E-value: 7.05e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22451    3 IDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKD-DPSGKIRITGARDGVEAATAKILNISDE 68
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 128-179 8.05e-06

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: 43.77  E-value: 8.05e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGT 179
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEVPVEIIGN 54
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 52-115 8.44e-06

first 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 KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 43.75  E-value: 8.44e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  52 DIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPV---QVCKAKAAI 115
Cdd:cd22459    1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVeDGVPGTEERVITISSSEApeaPVSPAQEAL 68
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 55-108 8.72e-06

first 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 first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 43.68  E-value: 8.72e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV----DTEDVGDERVLLISGFPVQV 108
Cdd:cd22435    4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLsknnDFYPGTTERVCLIQGEVEAV 61
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 56-115 9.47e-06

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411951  Cd Length: 68  Bit Score: 43.34  E-value: 9.47e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTE-DVGDERVLLISGFPVQVCKAKAAI 115
Cdd:cd22523    5 EFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQtEGTSERHVTITGSPVSITLAQYLI 65
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 129-194 9.55e-06

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411915  Cd Length: 72  Bit Score: 43.79  E-value: 9.55e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS-RLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22487    6 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNmKLFTIRGSPQQIDYARQLIEEKI 72
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 129-190 9.82e-06

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: 43.76  E-value: 9.82e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLS---RLIKISGTQKEVAAAKHLI 190
Cdd:cd22460    4 LLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCASpddRVVQISGEAQAVKKALELV 68
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 130-193 9.86e-06

fourth 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 fourth one.


Pssm-ID: 411917 [Multi-domain]  Cd Length: 69  Bit Score: 43.38  E-value: 9.86e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 130 SVPQRSVGRIIGRGGETIRSICKASGAKITCDKE-SEGTLLLSRLIKISGTQKEVAAAKHLILEK 193
Cdd:cd22489    5 TIPADKCGLVIGKGGENIKSINQQSGAHVELQRNpPPNTDPNVRIFTIRGVPQQIEHARQLIDEK 69
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 59-121 9.91e-06

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains 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 third one.


Pssm-ID: 411924  Cd Length: 76  Bit Score: 43.85  E-value: 9.91e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  59 VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDE--RVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22496    9 IPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSkvRMVIITGPPEAQFKAQGRIYGKLKE 73
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 124-196 1.11e-05

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: 43.93  E-value: 1.11e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRL------IKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22446    6 KVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDEDDddetveISIEGDAEGVELAKKEIEAIVKE 84
Tudor_TDRD9 cd20431
Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins; TDRD9 is ...
 318-413 1.47e-05

Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins; TDRD9 is an ATP-dependent DEAD-like RNA helicase required during spermatogenesis. It is involved in the biosynthesis of PIWI-interacting RNAs (piRNAs). A recessive deleterious mutation mutation in TDRD9 causes non-obstructive azoospermia in infertile men. TDRD9 contains an N-terminal HrpA-like RNA helicase module and a Tudor domain. 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: 410502  Cd Length: 101  Bit Score: 43.92  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 318 PNHFWIQIIGSRSL-QLDKLVSEMTQHYENSLPEDLtvHVGDIVAAPLS--TNGSWYRARVLGTLENgNLDLYFVDFGDN 394
Cdd:cd20431    6 VGHFWGYRIDENSSeILQQLTAEINQRQLVPLTTKP--VPNLLCLAPFTdaDMKKYYRAKILYVSGS-SAEVFFVDYGNT 82

                         90
                 ....*....|....*....
gi 291084699 395 GDCPLKDLRALRSDFLSLP 413
Cdd:cd20431   83 SQVPSSLLREIPETLLTLP 101
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 54-103 1.71e-05

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 42.55  E-value: 1.71e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 291084699  54 EIEMR--VPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEdvGDERVLLISG 103
Cdd:cd22432    1 VVELRllIPSKAAGAIIGKGGENIKRLRTEYNASVSVpDSS--GPERILTISA 51
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-120 1.78e-05

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411907 [Multi-domain]  Cd Length: 71  Bit Score: 43.01  E-value: 1.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQILT 120
Cdd:cd22479    4 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGlPERSVSLTGSPEAVQKAKMMLDDIVS 69
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 127-190 1.84e-05

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411885 [Multi-domain]  Cd Length: 64  Bit Score: 42.45  E-value: 1.84e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESeGTLLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22457    1 QNISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAP-HDETGERMFTITGTPEANDRALRLL 63
KH-I_ScSCP160_rpt7 cd22452
seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 124-192 2.12e-05

seventh 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 seventh one.


Pssm-ID: 411880 [Multi-domain]  Cd Length: 65  Bit Score: 42.31  E-value: 2.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEgtllLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22452    1 DFRGWIKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNK----ESDVITLRGTKEGVEKAEEMIKK 65
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 67-121 2.15e-05

second 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 second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 42.60  E-value: 2.15e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  67 IIGRQGANIKQLRKQTGARIDV----DTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22401   14 LIGKDGRNIKKIMEDTNTKITIsslqDLTSYNPERTITIKGSLEAMSEAESLISEKLRE 72
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-119 2.18e-05

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411909 [Multi-domain]  Cd Length: 71  Bit Score: 42.69  E-value: 2.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGAR---IDVDTEDVGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22481    5 EIMIPASKAGLVIGKGGETIKQLQERAGVKmvmIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELI 71
KH-I_Vigilin_rpt4 cd22408
fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 54-115 2.18e-05

fourth 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 fourth one.


Pssm-ID: 411836 [Multi-domain]  Cd Length: 62  Bit Score: 42.16  E-value: 2.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLIsGFPVQVCKAKAAI 115
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLR-GPADKLGAALTLV 61
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 67-118 2.70e-05

second 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 second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 42.26  E-value: 2.70e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 291084699  67 IIGRQGANIKQLRKQTGARIDVDTEDVGD--ERVLLISGFPVQVCKakaAIHQI 118
Cdd:cd02396   16 LIGKGGSKIKEIRESTGASVQVASEMLPNstERAVTISGSPEAITK---CVEQI 66
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 127-192 2.73e-05

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411909 [Multi-domain]  Cd Length: 71  Bit Score: 42.30  E-value: 2.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22481    4 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLE 69
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 128-199 3.02e-05

fourteenth 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 fourteenth one.


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 42.19  E-value: 3.02e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITC-DKESEGtlllSRLIKISGTQKEVAAAKHLILEKVSEDEE 199
Cdd:cd22417    4 TVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFpDKGDEN----DDEITITGYEKNAEAAKDAILKIVQELES 72
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 128-202 3.07e-05

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains 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 first one.


Pssm-ID: 411918  Cd Length: 76  Bit Score: 42.38  E-value: 3.07e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCD-KESEGTllLSRLIKISGTQKEVAAAKHLILEKVSEDEELRK 202
Cdd:cd22490    3 RLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHrKENAGA--AEKAISIHSTPEGCSAACKMILEIMQKEAKDTK 76
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 357-403 3.28e-05

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.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 41.42  E-value: 3.28e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 291084699 357 GDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDfGDNGDCPLKDLR 403
Cdd:cd04508    1 GDRVEAKWSDDGQWYPATVVAVNDDGKYTVLFDD-GNEEEVSEDDIR 46
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 56-123 3.29e-05

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411949  Cd Length: 76  Bit Score: 42.35  E-value: 3.29e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD-ERVLLISGFPVQVCKAKAAIHQILTENT 123
Cdd:cd22521    8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGStDRQVTITGSAASISLAQYLINARLSSEK 76
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 55-119 3.79e-05

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: 41.86  E-value: 3.79e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22486    5 IEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDgISPERVAQVMGPPDRCQHAAHIINELI 70
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 128-197 4.21e-05

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411949  Cd Length: 76  Bit Score: 41.96  E-value: 4.21e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILEKVSED 197
Cdd:cd22521    8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGS--TDRQVTITGSAASISLAQYLINARLSSE 75
KH-I_ANKRD17 cd22502
type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 ...
 127-190 5.90e-05

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411930 [Multi-domain]  Cd Length: 71  Bit Score: 41.28  E-value: 5.90e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22502    3 KKVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKT--GDRIITIRGGTESTRQATQLI 64
KH-I_RNaseY cd22431
type I K homology (KH) RNA-binding domain found in ribonuclease Y (RNase Y) and similar ...
 62-121 5.97e-05

type I K homology (KH) RNA-binding domain found in ribonuclease Y (RNase Y) and similar proteins; RNase Y is an endoribonuclease that initiates mRNA decay. It initiates the decay of all SAM-dependent riboswitches, such as yitJ riboswitch. RNase Y is involved in processing of the gapA operon mRNA and it cleaves between cggR and gapA. It is also the decay-initiating endonuclease for rpsO mRNA. It plays a role in degradation of type I toxin-antitoxin system bsrG/SR4 RNAs and also a minor role in degradation of type I toxin-antitoxin system bsrE/SR5 degradation.


Pssm-ID: 411859 [Multi-domain]  Cd Length: 79  Bit Score: 41.41  E-value: 5.97e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  62 EAVKLIIGRQGANIKQLRKQTGARIDVDTedvgDERVLLISGF-PVQVCKAKAAIHQILTE 121
Cdd:cd22431   13 EMKGRIIGREGRNIRAFEAATGVDLIIDD----TPEAVILSGFdPVRREVARRTLEKLVED 69
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 54-117 6.85e-05

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: 41.02  E-value: 6.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVdtEDVGD------ERVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd09031    2 VIELEVPENLVGAILGKGGKTLVEIQELTGARIQI--SKKGEfvpgtrNRKVTITGTPAAVQAAQYLIEQ 69
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-119 6.92e-05

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411906 [Multi-domain]  Cd Length: 75  Bit Score: 41.16  E-value: 6.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22478    7 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGlPERSCMLTGTPESVQSAKRLLDQIV 71
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-121 7.07e-05

second 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 second one.


Pssm-ID: 411911 [Multi-domain]  Cd Length: 83  Bit Score: 41.43  E-value: 7.07e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGAR---IDVDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22483    8 EILIPASKVGLVIGKGGETIKQLQERTGVKmimIQDGPLPTGADKPLRITGDPFKVQQAREMVLEIIRE 76
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 127-190 7.08e-05

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411951  Cd Length: 68  Bit Score: 41.03  E-value: 7.08e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22523    4 QEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGT--SERHVTITGSPVSITLAQYLI 65
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 134-197 7.21e-05

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 41.15  E-value: 7.21e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 134 RSVGRIIGRGGETIRSICKASGAKITCdkeSEGTlLLSRLIKISGTQKEVAAAKHLILEKVSED 197
Cdd:cd22515   11 KEVGSIIGKKGESVKKMREESGARINI---SEGN-CPERIITLAGPTNAIFKAFAMIIDKLEED 70
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 56-92 9.55e-05

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: 40.59  E-value: 9.55e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGAR-IDVDTED 92
Cdd:cd22426    5 EFKVDPDLIGLAIGSHGSNIQQARKIPGVEsIDVDEED 42
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 127-199 1.05e-04

second 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 second one.


Pssm-ID: 411911 [Multi-domain]  Cd Length: 83  Bit Score: 41.05  E-value: 1.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE 199
Cdd:cd22483    7 QEILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLPTGADKPLRITGDPFKVQQAREMVLEIIREKDQ 79
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 59-115 1.09e-04

third 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 third one.


Pssm-ID: 411835 [Multi-domain]  Cd Length: 62  Bit Score: 40.27  E-value: 1.09e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  59 VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDErVLLISGFPVQVCKAKAAI 115
Cdd:cd22407    6 IPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKD-EIVVSGEKEGVAQAVAKI 61
KH-I_FUBP2_rpt4 cd22488
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 54-117 1.20e-04

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411916  Cd Length: 69  Bit Score: 40.47  E-value: 1.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTE--DVGDE--RVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22488    1 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQppPNGDPnfKLFIIRGSPQQIDHAKQLIEE 68
KH_I_FMR1_FXR_rpt3 cd22427
third type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 127-190 1.22e-04

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: 40.67  E-value: 1.22e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGA---KITCDKESEGTLLLSRL--IKISGTQKEVAAAKHLI 190
Cdd:cd22427    4 EIFQVPRDLVGKVIGKNGRVIQEIVDKSGVvrvKIEGDNEDGPRPREEGLvpFIFVGTREAIANAKLLL 72
KH-I_FUBP2_rpt3 cd22485
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 55-119 1.25e-04

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411913  Cd Length: 68  Bit Score: 40.33  E-value: 1.25e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22485    3 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDgTGPEKIAHIMGPPDRCEHAARIINDLL 68
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 127-196 1.25e-04

fourth 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 fourth one.


Pssm-ID: 411877 [Multi-domain]  Cd Length: 70  Bit Score: 40.33  E-value: 1.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITC-DKESEGTlllsrlIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22449    6 VKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFeDKTGEGN------VEIKGSKKNVEEAKKRILSQIDE 70
KH-I_ANKHD1 cd22503
type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing ...
 127-190 1.49e-04

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.


Pssm-ID: 411931  Cd Length: 83  Bit Score: 40.50  E-value: 1.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22503    3 KKLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKN--GERMITIRGGTESTRYAVQLI 64
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 129-198 1.78e-04

sixth 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 sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 40.13  E-value: 1.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLILeKVSEDE 198
Cdd:cd22451    5 IDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDP----SGKIRITGARDGVEAATAKIL-NISDEE 69
Tudor_TDRD15_rpt1 cd20436
first Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 317-443 1.80e-04

first Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This 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: 410507  Cd Length: 147  Bit Score: 42.02  E-value: 1.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 317 HPNHFWIQIIGSRSLQLDKLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNGSWYRARVLgTLENGNLDLYFVDFGDNGD 396
Cdd:cd20436   10 HPKEVLVKFQGQYNSICELDYHILQNEIQNATKSKSSWGVGEFCLVEDTTSGEWYRGRVL-EKIDEKYEVFLIDRGEVLN 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 291084699 397 CPLKDLRALRSDFLSLPFQAIECSLARIAPSGEEWEEEALDEFDRLT 443
Cdd:cd20436   89 VHATNMASASGELFQLPPKAVCGIFANILPIGEKWSSTAVNYFSSLI 135
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
 128-194 2.05e-04

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 39.58  E-value: 2.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTlllsrLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22430    3 CFKIDSSLVGAVIGRGGSKIRELEESTGSKIKIIKGGQEA-----EVKIFGSDEAQQKAKELIDELV 64
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 134-197 2.12e-04

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 39.63  E-value: 2.12e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 134 RSVGRIIGRGGETIRSICKASGAKITCdkeSEGTlLLSRLIKISGTQKEVAAAKHLILEKVSED 197
Cdd:cd22517   11 KEVGSIIGKKGETVKRIREESSARITI---SEGS-CPERITTITGSTDAVFRAFSMIAFKLEED 70
KH-I_Vigilin_rpt13 cd22416
thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 124-202 2.40e-04

thirteenth 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 thirteenth one.


Pssm-ID: 411844 [Multi-domain]  Cd Length: 78  Bit Score: 39.91  E-value: 2.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 124 PVFEQLSVP---QRSvgrIIGRGGETIRSICKASGAKITCDKESegtlLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL 200
Cdd:cd22416    1 PVTEEVNVPfdlHRF---IIGQKGADVRKMMDEFDVNISIPPAE----LQSDIIKITGPPANVERAKAALLERVKELEAE 73


                 ..
gi 291084699 201 RK 202
Cdd:cd22416   74 KE 75
KH-I_ANKHD1 cd22503
type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing ...
 56-103 2.60e-04

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.


Pssm-ID: 411931  Cd Length: 83  Bit Score: 40.12  E-value: 2.60e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTE-DVGDERVLLISG 103
Cdd:cd22503    4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQkDKNGERMITIRG 52
KH-I_ANKRD17 cd22502
type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 ...
 56-103 2.68e-04

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.


Pssm-ID: 411930 [Multi-domain]  Cd Length: 71  Bit Score: 39.74  E-value: 2.68e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTE-DVGDERVLLISG 103
Cdd:cd22502    4 KVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQkDKTGDRIITIRG 52
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-119 2.87e-04

first 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 first one.


Pssm-ID: 411908 [Multi-domain]  Cd Length: 71  Bit Score: 39.50  E-value: 2.87e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22480    4 EYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGmPERPCVLTGTPESIEQAKRLLGQIV 68
KH-I_FUBP2_rpt4 cd22488
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 129-193 3.00e-04

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.


Pssm-ID: 411916  Cd Length: 69  Bit Score: 39.31  E-value: 3.00e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCDKE--SEGTLLLsRLIKISGTQKEVAAAKHLILEK 193
Cdd:cd22488    4 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQppPNGDPNF-KLFIIRGSPQQIDHAKQLIEEK 69
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 67-122 3.21e-04

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 39.23  E-value: 3.21e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  67 IIGRQGANIKQLRKQTGARIDVdTEDVGDERVLLISGFPVQVCKAKAAIHQILTEN 122
Cdd:cd22515   16 IIGKKGESVKKMREESGARINI-SEGNCPERIITLAGPTNAIFKAFAMIIDKLEED 70
KH-I_PNPT1 cd09033
type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide ...
 121-165 3.25e-04

type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) and similar proteins; PNPT1, also called 3'-5' RNA exonuclease OLD35, or PNPase old-35, or polynucleotide phosphorylase 1, or PNPase 1, or polynucleotide phosphorylase-like protein, is an RNA-binding protein implicated in numerous RNA metabolic processes. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'-to-5' direction. It acts as a mitochondrial intermembrane factor with RNA-processing exoribonulease activity. PNPT1 is a component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. It is involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules and required for correct processing and polyadenylation of mitochondrial mRNAs. PNPT1 also plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix.


Pssm-ID: 411809 [Multi-domain]  Cd Length: 67  Bit Score: 39.10  E-value: 3.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 291084699 121 ENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE 165
Cdd:cd09033    2 ENGPVTETLEVPPSKRAKFVGPGGYNIKKLQAETGVTITQVDEET 46
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 54-117 4.41e-04

fourth 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 fourth one.


Pssm-ID: 411917 [Multi-domain]  Cd Length: 69  Bit Score: 38.76  E-value: 4.41e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDE----RVLLISGFPVQVCKAKAAIHQ 117
Cdd:cd22489    1 EITYTIPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNTdpnvRIFTIRGVPQQIEHARQLIDE 68
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 129-179 4.66e-04

third 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 third one.


Pssm-ID: 411830 [Multi-domain]  Cd Length: 66  Bit Score: 38.77  E-value: 4.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGA--KITCDKESEGTlllSRLIKISGT 179
Cdd:cd22402    5 LYIPNKAVGAIIGTKGSHIRYIKRFSGAsiKIAPADSPDAP---ERKVTITGP 54
KH-I_MEX3_rpt1 cd22423
first type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding ...
 59-115 4.75e-04

first type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the first KH domain.


Pssm-ID: 411851  Cd Length: 73  Bit Score: 39.01  E-value: 4.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 291084699  59 VP-QEAVKLIIGRQGANIKQLRKQTGARIdvDTEDVGDERVLLISGFPVQVCKAKAAI 115
Cdd:cd22423    7 VPsSEHVAEIVGRQGCKIKALRAKTNTYI--KTPVRGEEPVFVVTGRKEDVAMAKREI 62
Tudor_TDRD15_rpt7 cd20442
seventh Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; ...
 367-419 4.79e-04

seventh Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the seventh 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: 410513  Cd Length: 160  Bit Score: 40.79  E-value: 4.79e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 291084699 367 NGSWYRARVLGTL-ENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIEC 419
Cdd:cd20442   63 NLKWYRAVVEHLYpETEKMLVFFVDHGITEVVSMGNIKQLSNDLLQIPRQAVLC 116
KH-I_ScSCP160_rpt7 cd22452
seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 58-88 5.27e-04

seventh 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 seventh one.


Pssm-ID: 411880 [Multi-domain]  Cd Length: 65  Bit Score: 38.46  E-value: 5.27e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 291084699  58 RVPQEAVKLIIGRQGANIKQLRKQTGARIDV 88
Cdd:cd22452    7 KVSPRYFGRIIGPGGSNINQIREKSGCFINV 37
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 124-196 5.54e-04

second 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 second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 38.79  E-value: 5.54e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKEsegTLLLS--RLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd02396    1 PITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASE---MLPNSteRAVTISGSPEAITKCVEQICCVMLE 72
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 53-124 6.19e-04

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 38.61  E-value: 6.19e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV--DTEDVGDERVLLISGFPVQVCKAKAAIHQILTENTP 124
Cdd:cd22519    6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVagDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESPP 79
KH-I_Vigilin_rpt13 cd22416
thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 53-115 7.41e-04

thirteenth 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 thirteenth one.


Pssm-ID: 411844 [Multi-domain]  Cd Length: 78  Bit Score: 38.37  E-value: 7.41e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVlLISGFPVQVCKAKAAI 115
Cdd:cd22416    2 VTEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDII-KITGPPANVERAKAAL 63
KH-I_FUBP1_rpt3 cd22484
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 55-115 8.09e-04

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411912  Cd Length: 68  Bit Score: 37.97  E-value: 8.09e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGfPVQVCKAKAAI 115
Cdd:cd22484    3 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDgTTPERIAQITG-PPDRCQHAAEI 63
Tudor_TDRD7_rpt2 cd20428
second Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; ...
 339-427 8.31e-04

second Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. 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: 410499  Cd Length: 140  Bit Score: 39.73  E-value: 8.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 339 EMTQHYENSLPedltvHVGDIVAAplSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL----SLPF 414
Cdd:cd20428   42 QMTSEYFVSLP-----FCGKICLA--RYKGKWARVEITNVHSSRALDVHFLDTGTVASVKVSELREIPPPFLreliSIPP 114

                         90
                 ....*....|...
gi 291084699 415 QAIECSLARIAPS 427
Cdd:cd20428  115 QALKCCLADLPLN 127
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 57-121 8.48e-04

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 42.34  E-value: 8.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291084699  57 MRVPQEAVKLIIGRQGANIKQLRKQTGARIDVdtEDVGdeRVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDI--EDDG--TVKIAATDGEAAEAAKERIEGITAE 618
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 67-129 9.49e-04

first 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 first one.


Pssm-ID: 411941 [Multi-domain]  Cd Length: 73  Bit Score: 38.19  E-value: 9.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  67 IIGRQGANIKQLRKQTGARIDVD-TEDV---GDERVLLISGfpvqvckakaAIHQILTENTPVFEQL 129
Cdd:cd22513   16 VIGKGGATINDFQAQSGARIQLSrAQEFfpgTTDRVLLVSG----------SLNEVLTALNLILEKL 72
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 55-88 9.69e-04

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains 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 first one.


Pssm-ID: 411918  Cd Length: 76  Bit Score: 38.15  E-value: 9.69e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV 88
Cdd:cd22490    2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDV 35
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 55-119 1.01e-03

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains 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 first one.


Pssm-ID: 411919  Cd Length: 74  Bit Score: 38.12  E-value: 1.01e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVD-TEDVG-DERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22491    2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHrKENAGaAEKPITIHATPEGCSAACRMILEIM 68
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 55-119 1.22e-03

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 37.66  E-value: 1.22e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV--GDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22456    2 IRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLplSTERILEVQGTPDAIHNATLEIGKTL 68
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 55-119 1.43e-03

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains 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 first one.


Pssm-ID: 411920  Cd Length: 76  Bit Score: 37.48  E-value: 1.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVD-TEDVG-DERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22492    2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHrKENAGaAEKSITILSTPEGTSAACKSILEIM 68
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 131-192 1.50e-03

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 37.23  E-value: 1.50e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKIT-----CDKESEgtlllsRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22433    8 VHQSQAGCIIGRAGFKIKELREKTGATIKvysecCPRSTD------RVVQIGGKPDKVVECIREILE 68
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 128-199 1.56e-03

first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains 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 first one.


Pssm-ID: 411920  Cd Length: 76  Bit Score: 37.48  E-value: 1.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCD-KESEGTllLSRLIKISGTQKEVAAAKHLILEKVSEDEE 199
Cdd:cd22492    3 RLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHrKENAGA--AEKSITILSTPEGTSAACKSILEIMHKEAQ 73
KH-I_AtC3H36_like cd22464
type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH ...
 128-192 1.61e-03

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins; The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance.


Pssm-ID: 411892 [Multi-domain]  Cd Length: 66  Bit Score: 37.07  E-value: 1.61e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITC-DKESEGTLllsRLIKISGTQKEVAAAKHLILE 192
Cdd:cd22464    2 KISVDASLAGAIIGKGGVNSKQICRETGVKLSIrDHERDPNL---KNVELEGSFEQIKEASGMVRE 64
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 115-150 1.83e-03

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


Pssm-ID: 441442  Cd Length: 76  Bit Score: 37.34  E-value: 1.83e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 291084699 115 IHQILTENTPVFEqLSVPQRSVGRIIGRGGETIRSI 150
Cdd:COG1837   21 VTEEEGERTVVLE-LRVAPEDLGKVIGKQGRTAKAI 55
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 53-115 1.95e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411944  Cd Length: 77  Bit Score: 37.39  E-value: 1.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVdTEDVGDERVLLISGFPVQVCKAKAAI 115
Cdd:cd22516    9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINI-SEGNCPERIVTITGPTDAIFKAFAMI 70
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 55-121 1.96e-03

second 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 second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 37.29  E-value: 1.96e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVlLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22406    7 VTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEI-KITGTKEGIEKARHEIQLISDE 72
KH-I_FUBP2_rpt2 cd22482
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 56-121 1.97e-03

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411910 [Multi-domain]  Cd Length: 73  Bit Score: 37.20  E-value: 1.97e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGAR---IDVDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22482    5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKmilIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 73
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 124-183 2.02e-03

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411948 [Multi-domain]  Cd Length: 72  Bit Score: 36.92  E-value: 2.02e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291084699 124 PVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKItcdkESEGTLL---LSRLIKISGTQKEV 183
Cdd:cd22520    1 PVTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQV----QVAGDLLpnsTERAVTVSGVPDAI 59
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 131-190 2.16e-03

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 36.89  E-value: 2.16e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22455    7 VSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPG--VHDRVLTVSGPLEGVAKAFGLI 64
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 50-88 2.69e-03

second type II K-homology (KH) RNA-binding domain found in transcription termination/antitermination protein NusA and similar proteins; NusA, also called N utilization substance protein A or transcription termination/antitermination L factor, is an essential multifunctional transcription elongation factor that participates in both transcription termination and antitermination. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNA polymerase pausing provides a mechanism for synchronizing transcription and translation. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology, KH1 and KH2. The K-homology (KH) domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the second KH domain of NusA and similar proteins.


Pssm-ID: 411786 [Multi-domain]  Cd Length: 61  Bit Score: 36.36  E-value: 2.69e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 291084699  50 EDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV 88
Cdd:cd22529   22 EDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDI 60
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 128-194 3.09e-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: 36.47  E-value: 3.09e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCdKESEGtLLLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22486    6 EVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQF-KPDDG-ISPERVAQVMGPPDRCQHAAHIINELI 70
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 129-197 3.15e-03

third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains 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 third one.


Pssm-ID: 411925  Cd Length: 77  Bit Score: 36.61  E-value: 3.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291084699 129 LSVPQRSVGRIIGRGGETIRSICKASGAKITCdKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSED 197
Cdd:cd22497    7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKI-APAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEE 74
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
 64-119 3.45e-03

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.


Pssm-ID: 411858 [Multi-domain]  Cd Length: 66  Bit Score: 36.11  E-value: 3.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  64 VKLIIGRQGANIKQLRKQTGARIDVDTEDvgDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22430   11 VGAVIGRGGSKIRELEESTGSKIKIIKGG--QEAEVKIFGSDEAQQKAKELIDELV 64
KH-I_PEPPER_like_rpt3 cd22461
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 56-115 4.23e-03

third 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 and flowering locus K homology domain protein (FLK). 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. The model corresponds to the KH3 domain of PEPPER and FLK.


Pssm-ID: 411889  Cd Length: 69  Bit Score: 35.99  E-value: 4.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAI 115
Cdd:cd22461    5 QMQIPLSYADAIIGTAGANISYIRRTSGATITIqETRGAPGEMTVEIHGTQSQVQTAQQLI 65
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 131-194 4.43e-03

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 36.00  E-value: 4.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 291084699 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDkESEGTlllSRLIKISGTQKEVAAakhlILEKV 194
Cdd:cd22432    8 IPSKAAGAIIGKGGENIKRLRTEYNASVSVP-DSSGP---ERILTISADRETVLG----ILTEI 63
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 53-121 4.57e-03

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411948 [Multi-domain]  Cd Length: 72  Bit Score: 36.15  E-value: 4.57e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV--DTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22520    2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVagDLLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72
KH-I_FUBP2_rpt2 cd22482
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 127-196 4.72e-03

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411910 [Multi-domain]  Cd Length: 73  Bit Score: 36.04  E-value: 4.72e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291084699 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22482    4 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 73
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 53-121 5.86e-03

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411946 [Multi-domain]  Cd Length: 78  Bit Score: 35.87  E-value: 5.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 291084699  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV--DTEDVGDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22518    7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVagDMLPNSTERAITIAGIPQSIIECVKQICVVMLE 77
KH-I_Vigilin_rpt10 cd22413
tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 139-190 6.79e-03

tenth 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 tenth one.


Pssm-ID: 411841 [Multi-domain]  Cd Length: 66  Bit Score: 35.31  E-value: 6.79e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699 139 IIGRGGETIRSICKASGAKITC----DKESEgtlllsrLIKISGTQKEVAAAKHLI 190
Cdd:cd22413   17 LIGRGGANIRKIRDNTGARIIFptarDEDQE-------LITIIGTKEAVEKAKEEL 65
Tudor_SPF30 cd20399
Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar ...
 356-403 7.38e-03

Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins; SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. Overexpression of SPF30 causes apoptosis. It contains one Tudor domain. 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: 410470 [Multi-domain]  Cd Length: 55  Bit Score: 34.97  E-value: 7.38e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 291084699 356 VGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLR 403
Cdd:cd20399    3 VGDKCMAVWSEDGQYYEATIEEISEDGTCTVTFDGYGNTEVTPLSQLK 50
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 67-122 7.90e-03

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 35.39  E-value: 7.90e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 291084699  67 IIGRQGANIKQLRKQTGARIDVdTEDVGDERVLLISGFPVQVCKAKAAIHQILTEN 122
Cdd:cd22517   16 IIGKKGETVKRIREESSARITI-SEGSCPERITTITGSTDAVFRAFSMIAFKLEED 70
KH_2 pfam07650
KH domain;
45-88 9.65e-03

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 35.22  E-value: 9.65e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 291084699   45 LTFVGEDDIEIEmrVPQEAVKL---------IIGRQGANIKQLRKQTGARIDV 88
Cdd:pfam07650  10 LKFAGVSKVEIE--RTPNAVIVvirasqpgiVIGKGGSRIKKIGKELRKDIEK 60
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 120-183 9.76e-03

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 35.53  E-value: 9.76e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 291084699 120 TENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKItcdkESEGTLL---LSRLIKISGTQKEV 183
Cdd:cd22519    1 TSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQV----QVAGDMLpnsTERAVTISGTPDAI 63
 
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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