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Conserved domains on  [gi|564365534|ref|XP_006243865|]
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poly(rC)-binding protein 4 isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 101-172 2.77e-42

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: 140.93  E-value: 2.77e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22520    1 PVTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 17-86 5.31e-41

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.


The actual alignment was detected with superfamily member cd22517:

Pssm-ID: 469614  Cd Length: 70  Bit Score: 137.47  E-value: 5.31e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22517    1 TLTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCPERITTITGSTDAVFRAFSMIAFKLEED 70
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 241-307 4.78e-38

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: 130.01  E-value: 4.78e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22523    1 TSSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLITT 67
UBCc_UEV super family cl49610
Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain/ubiquitin E2 variant (UEV) domain; ...
 166-194 8.12e-03

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain/ubiquitin E2 variant (UEV) domain; The family includes ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain and ubiquitin (Ub) E2 variant (UEV) domain. They belong to the ubiquitin-conjugating (UBC) superfamily that represents a structural domain with an alpha-beta(4)-alpha(3) core fold. E2 is part of the ubiquitin-mediated protein degradation pathway in which a thioester linkage forms between a conserved cysteine and the C-terminus of ubiquitin, and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thioester linkages without the use of E3s. Several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) contains the UEV domain, which lacks the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways.


The actual alignment was detected with superfamily member cd23805:

Pssm-ID: 483950  Cd Length: 146  Bit Score: 36.35  E-value: 8.12e-03
                         10        20
                 ....*....|....*....|....*....
gi 564365534 166 ICAVILESPPKGAtipYHPSLSLGTVLLS 194
Cdd:cd23805   81 ICLDILKMPPKGS---WKPSLNISTVLTS 106
 
Name Accession Description Interval E-value
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 101-172 2.77e-42

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: 140.93  E-value: 2.77e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22520    1 PVTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 17-86 5.31e-41

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: 137.47  E-value: 5.31e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22517    1 TLTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCPERITTITGSTDAVFRAFSMIAFKLEED 70
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 241-307 4.78e-38

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: 130.01  E-value: 4.78e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22523    1 TSSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLITT 67
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 243-307 6.93e-18

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: 76.55  E-value: 6.93e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 103-166 5.70e-14

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: 65.77  E-value: 5.70e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGTPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
19-80 6.21e-14

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 65.78  E-value: 6.21e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534    19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIA 80
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELIL 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 19-79 1.40e-13

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: 64.61  E-value: 1.40e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534   19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITI--SEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIppSESEGNERIVTITGTPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
243-305 1.60e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 61.93  E-value: 1.60e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534   243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNqaEGAGERHVTITGSPVSIALAQYLI 305
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPENVEKAAELI 64
KH smart00322
K homology RNA-binding domain;
101-170 2.01e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 61.54  E-value: 2.01e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534   101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGdllPNSTERAVTVSGVPDAIILCVRQICAVI 170
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEKAAELILEIL 68
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 20-139 8.31e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 42.55  E-value: 8.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  20 LRMLMHGK----EVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTA-AVFHAVSMI-----------AFKL 83
Cdd:PRK13763   1 MMMMEYVKipkdRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPlAVLKARDIVkaigrgfspekALRL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  84 --DE------DLCAAPANGGSVSRppvtlrlvipasQCGSLIGKAGTKIKEIRETTGAQVQVAG 139
Cdd:PRK13763  81 ldDDyvleviDLSDYGDSPNALRR------------IKGRIIGEGGKTRRIIEELTGVDISVYG 132
UBCc_UBE2T cd23805
Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T ...
 166-194 8.12e-03

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T and related enzymes; The E2T subfamily includes mammalian ubiquitin-conjugating enzymes E2 T (UBE2T/HSPC150/PIG50), plant ubiquitin-conjugating enzyme E2 37 (UBC37), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2T, also called cell proliferation-inducing gene 50 protein, catalyzes monoubiquitination. It is involved in mitomycin-C (MMC)-induced DNA repair. It acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway. UBE2T also mediates monoubiquitination of FANCL and FANCI. It may contribute to ubiquitination and degradation of BRCA1. In vitro, UBE2T can promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination.


Pssm-ID: 467425  Cd Length: 146  Bit Score: 36.35  E-value: 8.12e-03
                         10        20
                 ....*....|....*....|....*....
gi 564365534 166 ICAVILESPPKGAtipYHPSLSLGTVLLS 194
Cdd:cd23805   81 ICLDILKMPPKGS---WKPSLNISTVLTS 106
 
Name Accession Description Interval E-value
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 101-172 2.77e-42

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: 140.93  E-value: 2.77e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22520    1 PVTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 17-86 5.31e-41

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: 137.47  E-value: 5.31e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22517    1 TLTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCPERITTITGSTDAVFRAFSMIAFKLEED 70
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 241-307 4.78e-38

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: 130.01  E-value: 4.78e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22523    1 TSSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLITT 67
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 98-175 4.79e-38

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: 130.29  E-value: 4.79e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534  98 SRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILESPP 175
Cdd:cd22519    2 SKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVMLESPP 79
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 20-86 6.48e-37

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: 126.99  E-value: 6.48e-37
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22438    1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCPERIVTVTGTTDAVFKAFELICRKLEED 67
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 101-172 8.47e-37

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: 126.62  E-value: 8.47e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd02396    1 PITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTISGSPEAITKCVEQICCVMLE 72
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 96-173 8.66e-34

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: 119.07  E-value: 8.66e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534  96 SVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILES 173
Cdd:cd22518    1 AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVMLES 78
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 241-307 4.69e-33

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: 116.95  E-value: 4.69e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22439    1 QTTQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLAQYLINA 67
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 234-307 1.47e-32

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: 115.98  E-value: 1.47e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 234 GLDPSTQTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22522    1 GLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGSPANISLAQYLINA 74
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 17-86 3.31e-32

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: 114.72  E-value: 3.31e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22515    1 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKLEED 70
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 11-86 2.41e-31

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: 112.89  E-value: 2.41e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534  11 EPELSITLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22516    2 EGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIFKAFAMIAYKFEED 77
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 238-307 7.88e-28

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: 103.60  E-value: 7.88e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 238 STQTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22521    1 SAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINA 70
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 104-166 6.77e-18

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: 76.52  E-value: 6.77e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22433    4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQIGGKPDKVVECIREI 66
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 243-307 6.93e-18

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: 76.55  E-value: 6.93e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
 243-307 3.14e-17

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: 74.94  E-value: 3.14e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22404    2 SKKVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLINA 66
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 245-305 1.10e-15

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: 70.41  E-value: 1.10e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd00105    2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELI 62
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 238-305 2.74e-15

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: 69.66  E-value: 2.74e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 238 STQTSsqeflVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22434    3 TTQVT-----IPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNAQYLL 65
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 104-166 2.42e-14

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: 66.86  E-value: 2.42e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAG--DLLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22437    1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPkdQLLPGSSERIVTITGSFDQVVKAVALI 65
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 103-171 3.16e-14

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: 66.55  E-value: 3.16e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVIL 171
Cdd:cd22456    1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNATLEIGKTLL 69
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 103-166 5.70e-14

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: 65.77  E-value: 5.70e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGTPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
19-80 6.21e-14

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 65.78  E-value: 6.21e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534    19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMIA 80
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELIL 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 19-79 1.40e-13

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: 64.61  E-value: 1.40e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534   19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITI--SEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIppSESEGNERIVTITGTPEAVEAAKALI 63
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 244-306 1.63e-13

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: 64.40  E-value: 1.63e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 244 QEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ-AEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22457    1 QNISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKApHDETGERMFTITGTPEANDRALRLLY 64
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 242-305 2.81e-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: 63.81  E-value: 2.81e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 242 SSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22396    1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLI 64
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 242-306 3.58e-13

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: 63.59  E-value: 3.58e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 242 SSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKI---GNQAEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22514    1 TSVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKIsdrGDFVSGTRNRKVTITGPQDAVQMAQYLLE 68
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 103-168 5.03e-13

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: 63.41  E-value: 5.03e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQV-AGDLLP---NSTERAVTVSGVPDAIILCVRQICA 168
Cdd:cd22460    1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRIlPEEELPpcaSPDDRVVQISGEAQAVKKALELVSS 70
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 248-306 5.89e-13

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: 62.98  E-value: 5.89e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 248 VPNDLIGCVIGRQGSKISEIRQMSGAHIKI---GNQAEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd09031    7 VPENLVGAILGKGGKTLVEIQELTGARIQIskkGEFVPGTRNRKVTITGTPAAVQAAQYLIE 68
KH smart00322
K homology RNA-binding domain;
243-305 1.60e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 61.93  E-value: 1.60e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534   243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNqaEGAGERHVTITGSPVSIALAQYLI 305
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPENVEKAAELI 64
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 20-79 1.65e-12

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: 61.89  E-value: 1.65e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCP---ERITTITGSTAAVFHAVSMI 79
Cdd:cd22433    4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPrstDRVVQIGGKPDKVVECIREI 66
KH smart00322
K homology RNA-binding domain;
101-170 2.01e-12

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 61.54  E-value: 2.01e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534   101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGdllPNSTERAVTVSGVPDAIILCVRQICAVI 170
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEKAAELILEIL 68
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 20-85 2.71e-12

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: 61.47  E-value: 2.71e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS----EGSC-PERITTITGSTAAVFHAVSMIAFKLDE 85
Cdd:cd22401    2 LKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISslqdLTSYnPERTITIKGSLEAMSEAESLISEKLRE 72
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 104-166 6.26e-12

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: 60.00  E-value: 6.26e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKE-GEGSGERVVTITGTPEAVEKAKELI 62
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 20-79 1.02e-11

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: 59.62  E-value: 1.02e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPkeGEGSGERVVTITGTPEAVEKAKELI 62
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 18-80 1.53e-11

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: 59.23  E-value: 1.53e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  18 LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGSTAAVFHAVSMIA 80
Cdd:cd22455    1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVvpGVHDRVLTVSGPLEGVAKAFGLIA 65
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 17-76 2.62e-11

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: 58.39  E-value: 2.62e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGST---AAVFHAV 76
Cdd:cd22459    1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGvpGTEERVITISSSEapeAPVSPAQ 65
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 247-306 4.63e-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: 57.61  E-value: 4.63e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ---AEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22437    4 LVPNSSCGLIIGKGGSTIKELREDSNANIKISPKdqlLPGSSERIVTITGSFDQVVKAVALIL 66
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 101-172 8.62e-11

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: 57.16  E-value: 8.62e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQV--AGDLLPNSTERAVTVSGVPDAiilcVRQICAVILE 172
Cdd:cd22435    1 QCSLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLskNNDFYPGTTERVCLIQGEVEA----VNAVLDFILE 70
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 248-305 1.01e-10

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: 56.88  E-value: 1.01e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 248 VPNDLIGCVIGRQGSKISEIRQMSGAHIKIG-NQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22402    7 IPNKAVGAIIGTKGSHIRYIKRFSGASIKIApADSPDAPERKVTITGPPEAQWKAQLCI 65
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 102-154 1.04e-10

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: 56.85  E-value: 1.04e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVaGDLLPNSTERAVTVSG 154
Cdd:cd22459    2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV-EDGVPGTEERVITISS 53
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 19-83 1.86e-10

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: 56.09  E-value: 1.86e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS----EGSCPERITTITGSTAAVFHAVSMIAFKL 83
Cdd:cd22436    2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISqkpeSINLQERVVTVTGEPEANRKAVSLILQKI 70
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
 245-307 3.07e-10

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: 55.33  E-value: 3.07e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22462    2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLIEA 64
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 19-72 3.81e-10

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: 54.88  E-value: 3.81e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAV 72
Cdd:cd22432    3 ELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGPERILTISADRETV 56
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 94-161 5.59e-10

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: 55.12  E-value: 5.59e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534  94 GGSVSRPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAIIL 161
Cdd:cd22522    1 GLDASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIA-NATEGSSERQITITGSPANISL 67
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 20-83 7.23e-10

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: 54.53  E-value: 7.23e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS-----EGSCPERITTITGSTAAVFHAVSMIAFKL 83
Cdd:cd22437    1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISpkdqlLPGSSERIVTITGSFDQVVKAVALILEKL 69
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 243-305 1.12e-09

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: 54.26  E-value: 1.12e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22478    5 TEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLL 67
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 247-305 1.59e-09

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: 53.43  E-value: 1.59e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKI-GNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd02396    7 LVPASQCGSLIGKGGSKIKEIRESTGASVQVaSEMLPNSTERAVTISGSPEAITKCVEQI 66
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 103-172 1.61e-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: 53.39  E-value: 1.61e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVA-GDLLPNSTERAVTVSGVPDAIilcvRQICAVILE 172
Cdd:cd22436    2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISqKPESINLQERVVTVTGEPEAN----RKAVSLILQ 68
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 243-305 2.71e-09

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: 52.98  E-value: 2.71e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22480    2 TEEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMPERPCVLTGTPESIEQAKRLL 64
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 240-305 3.18e-09

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: 52.72  E-value: 3.18e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 240 QTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEG--AGERHVTITGSPVSIALAQYLI 305
Cdd:cd22428    3 RQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGgeLPERVLLIQGNPVQAQRAEEAI 70
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 103-158 3.57e-09

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: 52.25  E-value: 3.57e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDA 158
Cdd:cd22402    2 TTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPERKVTITGPPEA 57
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 243-305 3.67e-09

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: 52.64  E-value: 3.67e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22479    2 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGSPEAVQKAKMML 64
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 27-79 3.71e-09

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: 52.26  E-value: 3.71e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  27 KEVGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22396   10 KMVGLIIGRGGEQINRLQAESGAKIQIApdSGGLPERPCTLTGTPDAIETAKRLI 64
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 245-306 5.15e-09

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: 52.14  E-value: 5.15e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22395    3 EFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIR 64
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 101-159 5.98e-09

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: 51.94  E-value: 5.98e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAI 159
Cdd:cd22434    1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKID-EPLPGSEDRIITITGTQDQI 58
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 30-68 6.04e-09

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: 51.94  E-value: 6.04e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 564365534  30 GSIIGKKGETVKRIREQSSARITISE---GScPERITTITGS 68
Cdd:cd22434   14 GSIIGKGGQRIRQIRHESGASIKIDEplpGS-EDRIITITGT 54
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 247-305 7.06e-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: 51.85  E-value: 7.06e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEG--AGERHVTITGSPVSIALAQYLI 305
Cdd:cd22436    6 LVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESinLQERVVTVTGEPEANRKAVSLI 66
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 102-159 7.10e-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: 51.81  E-value: 7.10e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVA--GDLLPNSTERAVTVSGVPDAI 159
Cdd:cd09031    1 TVIELEVPENLVGAILGKGGKTLVEIQELTGARIQISkkGEFVPGTRNRKVTITGTPAAV 60
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 246-305 8.95e-09

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: 51.53  E-value: 8.95e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIG-NQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22456    4 LLIPHSLIGSIIGKGGARIKEIQDGSGARLVASkEFLPLSTERILEVQGTPDAIHNATLEI 64
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 103-166 9.70e-09

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: 51.08  E-value: 9.70e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22439    3 TQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIA-NSEDGSTERSVTITGTPEAVSLAQYLI 65
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 246-307 1.16e-08

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: 51.08  E-value: 1.16e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE-----GAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22460    4 LLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEElppcaSPDDRVVQISGEAQAVKKALELVSS 70
KH-I_ANKRD17 cd22502
type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 ...
 243-307 1.44e-08

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: 50.91  E-value: 1.44e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22502    2 SKKVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTGDRIITIRGGTESTRQATQLINA 66
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 104-167 1.64e-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: 50.72  E-value: 1.64e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPnstERAVTVSGVPDAIILCVRQIC 167
Cdd:cd22438    1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCP---ERIVTVTGTTDAVFKAFELIC 61
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 101-154 1.72e-08

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: 50.90  E-value: 1.72e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQV--AGDLLPNSTERAVTVSG 154
Cdd:cd22513    1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLsrAQEFFPGTTDRVLLVSG 56
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 245-305 1.99e-08

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: 50.30  E-value: 1.99e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIG-NQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22399    3 TFLVPANKCGLVIGKGGETIRQINQQSGAHVELDrNPPPNPNEKLFIIRGNPQQIEHAKQLI 64
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 247-307 2.76e-08

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: 49.92  E-value: 2.76e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE---GAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22401    5 LAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDltsYNPERTITIKGSLEAMSEAESLISE 68
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 245-305 3.11e-08

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: 50.01  E-value: 3.11e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22454    7 EVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSPDNVAAAKRLI 67
KH-I_IGF2BP2_rpt2 cd22494
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-85 4.28e-08

second 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 second one.


Pssm-ID: 411922  Cd Length: 77  Bit Score: 49.64  E-value: 4.28e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGS-----CPERITTITGSTAAVFHAVSMIAFKLDE 85
Cdd:cd22494    2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQdltiyNPERTITVKGSIEACSSAEVEIMKKLRE 72
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 103-172 5.11e-08

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: 49.63  E-value: 5.11e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22496    4 TVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKE 73
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 104-166 5.53e-08

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: 49.19  E-value: 5.53e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22400    2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAITIYGTPEGCSSACKQI 64
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 253-306 5.56e-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: 5.56e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 253 IGCVIGRQGSKISEIRQMSGAHIKIGNqaEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22438   10 VGSIIGKKGETIKKFREESGARINISD--GSCPERIVTVTGTTDAVFKAFELIC 61
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
 104-157 7.54e-08

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: 48.78  E-value: 7.54e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPD 157
Cdd:cd22462    1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVL-KPDSATGERIVLISGTPD 53
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 104-159 8.05e-08

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: 48.76  E-value: 8.05e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAG--DLLPNSTERAVTVSGVPDAI 159
Cdd:cd22401    2 LKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSlqDLTSYNPERTITIKGSLEAM 59
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 247-296 9.29e-08

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: 48.37  E-value: 9.29e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPV 296
Cdd:cd22459    7 LCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSSEA 56
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 29-79 9.36e-08

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: 48.48  E-value: 9.36e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  29 VGSIIGKKGETVKRIREQSSARI----TISEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22428   16 VGLIIGRQGATIKQIQKETGARIdfkdEGSGGELPERVLLIQGNPVQAQRAEEAI 70
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 247-295 9.71e-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: 48.40  E-value: 9.71e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ-AEGAGERHVTITGSP 295
Cdd:cd22433    7 LVHQSQAGCIIGRAGFKIKELREKTGATIKVYSEcCPRSTDRVVQIGGKP 56
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 18-79 1.02e-07

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: 48.47  E-value: 1.02e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  18 LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22454    4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFErvNGGSPNREVQITGSPDNVAAAKRLI 67
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 19-80 1.07e-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: 48.39  E-value: 1.07e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCP-------ERITTITGSTAAVFHAVSMIA 80
Cdd:cd22460    1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELppcaspdDRVVQISGEAQAVKKALELVS 69
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 29-79 1.12e-07

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: 48.02  E-value: 1.12e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISE--GSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22398   11 VGVVIGKGGEMIKKIQNETGARVQFKPddGNSPDRICVITGPPDQVQHAARMI 63
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 20-84 1.17e-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: 48.30  E-value: 1.17e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISE------GSCpERITTITGSTAAVFHAVSMIAFKLD 84
Cdd:cd22435    4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKnndfypGTT-ERVCLIQGEVEAVNAVLDFILEKIR 73
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 106-161 1.66e-07

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: 47.97  E-value: 1.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQVQVaGDLLPNSTERAVTVSGVPDAIIL 161
Cdd:cd22523    6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKI-GNQTEGTSERHVTITGSPVSITL 60
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 29-79 1.69e-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: 1.69e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITI--SEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22439   13 IGCIIGKGGTKINEIRQLSGATIKIanSEDGSTERSVTITGTPEAVSLAQYLI 65
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 102-159 2.05e-07

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: 47.70  E-value: 2.05e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDllpNSTERAVTVSGVPDAI 159
Cdd:cd22515    2 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG---NCPERIITLAGPTNAI 56
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 101-166 2.24e-07

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: 47.18  E-value: 2.24e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDllpNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22432    1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS---SGPERILTISADRETVLGILTEI 63
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 247-306 2.79e-07

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: 47.27  E-value: 2.79e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE-GAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22400    5 LVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENaGAAEKAITIYGTPEGCSSACKQIL 65
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 108-167 2.85e-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: 47.22  E-value: 2.85e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAIILCVRQIC 167
Cdd:cd22399    6 VPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNEKLFIIRGNPQQIEHAKQLIR 65
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 100-172 2.88e-07

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: 47.79  E-value: 2.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 100 PPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQV-------AGDLLPNSTERAVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22446    5 PKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIpkrneegNYDEDDDDETVEISIEGDAEGVELAKKEIEAIVKE 84
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 102-159 4.85e-07

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: 46.48  E-value: 4.85e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAI 159
Cdd:cd22396    1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPD-SGGLPERPCTLTGTPDAI 57
KH-I_ANKHD1 cd22503
type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing ...
 243-307 5.03e-07

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: 47.05  E-value: 5.03e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22503    2 SKKLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNGERMITIRGGTESTRYAVQLINA 66
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 18-86 5.24e-07

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: 46.94  E-value: 5.24e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  18 LTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGS----CPERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22429    2 ITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESddtlDLVRLITITGTKKEVDAAKSLILEKVSEE 74
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 102-159 5.46e-07

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: 46.63  E-value: 5.46e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDllpNSTERAVTVSGVPDAI 159
Cdd:cd22516    9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG---NCPERIVTITGPTDAI 63
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 103-158 5.83e-07

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: 46.60  E-value: 5.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDA 158
Cdd:cd22498    6 TVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGPPEA 61
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 29-79 5.89e-07

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: 46.04  E-value: 5.89e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITI-SEGSCPERItTITGSTAAVFHAVSMI 79
Cdd:cd22411   11 HKNIIGKGGATIKKIREETNTRIDLpEENSDSDVI-TITGKKEDVEKARERI 61
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
 246-305 6.14e-07

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: 46.12  E-value: 6.14e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIgnqAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22430    4 FKIDSSLVGAVIGRGGSKIRELEESTGSKIKI---IKGGQEAEVKIFGSDEAQQKAKELI 60
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 108-158 7.23e-07

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: 45.91  E-value: 7.23e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDA 158
Cdd:cd22457    5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDETGERMFTITGTPEA 55
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 106-161 8.83e-07

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: 46.20  E-value: 8.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAIIL 161
Cdd:cd22521    9 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIA-NPVEGSTDRQVTITGSAASISL 63
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 20-79 9.44e-07

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: 45.73  E-value: 9.44e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS---EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22400    2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHrkeNAGAAEKAITIYGTPEGCSSACKQI 64
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 102-159 9.66e-07

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: 45.75  E-value: 9.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAI 159
Cdd:cd22455    1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVS-KVVPGVHDRVLTVSGPLEGV 57
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 100-138 1.26e-06

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: 45.49  E-value: 1.26e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 564365534 100 PPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVA 138
Cdd:cd22447    2 PKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIP 40
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 108-159 1.29e-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: 45.31  E-value: 1.29e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTE--RAVTVSGVPDAI 159
Cdd:cd22489    6 IPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNTDPnvRIFTIRGVPQQI 59
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 25-79 2.26e-06

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: 44.48  E-value: 2.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  25 HGKEVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd02394    9 DPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEI 63
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 102-166 2.38e-06

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: 44.63  E-value: 2.38e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPnstERAVTVSGVPDAIILCVRQI 166
Cdd:cd22517    2 LTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCP---ERITTITGSTDAVFRAFSMI 63
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 19-83 3.27e-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: 44.35  E-value: 3.27e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGS-----CPERITTITGSTAAVFHAVSMIAFKL 83
Cdd:cd22513    3 VAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQeffpgTTDRVLLVSGSLNEVLTALNLILEKL 72
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 19-79 3.34e-06

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: 44.16  E-value: 3.34e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCP---ERITTITGSTAAVFHAVSMI 79
Cdd:cd22402    2 TTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPdapERKVTITGPPEAQWKAQLCI 65
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 246-307 4.02e-06

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: 43.86  E-value: 4.02e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKI-GNQAEGAGERHVTITGSPVSIALAQYLITA 307
Cdd:cd22520    6 LVIPASQCGSLIGKAGSKIKEIRESTGAQVQVaGDLLPNSTERAVTVSGVPDAIIQCVRQICA 68
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 106-158 4.35e-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: 43.93  E-value: 4.35e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDA 158
Cdd:cd22497    7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPDVSERMVIITGPPEA 59
KH-I_TDRKH_rpt2 cd22429
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 243-306 4.89e-06

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: 43.86  E-value: 4.89e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGE--RHVTITGSPVSIALAQYLIT 306
Cdd:cd22429    3 TEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDlvRLITITGTKKEVDAAKSLIL 68
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 102-166 4.97e-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: 43.59  E-value: 4.97e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGdlLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22458    1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIP--ISNSSQQTIHLSGTDKQIALAISSI 63
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 246-305 5.04e-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: 43.76  E-value: 5.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGN---QAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22489    4 YTIPADKCGLVIGKGGENIKSINQQSGAHVELQRnppPNTDPNVRIFTIRGVPQQIEHARQLI 66
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 101-166 5.11e-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: 43.57  E-value: 5.11e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLP-NSTERAVTVSGVPD----AIILCVRQI 166
Cdd:cd22463    1 RSKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPlEETQKILRISGTEEqlkrAQSLVEGLI 71
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 28-84 5.34e-06

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: 43.66  E-value: 5.34e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  28 EVGSIIGKKGETVKRIREQSSARITISEGSCPE--RITTITGSTAAVFHAVSMIAFKLD 84
Cdd:cd22395   10 LVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQnfQICSIEGTQQQIDKALKLIRKKFP 68
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 29-79 5.47e-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: 43.22  E-value: 5.47e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISEG---SCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22457   10 VGCIIGKGGSKIQEIRRLSGCKISIAKAphdETGERMFTITGTPEANDRALRLL 63
KH-I_IGF2BP3_rpt2 cd22495
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-85 5.65e-06

second 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 second one.


Pssm-ID: 411923  Cd Length: 77  Bit Score: 43.88  E-value: 5.65e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGS-----CPERITTITGSTAAVFHAVSMIAFKLDE 85
Cdd:cd22495    2 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQdltlyNPERTITVKGSIETCAKAEEEIMKKIRE 72
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-85 6.54e-06

second 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 second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 44.28  E-value: 6.54e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGS-----CPERITTITGSTAAVFHAVSMIAFKLDE 85
Cdd:cd22493    7 LKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQdltlyNPERTITVKGSIEACCRAEQEIMKKVRE 77
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 246-305 8.23e-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: 42.91  E-value: 8.23e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE---GAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22435    6 LLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDfypGTTERVCLIQGEVEAVNAVLDFI 68
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 256-310 1.20e-05

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: 42.56  E-value: 1.20e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 256 VIGRQGSKISEIRQMSGAHIKIGNQAEGAGErhVTITGSPVSIALAQYLITAWAT 310
Cdd:cd02394   16 IIGKGGANIKRIREESGVSIRIPDDEANSDE--IRIEGSPEGVKKAKAEILELVD 68
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
 105-170 1.22e-05

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: 42.58  E-value: 1.22e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 105 RLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAiilcVRQICAVI 170
Cdd:cd22404    4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQ-KGEQGDRRITIKGSADA----TRQAAQLI 64
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 103-159 1.50e-05

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: 42.41  E-value: 1.50e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVA--GDLLPNSTERAVTVSGVPDAI 159
Cdd:cd22514    2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKISdrGDFVSGTRNRKVTITGPQDAV 60
KH-I_FUBP_rpt4 cd22399
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 30-82 1.72e-05

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: 42.21  E-value: 1.72e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534  30 GSIIGKKGETVKRIREQSSARITISEGSCP---ERITTITGSTAAVFHAVSMIAFK 82
Cdd:cd22399   12 GLVIGKGGETIRQINQQSGAHVELDRNPPPnpnEKLFIIRGNPQQIEHAKQLIREK 67
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 245-305 2.23e-05

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: 42.03  E-value: 2.23e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERH--VTITGSPVSIALAQYLI 305
Cdd:cd22463    5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQkiLRISGTEEQLKRAQSLV 67
KH-I_FUBP1_rpt3 cd22484
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 29-80 2.60e-05

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: 41.43  E-value: 2.60e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMIA 80
Cdd:cd22484   12 VGIVIGRNGEMIKKIQNDAGVRIQFKpdDGTTPERIAQITGPPDRCQHAAEIIT 65
KH-I_MASK cd22404
type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family ...
 26-85 2.73e-05

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: 41.43  E-value: 2.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534  26 GKEVGSIIGKKGETVKRIREQSSARITI--SEGSCPERITTITGSTAAVFHAVSMIAFKLDE 85
Cdd:cd22404    9 NSAISRVIGRGGCNINAIREVSGAHIEIdkQKGEQGDRRITIKGSADATRQAAQLINALIKD 70
KH_I_FMR1_FXR_rpt2 cd22426
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 245-272 3.07e-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: 41.36  E-value: 3.07e-05
                         10        20
                 ....*....|....*....|....*...
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSG 272
Cdd:cd22426    5 EFKVDPDLIGLAIGSHGSNIQQARKIPG 32
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 246-298 3.32e-05

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: 41.70  E-value: 3.32e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKI-GNQAEGAGERHVTITGSPVSI 298
Cdd:cd22519   10 LVVPASQCGSLIGKGGSKIKEIRESTGAQVQVaGDMLPNSTERAVTISGTPDAI 63
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 19-86 3.58e-05

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: 41.54  E-value: 3.58e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPE---RITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22496    4 TVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDskvRMVIITGPPEAQFKAQGRIYGKLKEE 74
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 19-80 3.74e-05

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: 41.13  E-value: 3.74e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCP---ERITTITGSTAAVFHAVSMIA 80
Cdd:cd22456    1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPlstERILEVQGTPDAIHNATLEIG 65
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 240-302 3.79e-05

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: 41.60  E-value: 3.79e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 240 QTSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGnQAEG--AGERHVTITGSPVSIALAQ 302
Cdd:cd22498    3 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGpdAKLRMVIITGPPEAQFKAQ 66
KH-I_RCF3_like_rpt5 cd22463
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 19-79 4.34e-05

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: 40.88  E-value: 4.34e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPE----RITTITGSTAAVFHAVSMI 79
Cdd:cd22463    3 KIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLeetqKILRISGTEEQLKRAQSLV 67
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 114-170 4.66e-05

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: 41.02  E-value: 4.66e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 114 GSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTeraVTVSGVPDAIILCVRQICAVI 170
Cdd:cd02394   14 GHIIGKGGANIKRIREESGVSIRIPDDEANSDE---IRIEGSPEGVKKAKAEILELV 67
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 102-170 4.85e-05

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: 40.76  E-value: 4.85e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgDLLPNSTERAVTVSGVPDAIILCVRQICAVI 170
Cdd:cd22454    4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFE-RVNGGSPNREVQITGSPDNVAAAKRLIEDTI 71
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 29-79 5.07e-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: 40.69  E-value: 5.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22479   12 VGLIIGRGGEQINKIQQDSGCKVQISpdSGGLPERSVSLTGSPEAVQKAKMML 64
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 243-306 5.58e-05

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: 40.71  E-value: 5.58e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22398    1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPDQVQHAARMIQ 64
KH-I_IGF2BP3_rpt3 cd22498
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 17-86 6.44e-05

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: 40.83  E-value: 6.44e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  17 TLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEGSCPE---RITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22498    4 SETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDaklRMVIITGPPEAQFKAQGRIYGKLKEE 76
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 242-305 6.92e-05

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: 40.50  E-value: 6.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 242 SSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE---GAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22513    2 VVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQEffpGTTDRVLLVSGSLNEVLTALNLI 68
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 254-305 8.24e-05

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: 40.36  E-value: 8.24e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534 254 GCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22455   13 AVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKAFGLI 64
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 20-139 8.31e-05

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 42.55  E-value: 8.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  20 LRMLMHGK----EVGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTA-AVFHAVSMI-----------AFKL 83
Cdd:PRK13763   1 MMMMEYVKipkdRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPlAVLKARDIVkaigrgfspekALRL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534  84 --DE------DLCAAPANGGSVSRppvtlrlvipasQCGSLIGKAGTKIKEIRETTGAQVQVAG 139
Cdd:PRK13763  81 ldDDyvleviDLSDYGDSPNALRR------------IKGRIIGEGGKTRRIIEELTGVDISVYG 132
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 27-86 1.17e-04

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: 40.08  E-value: 1.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  27 KEVGSIIGKKGETVKRIREQSSARITISEGSCP---ERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22497   12 QAVGAIIGKKGQHIKQLARFAGASIKIAPAEGPdvsERMVIITGPPEAQFKAQGRIFGKLKEE 74
KH-I_PEPPER_like_rpt3 cd22461
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 243-305 1.43e-04

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: 39.46  E-value: 1.43e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22461    3 SQQMQIPLSYADAIIGTAGANISYIRRTSGATITIQETRGAPGEMTVEIHGTQSQVQTAQQLI 65
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 108-159 1.64e-04

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: 39.16  E-value: 1.64e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDlLPNSTERAVTVSGVPDAI 159
Cdd:cd22398    6 VPRFAVGVVIGKGGEMIKKIQNETGARVQFKPD-DGNSPDRICVITGPPDQV 56
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 19-81 1.64e-04

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: 39.15  E-value: 1.64e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534  19 TLRMLMHGKEVGSIIGKKGETVKRIREQSSARIT-ISEGSCP---ERITTITGSTAAVFHAVSMIAF 81
Cdd:cd22397    1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVmIQDGPQPtgqDKPLRITGDPQKVQRAKELVME 67
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 15-67 1.84e-04

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: 39.11  E-value: 1.84e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534  15 SITLTLRMLMHGKevgsIIGKKGETVKRIREQSSARITI-SEGSCPERITTITG 67
Cdd:cd22417    2 TLTVEVDPKYHPK----IIGRKGAVITKLRDDHDVNIQFpDKGDENDDEITITG 51
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 248-307 2.52e-04

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


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 39.32  E-value: 2.52e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 248 VPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERH--------VTITGSPVSIALAQYLITA 307
Cdd:cd22447   10 IPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPADedddtmveVTITGDEFNVQHAKQRIEE 77
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 7-79 2.57e-04

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: 38.94  E-value: 2.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534   7 GLEEEPELSitlTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITI---SEGSCpERITTITGSTAAVFHAVSMI 79
Cdd:cd22522    1 GLDASPPAS---THELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIanaTEGSS-ERQITITGSPANISLAQYLI 72
KH_I_FMR1_FXR_rpt3 cd22427
third type I K homology (KH) RNA-binding domain found in a family of fragile X mental ...
 242-305 2.62e-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: 39.13  E-value: 2.62e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 242 SSQEFLVPNDLIGCVIGRQGSKISEIRQMSG-AHIKIGNQAEgAGERHV-------TITGSPVSIALAQYLI 305
Cdd:cd22427    2 AEEIFQVPRDLVGKVIGKNGRVIQEIVDKSGvVRVKIEGDNE-DGPRPReeglvpfIFVGTREAIANAKLLL 72
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 29-83 3.00e-04

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: 38.56  E-value: 3.00e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISE-----GSCPERITTITGSTAAVFHAVSMIAFKL 83
Cdd:cd22514   12 IGAILGRGGRTINEIQQHSGARIKISDrgdfvSGTRNRKVTITGPQDAVQMAQYLLEQKL 71
KH-I_IGF2BP2_rpt3 cd22497
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 246-302 3.10e-04

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: 38.92  E-value: 3.10e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGnQAEG--AGERHVTITGSPVSIALAQ 302
Cdd:cd22497    7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIA-PAEGpdVSERMVIITGPPEAQFKAQ 64
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 99-159 3.14e-04

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: 38.85  E-value: 3.14e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  99 RPPVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDL--LPnstERAVTVSGVPDAI 159
Cdd:cd22478    1 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSggLP---ERSCMLTGTPESV 60
KH-I_FUBP2_rpt4 cd22488
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 246-305 3.15e-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: 38.54  E-value: 3.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGE---RHVTITGSPVSIALAQYLI 305
Cdd:cd22488    4 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQPPPNGDpnfKLFIIRGSPQQIDHAKQLI 66
KH-I_IGF2BP2_rpt2 cd22494
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 104-158 3.37e-04

second 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 second one.


Pssm-ID: 411922  Cd Length: 77  Bit Score: 38.86  E-value: 3.37e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAG--DLLPNSTERAVTVSGVPDA 158
Cdd:cd22494    2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSlqDLTIYNPERTITVKGSIEA 58
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 29-86 3.47e-04

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: 38.50  E-value: 3.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS---EGSCpERITTITGSTAAVFHAVSMIAFKLDED 86
Cdd:cd22521   16 IGCIIGRQGAKINEIRQMSGAQIKIAnpvEGST-DRQVTITGSAASISLAQYLINARLSSE 75
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 245-302 3.60e-04

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


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 38.38  E-value: 3.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERH--VTITGSPVSIALAQ 302
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEvpVEIIGNFYATQSAQ 62
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 108-166 4.02e-04

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


Pssm-ID: 411823 [Multi-domain]  Cd Length: 68  Bit Score: 38.27  E-value: 4.02e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGdlLPNSTE-RAVTVSGVPDAIILCVRQI 166
Cdd:cd22395    6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKP--HPYTQNfQICSIEGTQQQIDKALKLI 63
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 29-80 4.20e-04

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


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 38.55  E-value: 4.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITI---SEGSCPERI-------TTITGSTAAVFHAVSMIA 80
Cdd:cd22447   15 RARIIGKKGANLKQIREKTGVRIDIpprDADAAPADEdddtmveVTITGDEFNVQHAKQRIE 76
KH-I_FUBP2_rpt4 cd22488
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 108-159 4.27e-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: 38.16  E-value: 4.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTE--RAVTVSGVPDAI 159
Cdd:cd22488    6 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQPPPNGDPnfKLFIIRGSPQQI 59
KH-I_Vigilin_rpt4 cd22408
fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 103-166 4.49e-04

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: 37.92  E-value: 4.49e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAgdlLPNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVP---PNDSDSETITLRGPADKLGAALTLV 61
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 104-172 4.52e-04

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: 38.25  E-value: 4.52e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAiilcVRQICAVILE 172
Cdd:cd22492    2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEG----TSAACKSILE 66
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 246-298 4.88e-04

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: 38.18  E-value: 4.88e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKI-GNQAEGAGERHVTITGSPVSI 298
Cdd:cd22518   11 LVVPASQCGSLIGKGGCKIKEIRESTGAQVQVaGDMLPNSTERAITIAGIPQSI 64
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 104-178 5.17e-04

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: 5.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAiilcVRQICAVILESPPKGA 178
Cdd:cd22491    2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENAGAAEKPITIHATPEG----CSAACRMILEIMQKEA 72
KH-I_ScSCP160_rpt7 cd22452
seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 29-79 5.34e-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: 37.69  E-value: 5.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22452   13 FGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAEEMI 63
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 29-79 5.73e-04

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: 38.01  E-value: 5.73e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22486   14 VGIVIGRNGEMIKKIQNDAGVRIQFKpdDGISPERVAQVMGPPDRCQHAAHII 66
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 29-79 5.91e-04

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


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 37.94  E-value: 5.91e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISE------GScPERITTITGSTAAVFHAVSMI 79
Cdd:cd09031   12 VGAILGKGGKTLVEIQELTGARIQISKkgefvpGT-RNRKVTITGTPAAVQAAQYLI 67
KH-I_FUBP2_rpt1 cd22479
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 102-159 6.08e-04

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: 38.00  E-value: 6.08e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDL--LPnstERAVTVSGVPDAI 159
Cdd:cd22479    1 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGSPEAV 57
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 106-156 6.16e-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: 37.96  E-value: 6.16e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQ-VQVAGDLLPNSTERAVTVSGVP 156
Cdd:cd22483    9 ILIPASKVGLVIGKGGETIKQLQERTGVKmIMIQDGPLPTGADKPLRITGDP 60
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-79 6.17e-04

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: 37.73  E-value: 6.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITI---SEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22491    2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIhrkENAGAAEKPITIHATPEGCSAACRMI 64
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 104-172 6.29e-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: 6.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAVTVSGVPDAiilcVRQICAVILE 172
Cdd:cd22490    2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKAISIHSTPEG----CSAACKMILE 66
KH-I_FUBP1_rpt1 cd22478
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 29-72 6.88e-04

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: 37.70  E-value: 6.88e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAV 72
Cdd:cd22478   15 VGFIIGRGGEQISRIQQESGCKIQIApdSGGLPERSCMLTGTPESV 60
KH-I_FUBP2_rpt3 cd22485
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 29-79 7.02e-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: 37.63  E-value: 7.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22485   12 VGVVIGRSGEMIKKIQNDAGVRIQFKqdDGTGPEKIAHIMGPPDRCEHAARII 64
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 243-305 7.39e-04

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: 37.18  E-value: 7.39e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 243 SQEFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIgnQAEGAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDL--PEENSDSDVITITGKKEDVEKARERI 61
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 28-83 7.57e-04

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: 37.63  E-value: 7.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564365534  28 EVGSIIGKKGETVKRIREQSSARITISEGSCPE-----RITTITGSTAAVFHAVSMIAFKL 83
Cdd:cd22487   12 KTGLIIGKGGETIKSISQQSGARIELQRNPPPNadpnmKLFTIRGSPQQIDYARQLIEEKI 72
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 245-301 8.07e-04

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: 37.43  E-value: 8.07e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 245 EFLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAgERHVTITGSPVSIALA 301
Cdd:cd22458    4 EIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNSS-QQTIHLSGTDKQIALA 59
KH-I_Vigilin_rpt10 cd22413
tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 116-159 8.62e-04

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: 37.24  E-value: 8.62e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564365534 116 LIGKAGTKIKEIRETTGAQVqvagdLLPNSTER---AVTVSGVPDAI 159
Cdd:cd22413   17 LIGRGGANIRKIRDNTGARI-----IFPTARDEdqeLITIIGTKEAV 58
KH-I_HEN4_like_rpt5 cd22462
fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH ...
 20-79 9.48e-04

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: 37.23  E-value: 9.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITISEG--SCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22462    1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPdsATGERIVLISGTPDQARHAQNLI 62
KH-I_FUBP3_rpt1 cd22480
first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 27-84 9.57e-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: 37.18  E-value: 9.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534  27 KEVGSIIGKKGETVKRIREQSSARITIS--EGSCPERITTITGSTAAVFHAVSMIAFKLD 84
Cdd:cd22480   10 KMVGFIIGRGGEQISRIQLESGCKIQIApdSGGMPERPCVLTGTPESIEQAKRLLGQIVD 69
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 246-301 1.06e-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: 1.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE-GAGERHVTITGSPVSIALA 301
Cdd:cd22492    4 LLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENaGAAEKSITILSTPEGTSAA 60
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 101-140 1.47e-03

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: 36.69  E-value: 1.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGD 140
Cdd:cd02393    3 PRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDD 42
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 108-166 1.73e-03

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


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 36.54  E-value: 1.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQV----AGDLLPnstERAVTVSGVPDAII---LCVRQI 166
Cdd:cd22428   11 VPREAVGLIIGRQGATIKQIQKETGARIDFkdegSGGELP---ERVLLIQGNPVQAQraeEAIHQI 73
KH-I_IGF2BP3_rpt1 cd22492
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-71 1.86e-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: 36.71  E-value: 1.86e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITI----SEGSCPERITTIT---GSTAA 71
Cdd:cd22492    2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVhrkeNAGAAEKSITILStpeGTSAA 60
KH-I_IGF2BP1_rpt4 cd22499
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 108-150 1.94e-03

fourth 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 fourth one.


Pssm-ID: 411927  Cd Length: 76  Bit Score: 36.55  E-value: 1.94e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAV 150
Cdd:cd22499    8 VPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVI 50
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 29-79 2.08e-03

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: 36.30  E-value: 2.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISE-GscpeRITTITGSTAAVFHAVSMI 79
Cdd:cd02393   15 IGDVIGPGGKTIRAIIEETGAKIDIEDdG----TVTIFATDKESAEAAKAMI 62
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 106-156 2.13e-03

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: 36.14  E-value: 2.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQ-VQVAGDLLPNSTERAVTVSGVP 156
Cdd:cd22481    6 IMIPASKAGLVIGKGGETIKQLQERAGVKmVMIQDGPQNTGADKPLRITGDP 57
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 241-305 2.26e-03

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: 36.14  E-value: 2.26e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 241 TSSQEFLVPNDLIGCVIGRQGSKISEIRQMSGAH---IKIGNQAEGAgERHVTITGSPVSIALAQYLI 305
Cdd:cd22481    1 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKmvmIQDGPQNTGA-DKPLRITGDPYKVQQAKEMV 67
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 253-306 2.30e-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: 36.16  E-value: 2.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 253 IGCVIGRQGSKISEIRQMSGAHIKIgnqAEGAG-ERHVTITGSPVSIALAQYLIT 306
Cdd:cd22517   13 VGSIIGKKGETVKRIREESSARITI---SEGSCpERITTITGSTDAVFRAFSMIA 64
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
 29-79 2.57e-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: 35.72  E-value: 2.57e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISEGScPERITTITGSTAAVFHAVSMI 79
Cdd:cd22430   11 VGAVIGRGGSKIRELEESTGSKIKIIKGG-QEAEVKIFGSDEAQQKAKELI 60
KH-I_Vigilin_rpt4 cd22408
fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 32-79 3.12e-03

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: 35.61  E-value: 3.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564365534  32 IIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22408   14 VIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTLV 61
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 108-166 3.14e-03

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: 35.64  E-value: 3.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDllpNSTERAVTVSGVPDAIILCVRQI 166
Cdd:cd22411    6 IFKQFHKNIIGKGGATIKKIREETNTRIDLPEE---NSDSDVITITGKKEDVEKARERI 61
KH-I_IGF2BP1_rpt3 cd22496
third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 248-295 3.47e-03

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: 35.77  E-value: 3.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564365534 248 VPNDLIGCVIGRQGSKISEIRQMSGAHIKIG-NQAEGAGERHVTITGSP 295
Cdd:cd22496    9 IPAQAVGAIIGKKGQHIKQLSRFASASIKIApPETPDSKVRMVIITGPP 57
KH-I_Vigilin_rpt3 cd22407
third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 32-79 3.49e-03

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: 35.26  E-value: 3.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564365534  32 IIGKKGETVKRIREQSSARITISEGSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22407   14 IAGPNNENVKELQEETGVRINIPPPSVNKDEIVVSGEKEGVAQAVAKI 61
KH-I_FUBP3_rpt4 cd22489
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 30-79 3.83e-03

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: 35.68  E-value: 3.83e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534  30 GSIIGKKGETVKRIREQSSARITISEGSCPE-----RITTITGSTAAVFHAVSMI 79
Cdd:cd22489   12 GLVIGKGGENIKSINQQSGAHVELQRNPPPNtdpnvRIFTIRGVPQQIEHARQLI 66
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 108-172 3.90e-03

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: 35.51  E-value: 3.90e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTeraVTVSGVPDAIILCVRQICAVILE 172
Cdd:cd22451    7 IPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGK---IRITGARDGVEAATAKILNISDE 68
KH-I_BICC1_rpt2 cd22421
second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) ...
 102-166 3.91e-03

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411849  Cd Length: 70  Bit Score: 35.40  E-value: 3.91e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 102 VTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQvagdlLPNSTERA-------VTVSGVPDAIILCVRQI 166
Cdd:cd22421    3 VTLKMDVSHTDHSHVIGKGGNNIKKVMEDTGCHIH-----FPDSNRTSqaeksnqVSIAGQPAGVESARAQI 69
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 246-305 4.14e-03

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: 35.70  E-value: 4.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGERHV---TITGSPVSIALAQYLI 305
Cdd:cd22487    6 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMklfTIRGSPQQIDYARQLI 68
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 103-153 4.27e-03

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: 35.32  E-value: 4.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVagdllpNSTERAVTVS 153
Cdd:cd22449    5 TVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDF------EDKTGEGNVE 49
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 29-79 4.43e-03

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: 35.12  E-value: 4.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 564365534  29 VGSIIGKKGETVKRIREQSSARITISE-GSCPERITTITGSTAAVFHAVSMI 79
Cdd:cd22458   12 CGRLIGAKGKNIKALSEKSGASIRLIPiSNSSQQTIHLSGTDKQIALAISSI 63
KH-I_FUBP1_rpt4 cd22487
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 106-159 5.10e-03

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: 35.32  E-value: 5.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 564365534 106 LVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTE--RAVTVSGVPDAI 159
Cdd:cd22487    6 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPnmKLFTIRGSPQQI 61
KH-I_ANKHD1 cd22503
type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing ...
 105-176 5.27e-03

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: 35.49  E-value: 5.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564365534 105 RLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNStERAVTVSGVPDAIILCVRQICAVIlESPPK 176
Cdd:cd22503    4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNG-ERMITIRGGTESTRYAVQLINALI-QDPAK 73
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 103-159 5.50e-03

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: 34.91  E-value: 5.50e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 564365534 103 TLRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQVAGD-LLPNSTERAVTVSGVPDAI 159
Cdd:cd22397    1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDgPQPTGQDKPLRITGDPQKV 58
KH-I_DDX43_DDX53 cd22430
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ...
 104-137 5.71e-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: 34.95  E-value: 5.71e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564365534 104 LRLVIPASQCGSLIGKAGTKIKEIRETTGAQVQV 137
Cdd:cd22430    2 LCFKIDSSLVGAVIGRGGSKIRELEESTGSKIKI 35
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 246-307 6.06e-03

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: 35.46  E-value: 6.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 246 FLVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAEGAGER--------HVTITGSPVSIALAQYLITA 307
Cdd:cd22446   11 ISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDeddddetvEISIEGDAEGVELAKKEIEA 80
KH-I_IGF2BP1_rpt1 cd22490
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 20-71 6.26e-03

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: 35.06  E-value: 6.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564365534  20 LRMLMHGKEVGSIIGKKGETVKRIREQSSARITI----SEGSCPERI---TTITGSTAA 71
Cdd:cd22490    2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVhrkeNAGAAEKAIsihSTPEGCSAA 60
KH-I_IGF2BP2_rpt1 cd22491
first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 247-305 6.34e-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: 35.04  E-value: 6.34e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564365534 247 LVPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQAE-GAGERHVTITGSPVSIALAQYLI 305
Cdd:cd22491    5 LVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENaGAAEKPITIHATPEGCSAACRMI 64
KH-I_ScSCP160_rpt1 cd22446
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 13-54 6.55e-03

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: 35.46  E-value: 6.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 564365534  13 ELSITLTLRMLMHGKEVGSIIGKKGETVKRIREQSSARITIS 54
Cdd:cd22446    2 ELSPKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIP 43
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 253-306 7.22e-03

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: 34.60  E-value: 7.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564365534 253 IGCVIGRQGSKISEIRQMSGAHIKIgnqAEG-AGERHVTITGSPVSIALAQYLIT 306
Cdd:cd22515   13 VGSIIGKKGESVKKMREESGARINI---SEGnCPERIITLAGPTNAIFKAFAMII 64
KH-I_IGF2BP2_rpt4 cd22500
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 108-150 7.35e-03

fourth 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 fourth one.


Pssm-ID: 411928  Cd Length: 78  Bit Score: 35.11  E-value: 7.35e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564365534 108 IPASQCGSLIGKAGTKIKEIRETTGAQVQVAGDLLPNSTERAV 150
Cdd:cd22500    8 VPSSAAGRVIGKGGKTVNELQNLTSAEVIVPRDQTPDENEEVI 50
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 27-79 7.56e-03

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: 34.55  E-value: 7.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564365534  27 KEVGSIIGKKGETVKRIREQSSARITISE----GSCperitTITGSTAAVFHAVSMI 79
Cdd:cd22449   13 KYVPHIIGKKGANINKLREEYGVKIDFEDktgeGNV-----EIKGSKKNVEEAKKRI 64
KH-I_PNPT1 cd09033
type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide ...
 101-135 7.89e-03

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: 34.48  E-value: 7.89e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 564365534 101 PVTLRLVIPASQCGSLIGKAGTKIKEIRETTGAQV 135
Cdd:cd09033    5 PVTETLEVPPSKRAKFVGPGGYNIKKLQAETGVTI 39
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 248-293 8.03e-03

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: 34.49  E-value: 8.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564365534 248 VPNDLIGCVIGRQGSKISEIRQMSGAHIKIgNQAEGAGERHVTITG 293
Cdd:cd22417    7 VDPKYHPKIIGRKGAVITKLRDDHDVNIQF-PDKGDENDDEITITG 51
UBCc_UBE2T cd23805
Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T ...
 166-194 8.12e-03

Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T and related enzymes; The E2T subfamily includes mammalian ubiquitin-conjugating enzymes E2 T (UBE2T/HSPC150/PIG50), plant ubiquitin-conjugating enzyme E2 37 (UBC37), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2T, also called cell proliferation-inducing gene 50 protein, catalyzes monoubiquitination. It is involved in mitomycin-C (MMC)-induced DNA repair. It acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway. UBE2T also mediates monoubiquitination of FANCL and FANCI. It may contribute to ubiquitination and degradation of BRCA1. In vitro, UBE2T can promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination.


Pssm-ID: 467425  Cd Length: 146  Bit Score: 36.35  E-value: 8.12e-03
                         10        20
                 ....*....|....*....|....*....
gi 564365534 166 ICAVILESPPKGAtipYHPSLSLGTVLLS 194
Cdd:cd23805   81 ICLDILKMPPKGS---WKPSLNISTVLTS 106
 
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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