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Conserved domains on  [gi|18410189|ref|NP_565046|]
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RNA-binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
238-311 1.21e-16

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12451:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 79  Bit Score: 73.60  E-value: 1.21e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18410189 238 VTGFDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALELGRHDVGGWDLVVGKA 311
Cdd:cd12451   4 VKGFDASLGEDTIRDELREHFGECGEVTNVRIPTDRETGELKGFAYIEFstKEAKEKALELNGSDIAGGNLVVDEA 79
T4SS_IcmE_DotG super family cl41510
type IVB secretion system protein DotG/IcmE;
140-253 2.01e-04

type IVB secretion system protein DotG/IcmE;


The actual alignment was detected with superfamily member NF033900:

Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 43.17  E-value: 2.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189   140 TKDSLFSAGFKPAakdSLFSAGFKPDSLFSAGFEPAAkdsLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPDSLFSVGVK 219
Cdd:NF033900  550 TAAQLKAAGFTAA---ELKNAGFSAAELKAAGFSAKE---LKDAGFSAADLKDAGFSAGQ---LKAAGFSAADLKAAGFT 620
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 18410189   220 PAA-KDSLFSVGVNGRSFSVTGF------DASLPVDDIKSA 253
Cdd:NF033900  621 AAQlKAAGFSAKFSAKDLKAAGFsaaelkAAGFSAKELKAA 661
 
Name Accession Description Interval E-value
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
238-311 1.21e-16

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 73.60  E-value: 1.21e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18410189 238 VTGFDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALELGRHDVGGWDLVVGKA 311
Cdd:cd12451   4 VKGFDASLGEDTIRDELREHFGECGEVTNVRIPTDRETGELKGFAYIEFstKEAKEKALELNGSDIAGGNLVVDEA 79
RRM smart00360
RNA recognition motif;
245-308 2.96e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.90  E-value: 2.96e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189    245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALE-LGRHDVGGWDLVV 308
Cdd:smart00360   7 LPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFEseEDAEKALEaLNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
254-313 2.44e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 47.79  E-value: 2.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18410189 254 LSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE-LGRHDVGGWDLVVGKAEP 313
Cdd:COG0724  18 LRELFSEYGEVTSVKLITDRETGRSRGFGFVEMpdDEEAQAAIEaLNGAELMGRTLKVNEARP 80
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
140-253 2.01e-04

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 43.17  E-value: 2.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189   140 TKDSLFSAGFKPAakdSLFSAGFKPDSLFSAGFEPAAkdsLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPDSLFSVGVK 219
Cdd:NF033900  550 TAAQLKAAGFTAA---ELKNAGFSAAELKAAGFSAKE---LKDAGFSAADLKDAGFSAGQ---LKAAGFSAADLKAAGFT 620
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 18410189   220 PAA-KDSLFSVGVNGRSFSVTGF------DASLPVDDIKSA 253
Cdd:NF033900  621 AAQlKAAGFSAKFSAKDLKAAGFsaaelkAAGFSAKELKAA 661
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
251-295 2.04e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.14  E-value: 2.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 18410189   251 KSALSKYFSSFGEITRVFVPPShGTGGSLGYAYIDL--KEGAEKALE 295
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVRD-ETGRSKGFAFVEFedEEDAEKAIE 57
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
144-211 5.63e-04

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 41.63  E-value: 5.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18410189   144 LFSAGFkpAAKDsLFSAGFKPDSLFSAGFepAAKDsLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPD 211
Cdd:NF033900  303 LKNAGF--SAAD-LKNAGFTPAELKAAGF--SARD-LLNAGFSPSDLKDAGFSPAE---LKAAGFELP 361
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
155-225 4.19e-03

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 38.93  E-value: 4.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189   155 DSLFSAGFKPDSLFSAGFEPAakdSLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPDslFSVGVKPAAKDS 225
Cdd:NF033900  464 AALKAAGFSAKDLLDAGFTPQ---ELKAAGFTPKQLKQAGLNPAA---IIAAGRTAD--CSVASLAAARKA 526
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
140-225 8.41e-03

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 38.16  E-value: 8.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189   140 TKDSLFSAGFKPAAkdsLFSAGFKPDSLFSAGFepAAKDsLFSAGFKPGSLFSAGFEPAA-KDSLFSAGFKPDSLFSVGV 218
Cdd:NF033900  634 SAKDLKAAGFSAAE---LKAAGFSAKELKAAGF--SAGD-LKRAGFSADELGAAGFSAAElLNAGFSPGASVAGLQQAAL 707

                  ....*..
gi 18410189   219 KPAAKDS 225
Cdd:NF033900  708 VPSGITS 714
 
Name Accession Description Interval E-value
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
238-311 1.21e-16

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 73.60  E-value: 1.21e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18410189 238 VTGFDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALELGRHDVGGWDLVVGKA 311
Cdd:cd12451   4 VKGFDASLGEDTIRDELREHFGECGEVTNVRIPTDRETGELKGFAYIEFstKEAKEKALELNGSDIAGGNLVVDEA 79
RRM smart00360
RNA recognition motif;
245-308 2.96e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 49.90  E-value: 2.96e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189    245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALE-LGRHDVGGWDLVV 308
Cdd:smart00360   7 LPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFEseEDAEKALEaLNGKELDGRPLKV 73
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
241-300 6.41e-08

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 48.94  E-value: 6.41e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALELGRHD 300
Cdd:cd12448   2 FVGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETGQPKGFGYVDFStiDSAEAAIDALGGE 63
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
254-313 2.44e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 47.79  E-value: 2.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18410189 254 LSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE-LGRHDVGGWDLVVGKAEP 313
Cdd:COG0724  18 LRELFSEYGEVTSVKLITDRETGRSRGFGFVEMpdDEEAQAAIEaLNGAELMGRTLKVNEARP 80
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
245-308 7.93e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.12  E-value: 7.93e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189 245 LPVDDIKSALSKYFSSFGEITRVFVPPSHgTGGSLGYAYIDLK--EGAEKALE-LGRHDVGGWDLVV 308
Cdd:cd00590   6 LPPDTTEEDLRELFSKFGEVVSVRIVRDR-DGKSKGFAFVEFEspEDAEKALEaLNGTELGGRPLKV 71
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
254-284 5.73e-06

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 43.72  E-value: 5.73e-06
                        10        20        30
                ....*....|....*....|....*....|.
gi 18410189 254 LSKYFSSFGEITRVFVPPSHGTGGSLGYAYI 284
Cdd:cd12307  16 LRKYFSQFGTVTRLRLSRSKKTGKSKGYAFV 46
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
258-305 7.76e-06

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 43.31  E-value: 7.76e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 18410189 258 FSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALelgRHDVGGWD 305
Cdd:cd12365  19 FSVYGTVKNVDLPIDREPNLPRGYAYVEFesPEDAEKAI---KHMDGGQI 65
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
241-313 8.91e-06

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 43.08  E-value: 8.91e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYI--DLKEGAEKALELGRHDVGGWDLVVGKAEP 313
Cdd:cd12330   3 FVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHDTGRSRGFGFVtfDSESAVEKVLSKGFHELGGKKVEVKRATP 77
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
248-311 9.67e-06

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 43.04  E-value: 9.67e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189 248 DDIKSAlskyFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE-LGRHDVGGWDLVVGKA 311
Cdd:cd12371  15 DDIKSV----FEAFGKIKSCSLAPDPETGKHKGYGFIEYenPQSAQDAIAsMNLFDLGGQYLRVGRA 77
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
245-312 6.42e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 40.57  E-value: 6.42e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189 245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE-LGRHdvgGWDLVVGKAE 312
Cdd:cd12408   7 LSEDATEEDLRELFRPFGPISRVYLAKDKETGQSKGFAFVTFetREDAERAIEkLNGF---GYDNLILSVE 74
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
233-308 1.28e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 39.82  E-value: 1.28e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189 233 GRSFSVTGFDASLPVDDIKsalsKYFSSFGEITRVFVPPSH--GTGGSLGYAYIDL--KEGAEKALE-LGRHDVGGWDLV 307
Cdd:cd21619   1 SNTIYVGNIDMTINEDALE----KIFSRYGQVESVRRPPIHtdKADRTTGFGFIKYtdAESAERAMQqADGILLGRRRLV 76

                .
gi 18410189 308 V 308
Cdd:cd21619  77 V 77
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
239-313 1.65e-04

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 39.69  E-value: 1.65e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189 239 TGFDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALELGRHDVGGWDLVVGKAEP 313
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRDDGRSKGFGHVEFAsaESAQKALEKSGQDLGGREIRLDLANE 77
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
251-303 1.75e-04

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 39.55  E-value: 1.75e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 18410189 251 KSALSKYFSSFGEITRVFVPPSHGTGGSL---GYAYIDLK--EGAEKALELGRHDVGG 303
Cdd:cd12298  14 EEALRGIFEKFGEIESINIPKKQKNRKGRhnnGFAFVTFEdaDSAESALQLNGTLLDN 71
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
140-253 2.01e-04

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 43.17  E-value: 2.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189   140 TKDSLFSAGFKPAakdSLFSAGFKPDSLFSAGFEPAAkdsLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPDSLFSVGVK 219
Cdd:NF033900  550 TAAQLKAAGFTAA---ELKNAGFSAAELKAAGFSAKE---LKDAGFSAADLKDAGFSAGQ---LKAAGFSAADLKAAGFT 620
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 18410189   220 PAA-KDSLFSVGVNGRSFSVTGF------DASLPVDDIKSA 253
Cdd:NF033900  621 AAQlKAAGFSAKFSAKDLKAAGFsaaelkAAGFSAKELKAA 661
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
251-295 2.04e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 39.14  E-value: 2.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 18410189   251 KSALSKYFSSFGEITRVFVPPShGTGGSLGYAYIDL--KEGAEKALE 295
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVRD-ETGRSKGFAFVEFedEEDAEKAIE 57
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
254-311 3.50e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 38.69  E-value: 3.50e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189 254 LSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALE-LGRHDVGGWDLVVGKA 311
Cdd:cd21608  16 LRDLFSEFGEVESAKVITDRETGRSRGFGFVTFStaEAAEAAIDaLNGKELDGRSIVVNEA 76
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
245-303 5.20e-04

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 38.08  E-value: 5.20e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189 245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYI--DLKEGAEKALELGRHDVGG 303
Cdd:cd12271   6 IPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSGNFRGIAFItfKTEEAAKRALALDGEMLGN 66
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
144-211 5.63e-04

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 41.63  E-value: 5.63e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18410189   144 LFSAGFkpAAKDsLFSAGFKPDSLFSAGFepAAKDsLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPD 211
Cdd:NF033900  303 LKNAGF--SAAD-LKNAGFTPAELKAAGF--SARD-LLNAGFSPSDLKDAGFSPAE---LKAAGFELP 361
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
241-293 6.27e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 37.74  E-value: 6.27e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKA 293
Cdd:cd12384   4 FVGGLPYHTTDDSLREYFEQFGEIEEAVVITDRQTGKSRGYGFVTMadREAAERA 58
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
241-311 6.42e-04

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 37.88  E-value: 6.42e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKAL-ELGRHDVGGWDLVVGKA 311
Cdd:cd12399   2 YVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDRETKRPRGFGFVELqeEESAEKAIaKLDGTDFMGRTIRVNEA 75
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
241-308 8.71e-04

RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 37.33  E-value: 8.71e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALELGRHDVGGWDLVV 308
Cdd:cd12242   3 FVSNLPWTTGSSELKEYFSQFGKVKRCNLPFDKETGFHKGFGFVSFenEDGLRNALQKQKHIFEGNKVSV 72
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
245-303 9.20e-04

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 37.38  E-value: 9.20e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189 245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALElGRHDVGG 303
Cdd:cd12321   7 LPWKTTEQDLKEYFSTFGEVLMVQVKKDPKTGRSKGFGFVRFAsyETQVKVLS-QRHMIDG 66
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
241-303 1.51e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 36.87  E-value: 1.51e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLKE--GAEKALELGRHDVGG 303
Cdd:cd12757   8 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDaaSVDKVLEQKEHRLDG 72
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
245-308 2.21e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 36.09  E-value: 2.21e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18410189 245 LPVDDI-----KSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE-LGRHDVGGWDLVV 308
Cdd:cd12311   1 LKVDNLtyrttPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFydKRDAEDAIDaMDGAELDGRELRV 72
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
247-295 2.73e-03

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 36.26  E-value: 2.73e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 18410189 247 VDDikSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKALE 295
Cdd:cd12447  11 VDD--PWLKKEFEKYGGVISARVITDRGSGRSKGYGYVDFatPEAAQKALA 59
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
241-303 2.91e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 36.11  E-value: 2.91e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLKEGA--EKALELGRHDVGG 303
Cdd:cd12758   3 FIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAAsvDKVLELKEHKLDG 67
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
241-312 4.02e-03

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 35.50  E-value: 4.02e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALELG-RHDVGGWDLVVGKAE 312
Cdd:cd12397   2 FVGNLSFETTEEDLRKHFAPAGKIRKVRMATFEDSGKCKGFAFVDFKeiESATNAVKGPiNHSLNGRDLRVEYGE 76
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
155-225 4.19e-03

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 38.93  E-value: 4.19e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18410189   155 DSLFSAGFKPDSLFSAGFEPAakdSLFSAGFKPGSLFSAGFEPAAkdsLFSAGFKPDslFSVGVKPAAKDS 225
Cdd:NF033900  464 AALKAAGFSAKDLLDAGFTPQ---ELKAAGFTPKQLKQAGLNPAA---IIAAGRTAD--CSVASLAAARKA 526
RRM_TUT1 cd12279
RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase ...
234-308 4.90e-03

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).


Pssm-ID: 409721 [Multi-domain]  Cd Length: 74  Bit Score: 35.47  E-value: 4.90e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18410189 234 RSFSVTGFDASLPvddiKSALSKYFSSFGEITRVFVPPSHGTggslgYAYIDL--KEGAEKALELGRHDVGGWDLVV 308
Cdd:cd12279   3 RSVFVSGFKRGTS----ELELSDYFQAFGPVASVVMDKDKGV-----YAIVEMdsTETVEKVLSQPQHCLNGQRLRV 70
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
245-313 5.02e-03

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 35.47  E-value: 5.02e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18410189 245 LPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKALE-LGRHDVGGWDLVVGKAEP 313
Cdd:cd21609   7 IPRNVTSEELAKIFEEAGTVEIAEVMYDRYTGRSRGFGFVTMGsvEDAKAAIEkLNGTEVGGREIKVNITEK 78
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
239-301 5.17e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 36.52  E-value: 5.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18410189 239 TGFDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLK--EGAEKA-LELGRHDV 301
Cdd:cd21615  20 TLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKETGKSRGYAFIVFKseSDAKNAfKEGNGLRG 85
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
241-288 7.00e-03

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 35.09  E-value: 7.00e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLKE 288
Cdd:cd12566   6 FLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDKKTKKSKGFAYVLFLD 53
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
241-303 7.14e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 34.84  E-value: 7.14e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18410189 241 FDASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDLKEGA--EKALELGRHDVGG 303
Cdd:cd12575   2 FIGGLSWDTSKKDLKDYFSKFGEVVDCTIKLDPVTGRSRGFGFVLFKDAEsvDKVLDQKEHKLDG 66
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
243-293 7.26e-03

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 34.98  E-value: 7.26e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 18410189 243 ASLPVDDIKSALSKYFSSFGEITRVFVPPSHGTGGSLGYAYIDL--KEGAEKA 293
Cdd:cd12389   5 TNLPLSFTEEQFEELVRPYGNVERCFLVYSEVTGESKGYGFVEYtsKESAIRA 57
T4SS_IcmE_DotG NF033900
type IVB secretion system protein DotG/IcmE;
140-225 8.41e-03

type IVB secretion system protein DotG/IcmE;


Pssm-ID: 468233 [Multi-domain]  Cd Length: 1012  Bit Score: 38.16  E-value: 8.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18410189   140 TKDSLFSAGFKPAAkdsLFSAGFKPDSLFSAGFepAAKDsLFSAGFKPGSLFSAGFEPAA-KDSLFSAGFKPDSLFSVGV 218
Cdd:NF033900  634 SAKDLKAAGFSAAE---LKAAGFSAKELKAAGF--SAGD-LKRAGFSADELGAAGFSAAElLNAGFSPGASVAGLQQAAL 707

                  ....*..
gi 18410189   219 KPAAKDS 225
Cdd:NF033900  708 VPSGITS 714
 
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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