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Conserved domains on  [gi|1278988953|ref|NP_001344990|]
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ribosomal RNA-processing protein 7 homolog A isoform 2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_Rrp7A cd12294
RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar ...
 59-156 1.77e-42

RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain.


:

Pssm-ID: 409735 [Multi-domain]  Cd Length: 103  Bit Score: 138.22  E-value: 1.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278988953  59 RTLFILNVPPYCTQESLSRCLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLK-- 136
Cdd:cd12294     1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAEKIDSKTSKFFNPQPIKGFKVAYVVFKKPSSLKAALKLKst 80

                          90       100
                  ....*....|....*....|...
gi 1278988953 137 GPLLVSTESHLVKSGI---HSQY 156
Cdd:cd12294    81 KPFVLSTESHPVKTGLekwIKEY 103
dRRM_Rrp7p super family cl40585
deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and ...
 22-88 2.50e-10

deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet.


The actual alignment was detected with superfamily member cd12293:

Pssm-ID: 454777 [Multi-domain]  Cd Length: 105  Bit Score: 55.43  E-value: 2.50e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278988953  22 GYSAVPVKF----SAKQQAPHYLYMRQHRVRQgTQSTWPPDRTLFILNVPPYCTQESLSRCLSC-CGTIKTV 88
Cdd:cd12293     5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGLgGGRIESV 75
 
Name Accession Description Interval E-value
RRM_Rrp7A cd12294
RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar ...
 59-156 1.77e-42

RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain.


Pssm-ID: 409735 [Multi-domain]  Cd Length: 103  Bit Score: 138.22  E-value: 1.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278988953  59 RTLFILNVPPYCTQESLSRCLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLK-- 136
Cdd:cd12294     1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAEKIDSKTSKFFNPQPIKGFKVAYVVFKKPSSLKAALKLKst 80

                          90       100
                  ....*....|....*....|...
gi 1278988953 137 GPLLVSTESHLVKSGI---HSQY 156
Cdd:cd12294    81 KPFVLSTESHPVKTGLekwIKEY 103
dRRM_Rrp7p cd12293
deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and ...
 22-88 2.50e-10

deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet.


Pssm-ID: 410983 [Multi-domain]  Cd Length: 105  Bit Score: 55.43  E-value: 2.50e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278988953  22 GYSAVPVKF----SAKQQAPHYLYMRQHRVRQgTQSTWPPDRTLFILNVPPYCTQESLSRCLSC-CGTIKTV 88
Cdd:cd12293     5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGLgGGRIESV 75
RRM_Rrp7 pfam17799
Rrp7 RRM-like N-terminal domain; This domain corresponds to the N-terminal RNA-binding domain ...
 22-67 6.44e-05

Rrp7 RRM-like N-terminal domain; This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation.


Pssm-ID: 436053  Cd Length: 162  Bit Score: 41.68  E-value: 6.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1278988953  22 GYSAVPVKF----SAKQQAPHYLYMRQHrvrQGTQSTWPPDRTLFILNVP 67
Cdd:pfam17799   4 GFHVLPVRLppspSLPKKATHYIYFKKH---QTKNNDEASSRSLFLVNLP 50
 
Name Accession Description Interval E-value
RRM_Rrp7A cd12294
RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar ...
 59-156 1.77e-42

RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain.


Pssm-ID: 409735 [Multi-domain]  Cd Length: 103  Bit Score: 138.22  E-value: 1.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278988953  59 RTLFILNVPPYCTQESLSRCLSCCGTIKTVELQEKPDLAESPTEPKSQFFHPKPVPGFQVAYVVFQKPSGVSAALNLK-- 136
Cdd:cd12294     1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAEKIDSKTSKFFNPQPIKGFKVAYVVFKKPSSLKAALKLKst 80

                          90       100
                  ....*....|....*....|...
gi 1278988953 137 GPLLVSTESHLVKSGI---HSQY 156
Cdd:cd12294    81 KPFVLSTESHPVKTGLekwIKEY 103
dRRM_Rrp7p cd12293
deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and ...
 22-88 2.50e-10

deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins; Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet.


Pssm-ID: 410983 [Multi-domain]  Cd Length: 105  Bit Score: 55.43  E-value: 2.50e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278988953  22 GYSAVPVKF----SAKQQAPHYLYMRQHRVRQgTQSTWPPDRTLFILNVPPYCTQESLSRCLSC-CGTIKTV 88
Cdd:cd12293     5 GFLVLPVTVpspsASPEKTTHYLYIRKHASKN-PAETLPASRTLFLVNLPVDSTERHLRKLFGLgGGRIESV 75
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 59-140 8.83e-08

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 47.98  E-value: 8.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278988953  59 RTLFILNVPPYCTQESLSRCLSCCGTIKTVELQEKPdlAESPTEPK-----SQFFHPKPVPgfQVAYVVFQKPSGVSAAL 133
Cdd:cd12394     1 RTVFVGNLPVTVKKKALKKLFKEFGKIESVRFRSVA--VANPKLPKkvaviKKKFHPKRDS--MNAYVVFKEEESAQKAL 76


                  ....*..
gi 1278988953 134 NLKGPLL 140
Cdd:cd12394    77 KLNGTEF 83
RRM_Rrp7 pfam17799
Rrp7 RRM-like N-terminal domain; This domain corresponds to the N-terminal RNA-binding domain ...
 22-67 6.44e-05

Rrp7 RRM-like N-terminal domain; This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation.


Pssm-ID: 436053  Cd Length: 162  Bit Score: 41.68  E-value: 6.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1278988953  22 GYSAVPVKF----SAKQQAPHYLYMRQHrvrQGTQSTWPPDRTLFILNVP 67
Cdd:pfam17799   4 GFHVLPVRLppspSLPKKATHYIYFKKH---QTKNNDEASSRSLFLVNLP 50
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 61-134 1.41e-03

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: 36.11  E-value: 1.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1278988953  61 LFILNVPPYCTQESLSRCLSCCGTIKTVELQEKPDlaesptePKSQFFhpkpvpgfqvAYVVFQKPSGVSAALN 134
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRD-------GKSKGF----------AFVEFESPEDAEKALE 57
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 61-137 2.37e-03

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: 35.46  E-value: 2.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278988953  61 LFILNVPPYCTQESLSRCLSCCGTIKTVELqekpdlaesPTEPKSQffHPKpvpGFqvAYVVFQKPSGVSAALNLKG 137
Cdd:cd12448     1 LFVGNLPFSATQDALYEAFSQHGSIVSVRL---------PTDRETG--QPK---GF--GYVDFSTIDSAEAAIDALG 61
 
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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