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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166   6 EIAGFSILPLHFPATPAFPKPATHYLYLRAHEPRIPDADTPRSMFIVNIPVDTTETHLRHLFGTQLSAGRIERVefeaVP 85
Cdd:pfam17799   1 EIKGFHVLPVRLPPSPSLPKKATHYIYFKKHQTKNNDEASSRSLFLVNLPINTNFATLKKFFGTVALGATIESF----VS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166  86 TKKKGMQATPQGNIAsskkrkRVTAD-ELQAQLDD---VDLPatwdrqlqksGSHAIVVFADKPSMEASLKAARKAAKKG 161
Cdd:pfam17799  77 SLLTDEQEDVSIDLT------KLTSDlDLQDETDDeneAKLP----------KNCGIVVFVDKSSFQLAFNCLKKLSKSS 140

                         170       180
                  ....*....|....*....|....*
gi 2414169166 162 TEIVWGEGvegdRVPALGLQRYITH 186
Cdd:pfam17799 141 TKIVWPLG----KLPPLGSQRFLNK 161

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166   6 EIAGFSILPLHFPATPAFPKPATHYLYLRAHEPRIPDADTPRSMFIVNIPVDTTETHLRHLFGTQLSAGRIERVefeaVP 85
Cdd:pfam17799   1 EIKGFHVLPVRLPPSPSLPKKATHYIYFKKHQTKNNDEASSRSLFLVNLPINTNFATLKKFFGTVALGATIESF----VS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166  86 TKKKGMQATPQGNIAsskkrkRVTAD-ELQAQLDD---VDLPatwdrqlqksGSHAIVVFADKPSMEASLKAARKAAKKG 161
Cdd:pfam17799  77 SLLTDEQEDVSIDLT------KLTSDlDLQDETDDeneAKLP----------KNCGIVVFVDKSSFQLAFNCLKKLSKSS 140

                         170       180
                  ....*....|....*....|....*
gi 2414169166 162 TEIVWGEGvegdRVPALGLQRYITH 186
Cdd:pfam17799 141 TKIVWPLG----KLPPLGSQRFLNK 161

Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain; RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166 188 QLRYPDRAELLRTVNDYMTVFTQVAEVRKREEARRAQEPDEDGFITVTSGPKLA--EAAHEDEARQLVEKQKEKsKGLED 265
Cdd:pfam12923   1 RLSRPDPEALQQEVDEYMEEFDAEEEEEKRERKKARNEPDEDGFVTVTRGGPGGarKEAAEEKIAKKEKKKKKK-KELLD 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2414169166 266 FYRFQSREKRKEKQNQLLKKFDDDRRKLADMKKRK 300
Cdd:pfam12923  80 FYRFQIREKKKNELAELRKKFEEDKEKIEKLKESR 114

RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins; This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. 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. Rrp7A, also termed gastric cancer antigen Zg14, is the Rrp7p homolog mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166 179 GLQRYITHEQLRYPDRAELLRTVNDYMTVFTQVAEVRKREEARRAQEPDEDGFITVTSG---PKLAEAAHEDEARQLVEK 255
Cdd:cd12932     1 GLKKWVAEYKRSRPDPAELQSEVDEYMEEFDKREEEEKEEAKEARNEPDEDGFVTVTRGgrkGKTAREEAVEAKAKEKEK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2414169166 256 QKEKSKGLEDFYRFQSREKRKEKQNQLLKKFDDDRRKL 293
Cdd:cd12932    81 KKKKKKELEDFYRFQIREKKKEELAELRKKFEEDKKRI 118

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166   6 EIAGFSILPLHFPATPAFPKPATHYLYLRAHEPRIP--DADTPRSMFIVNIPVDTTETHLRHLFGtqLSAGRIERVefea 83
Cdd:cd12293     2 EINGFLVLPVTVPSPSASPEKTTHYLYIRKHASKNPaeTLPASRTLFLVNLPVDSTERHLRKLFG--LGGGRIESV---- 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2414169166  84 vptkkkgmqatpqgniasskkrkrvtadelqaqlddvdlpatwdrqLQKSGSHAIVVFADKPSMEASL 151
Cdd:cd12293    76 ----------------------------------------------LHSSGSTAHVVFVDKASLDLAM 97

RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins; The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2414169166 179 GLQRYITHEQLRYPDRAELLRTVNDYMTVFTQvAEVRKREEARRAQEPDEDGFITVTSG---PKLAEAAHEDEARQLVEK 255
Cdd:cd12951     1 GLKKWVEEYNASIPDPAELQSEIDEYMEEYDK-EEEEEKEEKEKEAEPDEDGWVTVTKKgrrPKTARKESVAAKAAEKEK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2414169166 256 QKEKSKGLEDFYRFQSREKRKEKQNQLLKKFDDDRRKLADMKK-RKGK 302
Cdd:cd12951    80 KKKKKKELKNFYRFQIRESKRNELAELRKKFEEDKKRIALLKAaRKFK 127

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2414169166  49 MFIVNIPVDTTETHLRHLFGTQ-----LSAGRIER-----VEFEAVPTKKKGMQATpQGNIASSKKR 105
Cdd:cd12245     5 LFVANLGPNVSEQELRQLFSRQpgfrrLRMHNKGGgpvcfVEFEDVPFATQALNHL-QGAILSSSDR 70