MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   829 LLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDMIAIREQGNGRLVCLLPSNQARQSPLGSSQSHDGS 908
Cdd:pfam19687    1 LLSSETISILQDAPACCLPLFKFTEIYEKKFGHKLIVSDLYKLTDTVAIREQGNGRLVCLLPSSQARQSPLGSSQSHDGS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   909 STNCSPVLFEELEYHESVCKQHCSNKDFSELVFDPDSYKVPFVVLSLKVFAPQVHSLLQTHEGTVPLLSFPDCYAAEFGD 988
Cdd:pfam19687   81 SANGSPIIFEELEYHEPVCRQHCLNKDFSEHEFDPDSYQIPFVILSLKTFAPQVHSLLQTHEGTVPLLSFPECYAAKFSP 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 564370724   989 LEITQDRDKGVPLEHFITCIPGVNIATAQNGVKVVKWIHNKPPPPNTDPWL 1039
Cdd:pfam19687  161 LQLGSETMEGVPLEHLITCVPSITIVTAQNGFKVIKWIHNKPPPPNTDPWL 211

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564370724 1051 LIQFSREVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDYGYSKLIELLEAVPHVLQILGMGSKRLLTLT 1122
Cdd:cd09979     1 LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72

RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564370724  461 CHTLLYVYNLPANKDGKSISNRLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSF 533
Cdd:cd12255     1 CHTLLYVYNLPTNRDVKSIRNRLRQLSDNCGGKVLSVSGGSAILRFANQESAERAQKRMEGEDVFGNKISVSF 73

RNA recognition motif 2 (RRM2) found in Limkain-b1 (LKAP) and similar proteins; This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724  738 FANGVDIQVSNVDYRLSRKELQQLLQEAFSKHGQVKSVELSPHTDYQLKAIVQMRNLHDAICAVNSLHRYKIGSKKILVS 817
Cdd:cd12256     1 FSNGVDLQVSNLDYRMSRKELQQMLHNQFKRHGKVKSVELSPQTDGSLKASVRVPSLQDAQYAVSQLHRYKIGSKRIQVS 80

                  ....*....
gi 564370724  818 LSTGAANKS 826
Cdd:cd12256    81 LATGSSNKS 89

C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains).

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1287 FKALAAQFVKLLRSQKGNCLMMTDLFTEYAKTFGYTFRLQDYDVSSVSALTQKLCHVVKVADMESGKQIQL 1357
Cdd:cd09982     1 VKALAAQLVKLLRSQKDSCLMMCDLLTEYSKTFGYTLRLQDYDVSSVPALMQKLCHVVKVVDTESGKQIQL 71

MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   829 LLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDMIAIREQGNGRLVCLLPSNQARQSPLGSSQSHDGS 908
Cdd:pfam19687    1 LLSSETISILQDAPACCLPLFKFTEIYEKKFGHKLIVSDLYKLTDTVAIREQGNGRLVCLLPSSQARQSPLGSSQSHDGS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   909 STNCSPVLFEELEYHESVCKQHCSNKDFSELVFDPDSYKVPFVVLSLKVFAPQVHSLLQTHEGTVPLLSFPDCYAAEFGD 988
Cdd:pfam19687   81 SANGSPIIFEELEYHEPVCRQHCLNKDFSEHEFDPDSYQIPFVILSLKTFAPQVHSLLQTHEGTVPLLSFPECYAAKFSP 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 564370724   989 LEITQDRDKGVPLEHFITCIPGVNIATAQNGVKVVKWIHNKPPPPNTDPWL 1039
Cdd:pfam19687  161 LQLGSETMEGVPLEHLITCVPSITIVTAQNGFKVIKWIHNKPPPPNTDPWL 211

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564370724 1051 LIQFSREVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDYGYSKLIELLEAVPHVLQILGMGSKRLLTLT 1122
Cdd:cd09979     1 LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72

RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564370724  461 CHTLLYVYNLPANKDGKSISNRLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSF 533
Cdd:cd12255     1 CHTLLYVYNLPTNRDVKSIRNRLRQLSDNCGGKVLSVSGGSAILRFANQESAERAQKRMEGEDVFGNKISVSF 73

The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1211 TKQFSKDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTL 1281
Cdd:cd09981     1 TKQFSKEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVLECGEEKYLQL 71

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724  304 PIGVFWDIENCSVPSGRSATTVVQRIR---EKFFRgHREAEFICVCDISKENKEVIQELNNCQVTVAHINATAKNAADDK 380
Cdd:cd10910     1 KTGVFWDIENCPVPDGYDARRVGPNIRralRKLGY-SGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 564370724  381 LRQSLRRFANTHTAPATVVLVSTDV-NFALELSDLRHRhGFHIILVH 426
Cdd:cd10910    80 ILVDMLLWALDNPPPANIMLISGDVrDFAYALSRLRSR-GYNVLLAY 125

The seventh LOTUS domain on Limkain b1(LKAP); The seventh LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564370724 1363 LRPLTVQLLVVLMSWEGDAYLPVDELKRHYETTHSTPLNPCEYGFMTLTELLKSLPSLVEVFMNDKAEECVKL 1435
Cdd:cd09983     1 LRSLTAQLLVLLMSWEGASDLSVEELRQHYESVHGTPLNPCEYGFMSLTELLKSLPYLVEVFTNGGGEEYVRL 73

MARF1, RNA recognition motif 1; MARF1 (also known as Limkain-b1) is an essential protein for controlling meiosis and retrotransposon surveillance in mouse oocytes, first described as a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. It may function both as an adaptor to recruit specific RNA targets and an effector to catalyze the specific cleavages of target RNAs. MARF1 contains an N-terminal NYN domain, two central RRMs, and C-terminal OST-HTH/LOTUS domains. This domain represents the RNA recognition motif 1 (RRM1) of MARF1.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   463 TLLYVYNLPANKDgKSISN----RLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKHR 538
Cdd:pfam11608    3 NLLFVRNLPVNCD-KSLQNavkhRLRRLSDNCGGKVLGISQGTAVLRFGSPEAASRACKRMENEDVYGHRISLSFSLGPR 81

                   .
gi 564370724   539 E 539
Cdd:pfam11608   82 D 82

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 564370724  1057 EVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDYGYSKLIELLEAVPHVLQILGMGSKRLLT 1120
Cdd:pfam12872    1 ELISLLRSDPDGWASLSELGSEYRKLFGEDFDPRNYGFSKLSDLLKAIPDVFEIEKRGGGGLVV 64

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 564370724  1369 QLLVVLMSWEgDAYLPVDELKRHYETTHSTPLNPCEYGFMTLTELLKSLPSLVEV 1423
Cdd:pfam12872    1 ELISLLRSDP-DGWASLSELGSEYRKLFGEDFDPRNYGFSKLSDLLKAIPDVFEI 54

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564370724   746 VSNVDYRLSRKELQQLlqeaFSKHGQVKSVELSPHTDYQLK--AIVQMRNLHDAICAVNSLHRYKIGSKKIL 815
Cdd:pfam00076    3 VGNLPPDTTEEDLKDL----FSKFGPIKSIRLVRDETGRSKgfAFVEFEDEEDAEKAIEALNGKELGGRELK 70

MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   829 LLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDMIAIREQGNGRLVCLLPSNQARQSPLGSSQSHDGS 908
Cdd:pfam19687    1 LLSSETISILQDAPACCLPLFKFTEIYEKKFGHKLIVSDLYKLTDTVAIREQGNGRLVCLLPSSQARQSPLGSSQSHDGS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   909 STNCSPVLFEELEYHESVCKQHCSNKDFSELVFDPDSYKVPFVVLSLKVFAPQVHSLLQTHEGTVPLLSFPDCYAAEFGD 988
Cdd:pfam19687   81 SANGSPIIFEELEYHEPVCRQHCLNKDFSEHEFDPDSYQIPFVILSLKTFAPQVHSLLQTHEGTVPLLSFPECYAAKFSP 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 564370724   989 LEITQDRDKGVPLEHFITCIPGVNIATAQNGVKVVKWIHNKPPPPNTDPWL 1039
Cdd:pfam19687  161 LQLGSETMEGVPLEHLITCVPSITIVTAQNGFKVIKWIHNKPPPPNTDPWL 211

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564370724 1051 LIQFSREVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDYGYSKLIELLEAVPHVLQILGMGSKRLLTLT 1122
Cdd:cd09979     1 LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72

RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564370724  461 CHTLLYVYNLPANKDGKSISNRLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSF 533
Cdd:cd12255     1 CHTLLYVYNLPTNRDVKSIRNRLRQLSDNCGGKVLSVSGGSAILRFANQESAERAQKRMEGEDVFGNKISVSF 73

The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1211 TKQFSKDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTL 1281
Cdd:cd09981     1 TKQFSKEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVLECGEEKYLQL 71

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724  304 PIGVFWDIENCSVPSGRSATTVVQRIR---EKFFRgHREAEFICVCDISKENKEVIQELNNCQVTVAHINATAKNAADDK 380
Cdd:cd10910     1 KTGVFWDIENCPVPDGYDARRVGPNIRralRKLGY-SGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 564370724  381 LRQSLRRFANTHTAPATVVLVSTDV-NFALELSDLRHRhGFHIILVH 426
Cdd:cd10910    80 ILVDMLLWALDNPPPANIMLISGDVrDFAYALSRLRSR-GYNVLLAY 125

The seventh LOTUS domain on Limkain b1(LKAP); The seventh LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564370724 1363 LRPLTVQLLVVLMSWEGDAYLPVDELKRHYETTHSTPLNPCEYGFMTLTELLKSLPSLVEVFMNDKAEECVKL 1435
Cdd:cd09983     1 LRSLTAQLLVLLMSWEGASDLSVEELRQHYESVHGTPLNPCEYGFMSLTELLKSLPYLVEVFTNGGGEEYVRL 73

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724 1213 QFSKDVVDLLRHQPHFRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTLT 1282
Cdd:cd09979     3 QFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724  306 GVFWDIENCSVPSGrsatTVVQRIREKFFRGhreAEFICVCDIsKENKEVIQELNNCQVTVAHINATAKNAADDKLRQSL 385
Cdd:cd06167     1 GVLVDADNCSNGFG----ALILRRYAGLFLQ---MGFEKYANI-NAQPLLVPPSNNRGFTVIRVAAKRKDAADVALVRQA 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 564370724  386 RRFANTHTaPATVVLVSTDvnfALELSDLRHR---HGFHIILVHK 427
Cdd:cd06167    73 GRLAYTGA-PDTVVLVSGD---KLDFSDLIEKakeAGLNVIVVGP 113

MARF1, RNA recognition motif 1; MARF1 (also known as Limkain-b1) is an essential protein for controlling meiosis and retrotransposon surveillance in mouse oocytes, first described as a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. It may function both as an adaptor to recruit specific RNA targets and an effector to catalyze the specific cleavages of target RNAs. MARF1 contains an N-terminal NYN domain, two central RRMs, and C-terminal OST-HTH/LOTUS domains. This domain represents the RNA recognition motif 1 (RRM1) of MARF1.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724   463 TLLYVYNLPANKDgKSISN----RLRRLSDNCGGKVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKHR 538
Cdd:pfam11608    3 NLLFVRNLPVNCD-KSLQNavkhRLRRLSDNCGGKVLGISQGTAVLRFGSPEAASRACKRMENEDVYGHRISLSFSLGPR 81

                   .
gi 564370724   539 E 539
Cdd:pfam11608   82 D 82

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1211 TKQFSKDVVDLLRHQPHfRMPFNKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTL 1281
Cdd:cd08824     1 LKQLAKQLRSLLQSYPG-GLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIVSL 70

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1127 VKRFTQDLLKLLKSQaSKQVIVSDFSQAYHWCFSKDWDVTEYGVCDLIDIISEIPDTTICLSQQDDDMVIC 1197
Cdd:cd08824     1 LKQLAKQLRSLLQSY-PGGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIVSL 70

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724 1288 KALAAQFVKLLRSQKgNCLMMTDLFTEYAKTFGYTFRLQDYDVSSVSALTQKLCHVVKVADMESGKQIQL 1357
Cdd:cd08824     2 KQLAKQLRSLLQSYP-GGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIVSL 70

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564370724  955 LKVFAPQVHSLLQTHEGTVPLLSFPDCYAAEFGDLEitQDRDKGVP-LEHFITCIPGVNIATAQNGVKVVKW 1025
Cdd:cd08824     1 LKQLAKQLRSLLQSYPGGLPLSKLPQLYKKKFGKPL--DLSEYGFSkLSDLLEALPGVVIVLSQGGERIVSL 70

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 564370724  1369 QLLVVLMSWEgDAYLPVDELKRHYETTHSTPLNPCEYGFMTLTELLKSLPSLVEV 1423
Cdd:pfam12872    1 ELISLLRSDP-DGWASLSELGSEYRKLFGEDFDPRNYGFSKLSDLLKAIPDVFEI 54

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564370724 1369 QLLVVLMSWEGdaYLPVDELKRHYETTHSTPLNPCEYGFMTLTELLKSLPSLVEVFmNDKAEECVKL 1435
Cdd:cd08824     7 QLRSLLQSYPG--GLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVL-SQGGERIVSL 70

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724  827 LSLLSTETMSILQDAPaCCLPLFKFIDIYEKKYGHKLNVSDL--YKLTDMI-------AIREQGNGRLVCL 888
Cdd:cd08824     1 LKQLAKQLRSLLQSYP-GGLPLSKLPQLYKKKFGKPLDLSEYgfSKLSDLLealpgvvIVLSQGGERIVSL 70

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724 1438 LYLFAKNVRSLLHTYHYQQIFLHEFAMAYTKYVGETLQPKTYGYSSVEELLGAIPQVVWIKGHGHKRIVVL 1508
Cdd:cd09979     1 LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTL 71

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564370724  744 IQVSNVDYRLSRKELQQLlqeaFSKHGQVKSVELSP-HTDYQLK----AIVQMRNLHDAICAVNSLHRYKIGSKKILV 816
Cdd:cd21619     4 IYVGNIDMTINEDALEKI----FSRYGQVESVRRPPiHTDKADRttgfGFIKYTDAESAERAMQQADGILLGRRRLVV 77

MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564370724  1053 QFSREVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDygysklielLEAVPHVLQILGMGSKRLLTLTHRAQVKR 1129
Cdd:pfam19687    1 LLSSETISILQDAPACCLPLFKFTEIYEKKFGHKLIVSD---------LYKLTDTVAIREQGNGRLVCLLPSSQARQ 68

The eighth LOTUS domain on Limkain b1(LKAP); The eighth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564370724 1213 QFSKDVVDLLrHQPHFRMPF-NKFIPSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTL 1281
Cdd:cd09984     3 QFAKNVRSLL-HTYHYQQIFlHEFSSAYSKYVGETLQPKNYGYNSLEELLGAIPQVVWIKGHGHKRIVVL 71

RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins; This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564370724  759 QQLLQEAFSKHGQVKSVELSPHTDYQLKAIVQMRNLHDAICAVNSLHRYKIGSKKILVSLS 819
Cdd:cd12433    18 QEELYSLFRPYGRINDITPPPPDSLPRYATVTFRRIRGAIAAKNCLHGYVVNEGGTRLRIQ 78

The second LOTUS domain on Tudor-containing protein 5 (TDRD5); The second LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be discovered. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564370724 1216 KDVVDLLRHQPHFRMPFNKfipSYHHHFGRQCKLAYYGFTKLLELLEAIPEILQVLECGEEKILTL 1281
Cdd:cd09975     6 SELKDLLSHSPVLLSELEK---AYVARFGRSFQYTQYGFFSMLEVLSAASDFIIVKQTRTGSLLLL 68

The first LOTUS domain on Limkain b1(LKAP); The first LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564370724 1054 FSREVIDLLKNQPSCILPISNFIPLYHHHFGKQCRVSDygysklielLEAVPHVLQILGMGSKRLLTL 1121
Cdd:cd09977     4 LSSETVSILQDAPACCLPLFKFTEIYEKKFGHKLAVSD---------LYRLTDTVAIREQGGGRLVCL 62