hypothetical protein DAPPUDRAFT_327607 [Daphnia pulex]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| RRM2_LKAP | cd12256 | RNA recognition motif 2 (RRM2) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
447-535 | 1.69e-39 | ||||
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. : Pssm-ID: 409701 [Multi-domain] Cd Length: 89 Bit Score: 141.35 E-value: 1.69e-39
|
||||||||
| LabA_like_C super family | cl14879 | C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ... |
931-1003 | 2.24e-36 | ||||
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). The actual alignment was detected with superfamily member cd09981: Pssm-ID: 472713 Cd Length: 71 Bit Score: 131.78 E-value: 2.24e-36
|
||||||||
| LabA_like_C super family | cl14879 | C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ... |
770-841 | 7.25e-36 | ||||
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). The actual alignment was detected with superfamily member cd09979: Pssm-ID: 472713 Cd Length: 72 Bit Score: 130.67 E-value: 7.25e-36
|
||||||||
| RRM1_LKAP | cd12255 | RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
185-258 | 1.77e-32 | ||||
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. : Pssm-ID: 409700 Cd Length: 73 Bit Score: 120.92 E-value: 1.77e-32
|
||||||||
| PIN_limkain_b1_N_like | cd10910 | N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ... |
26-148 | 9.20e-27 | ||||
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. : Pssm-ID: 350234 Cd Length: 126 Bit Score: 106.55 E-value: 9.20e-27
|
||||||||
| LabA_like_C super family | cl14879 | C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ... |
846-918 | 2.55e-24 | ||||
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). The actual alignment was detected with superfamily member cd09980: Pssm-ID: 472713 Cd Length: 72 Bit Score: 97.43 E-value: 2.55e-24
|
||||||||
| MARF1_LOTUS super family | cl45090 | MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis ... |
545-758 | 6.41e-24 | ||||
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). The actual alignment was detected with superfamily member pfam19687: Pssm-ID: 437519 [Multi-domain] Cd Length: 211 Bit Score: 101.30 E-value: 6.41e-24
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1152-1221 | 7.26e-15 | ||||
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. : Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 70.73 E-value: 7.26e-15
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1009-1080 | 1.59e-09 | ||||
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. : Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 55.32 E-value: 1.59e-09
|
||||||||
| Name | Accession | Description | Interval | E-value | ||||
| RRM2_LKAP | cd12256 | RNA recognition motif 2 (RRM2) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
447-535 | 1.69e-39 | ||||
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. Pssm-ID: 409701 [Multi-domain] Cd Length: 89 Bit Score: 141.35 E-value: 1.69e-39
|
||||||||
| LOTUS_5_Limkain_b1 | cd09981 | The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ... |
931-1003 | 2.24e-36 | ||||
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. Pssm-ID: 193595 Cd Length: 71 Bit Score: 131.78 E-value: 2.24e-36
|
||||||||
| LOTUS_3_Limkain_b1 | cd09979 | The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ... |
770-841 | 7.25e-36 | ||||
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. Pssm-ID: 193593 Cd Length: 72 Bit Score: 130.67 E-value: 7.25e-36
|
||||||||
| RRM1_LKAP | cd12255 | RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
185-258 | 1.77e-32 | ||||
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. Pssm-ID: 409700 Cd Length: 73 Bit Score: 120.92 E-value: 1.77e-32
|
||||||||
| PIN_limkain_b1_N_like | cd10910 | N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ... |
26-148 | 9.20e-27 | ||||
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. Pssm-ID: 350234 Cd Length: 126 Bit Score: 106.55 E-value: 9.20e-27
|
||||||||
| LOTUS_4_Limkain_b1 | cd09980 | The fourth LOTUS domain on Limkain b1(LKAP); The fourth LOTUS domain on Limkain b1(LKAP): ... |
846-918 | 2.55e-24 | ||||
The fourth LOTUS domain on Limkain b1(LKAP); The fourth 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. Pssm-ID: 193594 Cd Length: 72 Bit Score: 97.43 E-value: 2.55e-24
|
||||||||
| MARF1_LOTUS | pfam19687 | MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis ... |
545-758 | 6.41e-24 | ||||
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). Pssm-ID: 437519 [Multi-domain] Cd Length: 211 Bit Score: 101.30 E-value: 6.41e-24
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1152-1221 | 7.26e-15 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 70.73 E-value: 7.26e-15
|
||||||||
| LOTUS_2_Limkain_b1 | cd09978 | The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): ... |
679-746 | 1.17e-14 | ||||
The second LOTUS domain on Limkain b1(LKAP); The second 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 Pssm-ID: 193592 Cd Length: 71 Bit Score: 70.01 E-value: 1.17e-14
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
776-839 | 2.57e-12 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 62.96 E-value: 2.57e-12
|
||||||||
| NYN | pfam01936 | NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ... |
26-156 | 5.08e-11 | ||||
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs. Pssm-ID: 426520 Cd Length: 137 Bit Score: 61.92 E-value: 5.08e-11
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
937-990 | 1.02e-09 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 55.64 E-value: 1.02e-09
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1009-1080 | 1.59e-09 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 55.32 E-value: 1.59e-09
|
||||||||
| MARF1_RRM1 | pfam11608 | MARF1, RNA recognition motif 1; MARF1 (also known as Limkain-b1) is an essential protein for ... |
189-260 | 5.91e-09 | ||||
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. Pssm-ID: 463307 Cd Length: 89 Bit Score: 54.35 E-value: 5.91e-09
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
1159-1220 | 1.72e-06 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 46.78 E-value: 1.72e-06
|
||||||||
| Name | Accession | Description | Interval | E-value | ||||
| RRM2_LKAP | cd12256 | RNA recognition motif 2 (RRM2) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
447-535 | 1.69e-39 | ||||
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. Pssm-ID: 409701 [Multi-domain] Cd Length: 89 Bit Score: 141.35 E-value: 1.69e-39
|
||||||||
| LOTUS_5_Limkain_b1 | cd09981 | The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ... |
931-1003 | 2.24e-36 | ||||
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. Pssm-ID: 193595 Cd Length: 71 Bit Score: 131.78 E-value: 2.24e-36
|
||||||||
| LOTUS_3_Limkain_b1 | cd09979 | The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ... |
770-841 | 7.25e-36 | ||||
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. Pssm-ID: 193593 Cd Length: 72 Bit Score: 130.67 E-value: 7.25e-36
|
||||||||
| RRM1_LKAP | cd12255 | RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins; This subfamily ... |
185-258 | 1.77e-32 | ||||
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. Pssm-ID: 409700 Cd Length: 73 Bit Score: 120.92 E-value: 1.77e-32
|
||||||||
| PIN_limkain_b1_N_like | cd10910 | N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ... |
26-148 | 9.20e-27 | ||||
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. Pssm-ID: 350234 Cd Length: 126 Bit Score: 106.55 E-value: 9.20e-27
|
||||||||
| LOTUS_3_Limkain_b1 | cd09979 | The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ... |
933-995 | 6.72e-25 | ||||
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. Pssm-ID: 193593 Cd Length: 72 Bit Score: 99.08 E-value: 6.72e-25
|
||||||||
| LOTUS_5_Limkain_b1 | cd09981 | The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ... |
775-840 | 8.03e-25 | ||||
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. Pssm-ID: 193595 Cd Length: 71 Bit Score: 99.04 E-value: 8.03e-25
|
||||||||
| LOTUS_4_Limkain_b1 | cd09980 | The fourth LOTUS domain on Limkain b1(LKAP); The fourth LOTUS domain on Limkain b1(LKAP): ... |
846-918 | 2.55e-24 | ||||
The fourth LOTUS domain on Limkain b1(LKAP); The fourth 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. Pssm-ID: 193594 Cd Length: 72 Bit Score: 97.43 E-value: 2.55e-24
|
||||||||
| MARF1_LOTUS | pfam19687 | MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis ... |
545-758 | 6.41e-24 | ||||
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). Pssm-ID: 437519 [Multi-domain] Cd Length: 211 Bit Score: 101.30 E-value: 6.41e-24
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
775-840 | 5.26e-15 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 71.11 E-value: 5.26e-15
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1152-1221 | 7.26e-15 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 70.73 E-value: 7.26e-15
|
||||||||
| LOTUS_2_Limkain_b1 | cd09978 | The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): ... |
679-746 | 1.17e-14 | ||||
The second LOTUS domain on Limkain b1(LKAP); The second 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 Pssm-ID: 193592 Cd Length: 71 Bit Score: 70.01 E-value: 1.17e-14
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
931-1001 | 3.17e-14 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 68.80 E-value: 3.17e-14
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
776-839 | 2.57e-12 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 62.96 E-value: 2.57e-12
|
||||||||
| NYN | pfam01936 | NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ... |
26-156 | 5.08e-11 | ||||
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs. Pssm-ID: 426520 Cd Length: 137 Bit Score: 61.92 E-value: 5.08e-11
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
937-990 | 1.02e-09 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 55.64 E-value: 1.02e-09
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
1009-1080 | 1.59e-09 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 55.32 E-value: 1.59e-09
|
||||||||
| LOTUS_3_Limkain_b1 | cd09979 | The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ... |
1152-1221 | 3.97e-09 | ||||
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. Pssm-ID: 193593 Cd Length: 72 Bit Score: 54.40 E-value: 3.97e-09
|
||||||||
| MARF1_RRM1 | pfam11608 | MARF1, RNA recognition motif 1; MARF1 (also known as Limkain-b1) is an essential protein for ... |
189-260 | 5.91e-09 | ||||
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. Pssm-ID: 463307 Cd Length: 89 Bit Score: 54.35 E-value: 5.91e-09
|
||||||||
| OST-HTH | pfam12872 | OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ... |
1159-1220 | 1.72e-06 | ||||
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. Pssm-ID: 463735 Cd Length: 64 Bit Score: 46.78 E-value: 1.72e-06
|
||||||||
| LOTUS | cd08824 | LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ... |
846-918 | 1.84e-06 | ||||
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. Pssm-ID: 193585 [Multi-domain] Cd Length: 70 Bit Score: 46.84 E-value: 1.84e-06
|
||||||||
| LOTUS_5_Limkain_b1 | cd09981 | The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ... |
1154-1221 | 3.89e-06 | ||||
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. Pssm-ID: 193595 Cd Length: 71 Bit Score: 45.88 E-value: 3.89e-06
|
||||||||
| LOTUS_1_Limkain_b1 | cd09977 | The first LOTUS domain on Limkain b1(LKAP); The first LOTUS domain on Limkain b1(LKAP): ... |
546-602 | 6.92e-06 | ||||
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. Pssm-ID: 193591 Cd Length: 62 Bit Score: 44.88 E-value: 6.92e-06
|
||||||||
| LOTUS_4_Limkain_b1 | cd09980 | The fourth LOTUS domain on Limkain b1(LKAP); The fourth LOTUS domain on Limkain b1(LKAP): ... |
776-824 | 6.96e-05 | ||||
The fourth LOTUS domain on Limkain b1(LKAP); The fourth 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. Pssm-ID: 193594 Cd Length: 72 Bit Score: 42.35 E-value: 6.96e-05
|
||||||||
| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
453-525 | 2.14e-04 | ||||
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: 41.11 E-value: 2.14e-04
|
||||||||
| LOTUS_4_Limkain_b1 | cd09980 | The fourth LOTUS domain on Limkain b1(LKAP); The fourth LOTUS domain on Limkain b1(LKAP): ... |
932-995 | 2.31e-04 | ||||
The fourth LOTUS domain on Limkain b1(LKAP); The fourth 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. Pssm-ID: 193594 Cd Length: 72 Bit Score: 40.81 E-value: 2.31e-04
|
||||||||
| LOTUS_8_Limkain_b1 | cd09984 | The eighth LOTUS domain on Limkain b1(LKAP); The eighth LOTUS domain on Limkain b1(LKAP): ... |
1154-1225 | 6.80e-04 | ||||
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. Pssm-ID: 193598 Cd Length: 76 Bit Score: 39.89 E-value: 6.80e-04
|
||||||||
| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
191-257 | 3.66e-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: 37.65 E-value: 3.66e-03
|
||||||||
| LOTUS_2_TDRD5 | cd09975 | The second LOTUS domain on Tudor-containing protein 5 (TDRD5); The second LOTUS domain on ... |
775-840 | 3.98e-03 | ||||
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. Pssm-ID: 193589 Cd Length: 70 Bit Score: 37.55 E-value: 3.98e-03
|
||||||||
| LOTUS_8_Limkain_b1 | cd09984 | The eighth LOTUS domain on Limkain b1(LKAP); The eighth LOTUS domain on Limkain b1(LKAP): ... |
772-847 | 5.09e-03 | ||||
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. Pssm-ID: 193598 Cd Length: 76 Bit Score: 37.20 E-value: 5.09e-03
|
||||||||
| LOTUS_6_Limkain_b1 | cd09982 | The sixth LOTUS domain on Limkain b1(LKAP); The sixth LOTUS domain on Limkain b1(LKAP): ... |
773-840 | 8.30e-03 | ||||
The sixth LOTUS domain on Limkain b1(LKAP); The sixth 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. Pssm-ID: 193596 Cd Length: 71 Bit Score: 36.39 E-value: 8.30e-03
|
||||||||
| Blast search parameters | ||||
|
