first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    1 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSGTKLLLLHEQETLTQVTQRPSSHKM 80
Cdd:cd17170      2 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRTEGSGTKLLLLHEQETLTQVTQRPGSHKM 81

                           90
                   ....*....|...
gi 2024343435   81 RCLFRISFVPKDP 93
Cdd:cd17170     82 RCLFRISFVPKDP 94

Band 4.1 homologues; Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435     4 VLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSgtKLLLLHEQETLTQVTQrpsSHKMRCL 83
Cdd:smart00295    1 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDL--RHWLDPAKTLLDQDVK---SEPLTLY 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    84 FRISFVPKDPIDlLRRDPVAFEYLYVQSCNDVVQERFgpELKYDIALRLAALQMYIatvtTKQTQKISLKYIEKEWGLET 163
Cdd:smart00295   76 FRVKFYPPDPNQ-LKEDPTRLNLLYLQVRNDILEGRL--PCPEEEALLLAALALQA----EFGDYDEELHDLRGELSLKR 148

                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435   164 FLPSAVLQSMKEKNIKKALSHLVKanqnlvpPGKKLSALQAKVHYLKFLSDLRLYGGRVF 223
Cdd:smart00295  149 FLPKQLLDSRKLKEWRERIVELHK-------ELIGLSPEEAKLKYLELARKLPTYGVELF 201

FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 4 (FRMPD4); FRMPD4, also termed PDZ domain-containing protein 10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a multiscaffolding protein that modulates both Homer1 and postsynaptic density protein 95 activity. It can associate with the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. Moreover, FRMPD4 is asymmetrically distributed in the cytosol and nuclei of neural stem/progenitor cells in the adult brain, suggesting a significant role in cell differentiation via association with cell polarity machinery. FRMPD4 contains a WW domain, a PDZ domain, and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    1 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSGTKLLLLHEQETLTQVTQRPSSHKM 80
Cdd:cd17170      2 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRTEGSGTKLLLLHEQETLTQVTQRPGSHKM 81

                           90
                   ....*....|...
gi 2024343435   81 RCLFRISFVPKDP 93
Cdd:cd17170     82 RCLFRISFVPKDP 94

Band 4.1 homologues; Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435     4 VLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSgtKLLLLHEQETLTQVTQrpsSHKMRCL 83
Cdd:smart00295    1 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDL--RHWLDPAKTLLDQDVK---SEPLTLY 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    84 FRISFVPKDPIDlLRRDPVAFEYLYVQSCNDVVQERFgpELKYDIALRLAALQMYIatvtTKQTQKISLKYIEKEWGLET 163
Cdd:smart00295   76 FRVKFYPPDPNQ-LKEDPTRLNLLYLQVRNDILEGRL--PCPEEEALLLAALALQA----EFGDYDEELHDLRGELSLKR 148

                           170       180       190       200       210       220
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435   164 FLPSAVLQSMKEKNIKKALSHLVKanqnlvpPGKKLSALQAKVHYLKFLSDLRLYGGRVF 223
Cdd:smart00295  149 FLPKQLLDSRKLKEWRERIVELHK-------ELIGLSPEEAKLKYLELARKLPTYGVELF 201

FERM central domain; This domain is the central structural domain of the FERM domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435   93 PIDLLRRDPVAFEYLYVQSCNDVVQERFGPELkyDIALRLAALQMYIATVTTKQTQKISlkyieKEWGLETFLPSAVLQS 172
Cdd:pfam00373    1 DLELLLQDEVTRHLLYLQAKDDILEGRLPCSE--EEALLLAALQLQAEFGDYQPSSHTS-----EYLSLESFLPKQLLRK 73

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2024343435  173 MKEKNIKKALSHLVKANQNlvppgkkLSALQAKVHYLKFLSDLRLYGGRVF 223
Cdd:pfam00373   74 MKSKELEKRVLEAHKNLRG-------LSAEEAKLKYLQIAQSLPTYGVEFF 117

FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 4 (FRMPD4); FRMPD4, also termed PDZ domain-containing protein 10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a multiscaffolding protein that modulates both Homer1 and postsynaptic density protein 95 activity. It can associate with the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. Moreover, FRMPD4 is asymmetrically distributed in the cytosol and nuclei of neural stem/progenitor cells in the adult brain, suggesting a significant role in cell differentiation via association with cell polarity machinery. FRMPD4 contains a WW domain, a PDZ domain, and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    1 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSGTKLLLLHEQETLTQVTQRPSSHKM 80
Cdd:cd17170      2 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRTEGSGTKLLLLHEQETLTQVTQRPGSHKM 81

                           90
                   ....*....|...
gi 2024343435   81 RCLFRISFVPKDP 93
Cdd:cd17170     82 RCLFRISFVPKDP 94

FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing proteins FRMPD1, FRMPD3, FRMPD4, and similar proteins; This family includes FERM and PDZ domain-containing proteins FRMPD1, FRMPD3, and FRMPD4, which all contain a PDZ domain and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). FRMPD1, also termed FERM domain-containing protein 2, is an activator of G-protein signaling 3 (AGS3)-binding protein that regulates the subcellular location of AGS3 and its interaction with G-proteins. FRMPD4, also termed PDZ domain-containing protein 10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a multiscaffolding protein that modulates both Homer1 and post-synaptic density protein 95 activity. Both FRMPD1 and FRMPD4 can associate with the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. The biological role of FRMPD3 remains unclear.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    1 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSGTKLLLLHEQETLTQVTQRPSSHKM 80
Cdd:cd17088      1 MPNVLKVYLENGQTKSFKYDQSTTVKDVLLSLQEKLGIKSMEHFSLVLEYVKSPRTNKLSLLQPDESLAQVAARPGSHHL 80

                           90
                   ....*....|
gi 2024343435   81 RCLFRISFVP 90
Cdd:cd17088     81 RCLFRISFVP 90

FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 3 (FRMPD3); FRMPD3 is an uncharacterized FERM and PDZ domain-containing protein. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    1 MPNVLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLMLEQRVEGSGTKLLLLHEQETLTQVTQRPSSHKM 80
Cdd:cd17169      1 IPNVLKVFLENGQIKSFTFDGRTTVKDVMLTLQDRLSLRHIEHFALVLEYGGPEQNHKFLLLQDKQPLAHVVQRTHYQGM 80

                           90
                   ....*....|...
gi 2024343435   81 RCLFRISFVPKDP 93
Cdd:cd17169     81 KCLFRICFFPKDP 93

LGN tetratricopeptide repeat-binding domain found in FERM and PDZ domain-containing protein 4; FRMPD4, also called PDZ domain-containing protein 10 (PDZD10), PDZK10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a novel PSD-95-interacting FERM and PDZ domain protein that regulates dendritic spine morphogenesis. It acts as a positive regulator of dendritic spine morphogenesis and density. It is required for the maintenance of excitatory synaptic transmission. It binds phosphatidylinositol 4,5-bisphosphate. FRMPD4 contains WW, PDZ and FERM domains in the N-terminal region. This model corresponds to a conserved region in the C-terminal region of FRMPD4 that binds to tetratricopeptide (TPR) repeats present in the N-terminal domain of adaptor protein LGN. LGN plays a crucial role in mitotic spindle orientation and cell polarization via interaction with multiple targets including FRMPD4.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2024343435  772 QAADLQSKVVPSKQILHSDNMEMEPETMETKSVTDYFSKLHMGSLVYSC 820
Cdd:cd21943      1 QETELQSKVVPSKQILHSDNIEMEPETMETKSLTDYFSKLHMGSLVYSC 49

FERM domain B-lobe; The FERM domain has a cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases, the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains and consequently is capable of binding to both peptides and phospholipids at different sites.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435  103 AFEYLYVQSCNDVVQERFgpELKYDIALRLAALQMYIATVTTKQTqkislKYIEKEWGLETFLPSAVLQSMKEKNIKKAL 182
Cdd:cd14473      1 TRYLLYLQVKRDILEGRL--PCSEETAALLAALALQAEYGDYDPS-----EHKPKYLSLKRFLPKQLLKQRKPEEWEKRI 73

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2024343435  183 SHLVKANQNLvppgkklSALQAKVHYLKFLSDL 215
Cdd:cd14473     74 VELHKKLRGL-------SPAEAKLKYLKIARKL 99

FERM domain C-lobe of Focal Adhesion Kinase 1 and 2; FAK1 (also called FRNK/Focal adhesion kinase-related nonkinase; p125FAK/pp125FAK;PTK2/Protein-tyrosine kinase 2 protein tyrosine kinase 2 (PTK2) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. It has been implicated in diverse cellular roles including cell locomotion, mitogen response and cell survival. The N-terminal region of FAK1 contains a FERM domain, a linker, a kinase domain, and a C-terminal FRNK (FAK-related-non-kinase) domain. Three subdomains of FERM: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3), form a cloverleaf fold, similar to those of known FERM structures despite the low sequence conservation. The C-lobe/F3 within the FERM domain is part of the PH domain family. The phosphoinositide-binding site found in ERM family proteins is not present in the FERM domain of FAK1. The adjacent Src SH3 and SH2 binding sites in the linker of FAK1 associates with the F3 and F1 lobes and are thought to be involved in regulation. The FERM domain of FAK1 can inhibit enzymatic activity and repress FAK signaling. In an inactive state of FAK1, the FERM domain is thought to interact with the catalytic domain of FAK1 to repress its activity. Upon activation this interaction is disrupted and its kinase activity restored. The FRNK domain is thought to function as a negative regulator of kinase activity. The C-lobe/F3 is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435  222 VFKATLVQGEKRSeVTLLVGPRYGISHVINTKTNLVaLLADFSHVNRIEMFTEDESSVRVELHvLDVK----PITLLMES 297
Cdd:cd13190      4 IFKCALGSGWSIP-VDLVIGPEVGISYLTDKGSAPT-HLADFEQIQSIQTSKSEDKDGKALLQ-LKIAgasePLSITCSS 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2024343435  298 SD-AMNLACLTAGYYRLLVDSRRSIFNMANK 327
Cdd:cd13190     81 LAtAESLADLIDGYCRLVNQTDSSLIIRPEK 111

FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain and F1 sub-domain, found in FERM (Four.1/Ezrin/Radixin/Moesin) family proteins; FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain is present at the N-terminus of a large and diverse group of proteins that mediate linkage of the cytoskeleton to the plasma membrane. FERM-containing proteins are ubiquitous components of the cytocortex and are involved in cell transport, cell structure and signaling functions. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N), which is structurally similar to ubiquitin.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2024343435    4 VLKVYLENGQTKSFRFDCSTSIKDVILTLQEKLSIKCIEHFSLmleQRVEGSGTKLLLLHEqETLTQvtQRPSSHKMRCL 83
Cdd:cd01765      2 SCRVRLLDGTELTLEVSKKATGQELFDKVCEKLNLLEKDYFGL---FYEDNDGQKHWLDLD-KKISK--QLKRSGPYQFY 75

                   ....*
gi 2024343435   84 FRISF 88
Cdd:cd01765     76 FRVKF 80