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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502276558  161 RRLTLVKNGYPGCQQTVVLSHKNTRNLAGFLSKASELLRFPVKQVYTTHGKKVDSLQTLLDGPSLLVCAGNEAFR 235
Cdd:cd17148      1 KKITLVKNGDPDVRRSIILNRRNARNLRTFLDEISDLLQFPVKKLYTLEGRKIDSIQALLHCPSVLVCVGREPFK 75

Dublecortin-like domain 2 found in retinitis pigmentosa 1-like 1 (RP1L1) protein; RP1L1 is a member of doublecortin (DCX) family. Its protein domains occur in tandem repeats. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX-domain of RP1L1 localizes to the photoreceptor and is genetically associated with retinitis pigmentosa.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502276558  161 RRLTLVKNGYPGCQQTVVLSHKNTRNLAGFLSKASELLRFPVKQVYTTHGKKVDSLQTLLDGPSLLVCAGNEAFR 235
Cdd:cd17148      1 KKITLVKNGDPDVRRSIILNRRNARNLRTFLDEISDLLQFPVKKLYTLEGRKIDSIQALLHCPSVLVCVGREPFK 75

Doublecortin;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502276558   60 AVHQRTFKTFSALMDELSQRMP-LSFG-VRSVTTPRGlHGLSALEQLQDGGCYLCSDRKP 117
Cdd:pfam03607    1 VVNKRRFRSFDALLDELTEKVVkLPFGaVRKLYTLDG-KRVTSLDELEDGGVYVAAGREK 59

Domain in the Doublecortin (DCX) gene product; Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502276558   156 NPMAPRRLTLVKNG---YPGCQqtVVLSHKNTRNLAGFLSKASELLR----FPVKQVYTTHGKKVDSLQTLLDGPSlLVC 228
Cdd:smart00537    1 SLVKPKRIRFYRNGdrfFKGVR--LVVNRKRFKSFEALLQDLTEVVKldlpHGVRKLYTLDGKKVTSLDELEDGGS-YVA 77

                            90
                    ....*....|
gi 2502276558   229 AGNEAFRRLE 238
Cdd:smart00537   78 SGTEAFKKVD 87

Doublecortin-like domain 1 found in retinitis pigmentosa (RP)-like protein; RP-like protein family is part of doublecortin (DCX) family. It has double tandem DCX repeats that are associated with retinitis pigmentosa. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. RP-like proteins are colocalized to the photoreceptor and share a function in outer segment disc morphogenesis.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502276558   42 KKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDELSQRMPLSFGVRSVTTPRGLHGLSALEQLQDGGCYLCSDRK 116
Cdd:cd16110      1 KNVTFYKDGDVHFSGVRVAINPRRYRTFDALLDELSRKVPLPFGVRSITTPRGRHSITSLEQLEDGGKYVCSSKR 75

Doublecortin-like domain 1 found in retinitis pigmentosa 1 (RP1)-like protein; RP1, also termed oxygen-regulated protein 1, is a member of the doublecortin (DCX) family. Its DCX domains occur in double tandem repeats. RP1 is associated with retinitis pigmentosa, which is a type of inherited blindness. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The RP1 protein is expressed in photoreceptors and is required for correct stacking of outer segment discs. It interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2502276558   42 KKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDELSQRMPLSFGVRSVTTPRGLHGLSALEQLQDGGCYLCSDRKPPK 119
Cdd:cd17145      1 KRVCFYKSGDPQFGGLRMVVNSRSFKTFDALLDNLSKKVPLPFGVRNITTPRGVHHITSLEDLEDGKSYICSHQKKVK 78

Dublecortin-like domain 2 found in retinitis pigmentosa (RP)-like protein; RP-like protein family is part of doublecortin (DCX) superfamily with double tandem DCX repeats that are associated with retinitis pigmentosa. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. RP-like proteins are colocalized to the photoreceptor and share a function in outer segment disc morphogenesis.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2502276558  161 RRLTLVKNGYPGCQQTVVLSHKNTRNLAGFLSKASELLRFPVKQVYTTHGKKVDSLQTLLDGPSLLVCA 229
Cdd:cd17070      1 KVITVISNGDPHSRHTILLNRRTTQSFEQVLQDLSELLKGPVRKLYTTDGKKVESLSALFHGPDEYVAA 69

Dublecortin-like domain 2 found in retinitis pigmentosa 1 (RP1)-like protein; RP1, also termed oxygen-regulated protein 1, is a member of doublecortin (DCX) superfamily that contains double tandem repeats of the DCX domains. RP1 is associated with retinitis pigmentosa, which is a type of inherited blindness. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The RP1 protein is expressed in photoreceptors that is required for correct stacking of outer segment discs. RP1 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502276558  161 RRLTLVKNGYPGCQQTVVLSHKNTRNLAGFLSKASELLRFPVKQVYTTHGKKVDSLQTLLDGPSLLVCAGNEAFR 235
Cdd:cd17147      1 RKLIVFKNGDPGFKHTLILNKKTTQSFEALLDHVSELMQFPVVKLYTTDGRRVDSLQALILSSGAVVAAGREPFK 75

Dublecortin-like domain 1 found in doublecortin domain-containing protein 2 (DCDC2) and similar proteins; DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502276558   42 KKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDELSQRMPLSFG-VRSVTTPRGLHGLSALEQLQDGGCY 110
Cdd:cd17071      1 KIIVVYKNGDPFFPGKKFVVNERQVRTFDAFLNEVTSGIKAPFGaVRSIYTPTGGHRVKDLDSLQNGGVY 70

Dublecortin-like domain structurally similar to a beta-grasp ubiquitin-like fold; Dublecortin (DCX) is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX gene family consists of eleven paralogs in human and mouse, and its DCX protein domains can occur in double tandem or as single DCX repeats. Proteins with DCX tandem domains in general have roles in microtubule (MT) regulation and signal transduction such as X-linked doublecortin (DCX), retinitis pigmentosa-1 (RP1) and doublecortin-like kinase (DCLK). Single DCX repeat proteins are normally localized to actin-rich subcellular structures, or the nucleus such as DCDC2. DCX is not only a unique MAP in terms of structure, it also interacts with multiple additional proteins. Mutations in human DCX genes are associated with abnormal neuronal migration, epilepsy, and mental retardation.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2502276558  161 RRLTLVKNGYPGCQQTVVLSHKN-TRNLAGFLSKASELLR---FPVKQVYTTHGKKVDSLQTLLDGPSLLVCA 229
Cdd:cd01617      1 KRITVFRNGDKNFKGVKVLVKPRrFRTFDQLLDELTEKLGlptGGVRKLYTPSGKLVKSLSDLEDGESYVVCG 73

Dublecortin-like domain 1 found in doublecortin domain-containing protein 2C (DCDC2C); DCDC2 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2502276558   42 KKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDELSQRMPLSFGVRSVTTPRGLHGLSALEQLQDGGCYLCSDRK 116
Cdd:cd17151      1 KTILVYRNGDPFYQAHKVVIHRRRVKTFDALLRQLTETVKVPFGVRCLYTPRNGHRVKGLDDLQGGGKYVAAGRE 75

Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1); DCLK1 is a member of doublecortin (DCX) protein superfamily that functions as a microtubule-associated protein (MAP), and contains two conserved tubulin binding domains. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule-binding domains, DCLK encodes a serine/threonine kinase domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. DCLK1 appears to regulate cyclic AMP signaling and is involved in neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. Unlike DCX, this DCLK has varying levels of expression throughout embryonic and adult life.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502276558   41 AKKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDELSQRMP----LSFGVRSVTTPRGLHGLSALEQLQDGGCYLCSDRK 116
Cdd:cd17140      2 AKKVRFYRNGDRYFKGIVYAISPDRFRSFEALLADLTRTLSdnvnLPQGVRTIYTIDGLKKISSLDQLVEGESYVCGSIE 81

                   ...
gi 2502276558  117 PPK 119
Cdd:cd17140     82 PFK 84

Dublecortin-like domain 1 found in neuronal migration protein doublecortin (DCX); DCX, also termed doublin or lissencephalin-X (Lis-XDCX), is a microtubule-associated protein (MAP). It belongs to the doublecortin (DCX) family, has double tandem DCX repeats, and is expressed in migrating neurons. Structure studies show that the N-terminal DCX domain has a stable ubiquitin-like fold. DCX is not only a unique MAP in terms of structure, it also interacts with multiple additional proteins. Mutations in the human DCX genes are associated with abnormal neuronal migration, epilepsy, and mental retardation.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2502276558   41 AKKITFLKRGDPQFAGVRLAVHQRTFKTFSALMDEL----SQRMPLSFGVRSVTTPRGLHGLSALEQLQDGGCYLCS 113
Cdd:cd16112      2 AKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLtrslSDNINLPQGVRYIYTIDGSRKIGSMDELEEGESYVCS 78

Domain in the Doublecortin (DCX) gene product; Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2502276558   156 NPMAPRRLTLVKNG---YPGCQqtVVLSHKNTRNLAGFLSKASELLR----FPVKQVYTTHGKKVDSLQTLLDGPSlLVC 228
Cdd:smart00537    1 SLVKPKRIRFYRNGdrfFKGVR--LVVNRKRFKSFEALLQDLTEVVKldlpHGVRKLYTLDGKKVTSLDELEDGGS-YVA 77

                            90
                    ....*....|
gi 2502276558   229 AGNEAFRRLE 238
Cdd:smart00537   78 SGTEAFKKVD 87