ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins; Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846 702 PATIRVSKPNE-------NDGQFMEITVQsLSENVGSLKEKIAGEIQIPANKQKLS-GKAGFLKDNMSLAHYNVGAGEIL 773
Cdd:cd01800   1 PVTLKVQVPNVpdkpewkLNGQVLELTLP-LTDTISVLKEKIHEELGMPANKQKLQvEGGGFLKDSNSLAFYNLGSGTVL 79

                ....*
gi 15223846 774 TLSLR 778
Cdd:cd01800  80 TLSLK 84

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 15223846    191 LDIIKLTAQFVARNGKSFLTGLSNRENNNPQFHFMKPTHSMFTFFTSLVDAYSE 244
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKPNDPYHAYYRKKLAEYRQ 54

ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins; Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846 702 PATIRVSKPNE-------NDGQFMEITVQsLSENVGSLKEKIAGEIQIPANKQKLS-GKAGFLKDNMSLAHYNVGAGEIL 773
Cdd:cd01800   1 PVTLKVQVPNVpdkpewkLNGQVLELTLP-LTDTISVLKEKIHEELGMPANKQKLQvEGGGFLKDSNSLAFYNLGSGTVL 79

                ....*
gi 15223846 774 TLSLR 778
Cdd:cd01800  80 TLSLK 84

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 15223846    191 LDIIKLTAQFVARNGKSFLTGLSNRENNNPQFHFMKPTHSMFTFFTSLVDAYSE 244
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKPNDPYHAYYRKKLAEYRQ 54

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15223846   192 DIIKLTAQFVARNGKSFLTGLSNRENNNPQFHFMKPT-HSMFTFFTSLVDAY 242
Cdd:pfam01805   1 DIIKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPdDPLHAYYRWKLEEY 52

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15223846   714 DGQFMEITVqSLSENVGSLKEKIAGEIQIPANKQKL--SGKagFLKDNMSLAHYNVGAGEILTLSLRER 780
Cdd:pfam00240   7 DGKKITLEV-DPTDTVLELKEKIAEKEGVPPEQQRLiySGK--VLEDDQTLGEYGIEDGSTIHLVLRQR 72

EBNA-3B; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846  536 PNSFPGPAAlPPPRPGVPIVRPLPPPPNLalnlprPPPSAQYPGAPRPLGVPMMQPMHQQHQLTMPGPPGHPQMMmnRPP 615
Cdd:PHA03378 697 PPRAPTPMR-PPAAPPGRAQRPAAATGRA------RPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRA--RPP 767

                         90       100       110
                 ....*....|....*....|....*....|...
gi 15223846  616 QMQPGMHVPPPPGSQFAHHMQIPR--PYGQLPP 646
Cdd:PHA03378 768 AAAPGAPTPQPPPQAPPAPQQRPRgaPTPQPPP 800

ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins; Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846 702 PATIRVSKPNE-------NDGQFMEITVQsLSENVGSLKEKIAGEIQIPANKQKLS-GKAGFLKDNMSLAHYNVGAGEIL 773
Cdd:cd01800   1 PVTLKVQVPNVpdkpewkLNGQVLELTLP-LTDTISVLKEKIHEELGMPANKQKLQvEGGGFLKDSNSLAFYNLGSGTVL 79

                ....*
gi 15223846 774 TLSLR 778
Cdd:cd01800  80 TLSLK 84

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 15223846    191 LDIIKLTAQFVARNGKSFLTGLSNRENNNPQFHFMKPTHSMFTFFTSLVDAYSE 244
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKPNDPYHAYYRKKLAEYRQ 54

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15223846   192 DIIKLTAQFVARNGKSFLTGLSNRENNNPQFHFMKPT-HSMFTFFTSLVDAY 242
Cdd:pfam01805   1 DIIKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPdDPLHAYYRWKLEEY 52

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15223846    714 DGQFMEITVQSlSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR 778
Cdd:smart00213   9 DGKTITLEVKP-SDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15223846 704 TIRVSkpneNDGQFmEITVqSLSENVGSLKEKIAGEIQIPANKQKL--SGKagFLKDNMSLAHYNVGAG 770
Cdd:cd16106   4 TVKCS----NGKKF-TVEV-EPDATVLELKELIAEKSDIPAEQQRLiyKGK--ILKDEETLSSYKIQDG 64

ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15223846 719 EITVQ-SLSENVGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLSLR 778
Cdd:cd01807  12 ECTIEvSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLVVK 72

ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; BAG6, also termed large proline-rich protein BAG6, or BAG family molecular chaperone regulator 6, or HLA-B-associated transcript 3 (Bat3), or protein Scythe, or protein G3, is a nucleo-cytoplasmic shuttling chaperone protein that is highly conserved in eukaryotes. It functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored transmembrane protein biogenesis in mammals. BAG6 is a component of the heterotrimeric BAG6 sortase complex composed of BAG6, transmembrane recognition complex 35 (TRC35) and ubiquitin-like protein 4A (UBL4A). The BAG6 complex together with the cochaperone small, glutamine-rich, tetratricopeptide repeat-containing, protein alpha (SGTA) plays a role in the biogenesis of tail-anchored membrane proteins and subsequently shown to regulate the ubiquitination and proteasomal degradation of mislocalized proteins. Moreover, BAG6 acts as an apoptotic regulator that binds reaper, a potent apoptotic inducer. BAG6/reaper is thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. It is also likely a key regulator of the molecular chaperone Heat Shock Protein A2 (HSPA2) stability/function in human germ cells. Furthermore, aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. BAG6 contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15223846 718 MEITVQSL-SEN----------VGSLKEKIAGEIQIPANKQKLSGKAGFLKDNMSLAHYNVGaGEILTLSLR 778
Cdd:cd01809   1 LEVTVKTLdSQNrtftvpeeitVKEFKEHIASSVNIPAEKQRLIFQGRVLQDDKKLKEYDVD-GKVIHLVER 71

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846   542 PAALPPPRPGVPIVRPLPPPPNLALNLPRPPPSAQYPGAPrplgvPMMQPMHQQHQLTMPGPPGHPQMMMNRPPQMQPGM 621
Cdd:pfam15279 219 PGIGPPPKPPRNLGPPSNPMHRPPFSPHHPPPPPTPPGPP-----PGLPPPPPRGFTPPFGPPFPPVNMMPNPPEMNFGL 293

                          90
                  ....*....|
gi 15223846   622 -----HVPPP 626
Cdd:pfam15279 294 pslapLVPPV 303

EBNA-3B; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15223846  536 PNSFPGPAAlPPPRPGVPIVRPLPPPPNLalnlprPPPSAQYPGAPRPLGVPMMQPMHQQHQLTMPGPPGHPQMMmnRPP 615
Cdd:PHA03378 697 PPRAPTPMR-PPAAPPGRAQRPAAATGRA------RPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRA--RPP 767

                         90       100       110
                 ....*....|....*....|....*....|...
gi 15223846  616 QMQPGMHVPPPPGSQFAHHMQIPR--PYGQLPP 646
Cdd:PHA03378 768 AAAPGAPTPQPPPQAPPAPQQRPRgaPTPQPPP 800

ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin (Ub) regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the first Ubl domain.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 15223846 726 SENVGSLKEKIAGEIQIPANKQKLSG-KAGFLKDNMSL 762
Cdd:cd17129  20 TETVGDIKQILENELGIPPCKQILKGwKARTVSDSTVL 57