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 165932270 702 PVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYE-GIFIKDSNSLAYYNMASGAVIH 780
Cdd:cd01800    1 PVTLKVQVPNVPDKPEWKLNGQVLELTLPLTDTISVLKEKIHEELGMPANKQKLQVEgGGFLKDSNSLAFYNLGSGTVLT 80

                 ....
gi 165932270 781 LALK 784
Cdd:cd01800   81 LSLK 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 165932270    50 RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKE 103
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 165932270 702 PVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYE-GIFIKDSNSLAYYNMASGAVIH 780
Cdd:cd01800    1 PVTLKVQVPNVPDKPEWKLNGQVLELTLPLTDTISVLKEKIHEELGMPANKQKLQVEgGGFLKDSNSLAFYNLGSGTVLT 80

                 ....
gi 165932270 781 LALK 784
Cdd:cd01800   81 LSLK 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 165932270    50 RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKE 103
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 165932270  165 DVVKLTAQFVARNGRQFLTQLMQKEQRNYQFDFLRPQ-HSLFNYFTKLVEQY 215
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 165932270   716 TEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALK 784
Cdd:smart00213   4 TVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72

ubiquitin; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 165932270 720 LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERGG 788
Cdd:PTZ00044   8 LTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQLRGG 76

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 165932270 702 PVSIKVQVPNMQDKTEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYE-GIFIKDSNSLAYYNMASGAVIH 780
Cdd:cd01800    1 PVTLKVQVPNVPDKPEWKLNGQVLELTLPLTDTISVLKEKIHEELGMPANKQKLQVEgGGFLKDSNSLAFYNLGSGTVLT 80

                 ....
gi 165932270 781 LALK 784
Cdd:cd01800   81 LSLK 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 165932270    50 RNIVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPNDPYHAYYRHKVSEFKE 103
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 165932270  165 DVVKLTAQFVARNGRQFLTQLMQKEQRNYQFDFLRPQ-HSLFNYFTKLVEQY 215
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 165932270   716 TEWKLNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALK 784
Cdd:smart00213   4 TVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 165932270 720 LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHL 781
Cdd:cd17039    6 LDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHL 67

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 165932270 720 LNGQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKERGG 788
Cdd:cd01803    8 LTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 76

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 165932270 723 QGLVFTLPLTDQVSVIKVK--IHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALK 784
Cdd:cd01807    9 QGKECTIEVSPTESVLTVKqlVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLVVK 72

ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein that upon viral infection it modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other ubiquitin-like (Ubl) molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the second Ubl domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 165932270 722 GQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMASGAVIHLALKER 786
Cdd:cd01810   10 GQSHTYEVRLTQTVDQLKQKVSGREGVHDDQFWLTFEGRPLEDQLPLGEYGLKPQSTIHMNLRLR 74

ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein (Ubl) that upon viral infection, modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other Ubl molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the first Ubl domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 165932270 724 GLVFTLPLTD--QVSVIKVKIHEATGMPAGKQKL--QYEGIFIKDSNSLAYYNMASGAVIHLALKE 785
Cdd:cd01792   10 GNEFQVSVSPsmTVSELKAQITQKIGVPAFQQRLavQPSGVELQDGVRLASQGLGPSSTVLLVVKK 75

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein UBFD1 and similar proteins; UBFD1, also termed ubiquitin-binding protein homolog (UBPH), is a polyubiquitin binding protein containing a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. It may play a role as nuclear factor-kappaB (NF-kappaB) regulator.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 165932270 728 TLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIfIKDSNSLAYYNMASGA 777
Cdd:cd17047   15 KFPLDSTIAELKEHIETLTGVPPAMQKLMYKGL-LKDDKTLRELKVTKGA 63