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Conserved domains on  [gi|1981806245|ref|XP_039271093|]
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ubiquitin-like protein FUBI isoform X2 [Styela clava]

Protein Classification

Ubl1_cv_Nsp3_N-like and Ribosomal_S30 domain-containing protein( domain architecture ID 13219004)

Ubl1_cv_Nsp3_N-like and Ribosomal_S30 domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ribosomal_S30 pfam04758
Ribosomal protein S30;
75-132 5.25e-37

Ribosomal protein S30;


:

Pssm-ID: 398432  Cd Length: 58  Bit Score: 120.45  E-value: 5.25e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1981806245  75 KVHGSLARAGKVKGQTPKVDKQEKKKQKTGRAKRRMQYNRRFVNVVPTFGRRRGPNSN 132
Cdd:pfam04758   1 KVHGSLARAGKVRNQTPKVEKQEKKKKPTGRAKKRLQYNRRFVNVVPGGGRKKGPNSQ 58
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
1-74 1.88e-30

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.


The actual alignment was detected with superfamily member cd01793:

Pssm-ID: 475130  Cd Length: 74  Bit Score: 104.29  E-value: 1.88e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1981806245   1 MQLFLQAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRLLGG 74
Cdd:cd01793     1 MQLFVRAQSLHTLEVSGNETVADIKAHIAALEGIAVEDQVLLYAGAPLEDDVVLGQCGIPDLATLEVAVRLLGG 74
 
Name Accession Description Interval E-value
Ribosomal_S30 pfam04758
Ribosomal protein S30;
75-132 5.25e-37

Ribosomal protein S30;


Pssm-ID: 398432  Cd Length: 58  Bit Score: 120.45  E-value: 5.25e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1981806245  75 KVHGSLARAGKVKGQTPKVDKQEKKKQKTGRAKRRMQYNRRFVNVVPTFGRRRGPNSN 132
Cdd:pfam04758   1 KVHGSLARAGKVRNQTPKVEKQEKKKKPTGRAKKRLQYNRRFVNVVPGGGRKKGPNSQ 58
Ubl_FUBI cd01793
ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is ...
1-74 1.88e-30

ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.


Pssm-ID: 340491  Cd Length: 74  Bit Score: 104.29  E-value: 1.88e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1981806245   1 MQLFLQAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRLLGG 74
Cdd:cd01793     1 MQLFVRAQSLHTLEVSGNETVADIKAHIAALEGIAVEDQVLLYAGAPLEDDVVLGQCGIPDLATLEVAVRLLGG 74
PTZ00467 PTZ00467
40S ribosomal protein S30; Provisional
74-117 1.30e-16

40S ribosomal protein S30; Provisional


Pssm-ID: 185646  Cd Length: 66  Bit Score: 69.03  E-value: 1.30e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1981806245  74 GKVHGSLARAGKVKGQTPKVDKQEKKKQKTGRAKRRMQYNRRFV 117
Cdd:PTZ00467    2 GKIHGSLARAGKVKNQTPKVAKQEKPKQPRGRALKRLKYTRRFL 45
RPS30 COG4919
Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S30 ...
77-117 3.81e-09

Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S30 is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 443947  Cd Length: 52  Bit Score: 49.24  E-value: 3.81e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1981806245  77 HGSLARAGKVKGQTPKVDKQEKKKqKTGRAKRRMQYNRRFV 117
Cdd:COG4919     4 HGSLTKAGKVRSQTPKIPAKPRKN-PPPRVRNRREYRKRFV 43
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
11-71 4.84e-09

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.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 49.48  E-value: 4.84e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1981806245  11 HCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRL 71
Cdd:pfam00240  11 ITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQ 71
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
1-67 1.38e-08

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


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 48.41  E-value: 1.38e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1981806245    1 MQLFL--QAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDV 67
Cdd:smart00213   1 IELTVktLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHL 69
 
Name Accession Description Interval E-value
Ribosomal_S30 pfam04758
Ribosomal protein S30;
75-132 5.25e-37

Ribosomal protein S30;


Pssm-ID: 398432  Cd Length: 58  Bit Score: 120.45  E-value: 5.25e-37
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1981806245  75 KVHGSLARAGKVKGQTPKVDKQEKKKQKTGRAKRRMQYNRRFVNVVPTFGRRRGPNSN 132
Cdd:pfam04758   1 KVHGSLARAGKVRNQTPKVEKQEKKKKPTGRAKKRLQYNRRFVNVVPGGGRKKGPNSQ 58
Ubl_FUBI cd01793
ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is ...
1-74 1.88e-30

ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.


Pssm-ID: 340491  Cd Length: 74  Bit Score: 104.29  E-value: 1.88e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1981806245   1 MQLFLQAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRLLGG 74
Cdd:cd01793     1 MQLFVRAQSLHTLEVSGNETVADIKAHIAALEGIAVEDQVLLYAGAPLEDDVVLGQCGIPDLATLEVAVRLLGG 74
PTZ00467 PTZ00467
40S ribosomal protein S30; Provisional
74-117 1.30e-16

40S ribosomal protein S30; Provisional


Pssm-ID: 185646  Cd Length: 66  Bit Score: 69.03  E-value: 1.30e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1981806245  74 GKVHGSLARAGKVKGQTPKVDKQEKKKQKTGRAKRRMQYNRRFV 117
Cdd:PTZ00467    2 GKIHGSLARAGKVKNQTPKVAKQEKPKQPRGRALKRLKYTRRFL 45
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
9-67 1.68e-10

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.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 52.98  E-value: 1.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1981806245   9 QLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDV 67
Cdd:cd17039     9 KTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHL 67
Ubl2_ISG15 cd01810
ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar ...
1-71 3.60e-10

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.


Pssm-ID: 340508 [Multi-domain]  Cd Length: 74  Bit Score: 52.45  E-value: 3.60e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1981806245   1 MQLFLQAE--QLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRL 71
Cdd:cd01810     1 LSIFVRNEkgQSHTYEVRLTQTVDQLKQKVSGREGVHDDQFWLTFEGRPLEDQLPLGEYGLKPQSTIHMNLRL 73
PRK09336 PRK09336
30S ribosomal protein S30e; Provisional
77-119 1.32e-09

30S ribosomal protein S30e; Provisional


Pssm-ID: 181786  Cd Length: 50  Bit Score: 50.55  E-value: 1.32e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1981806245  77 HGSLARAGKVKGQTPKVDKQEKKKqKTGRAKRRMQYNRRFVNV 119
Cdd:PRK09336    4 HGSLTKAGKVRSQTPKIPPKPKKN-EVPRVRNRREYERRVLKA 45
RPS30 COG4919
Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S30 ...
77-117 3.81e-09

Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S30 is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 443947  Cd Length: 52  Bit Score: 49.24  E-value: 3.81e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1981806245  77 HGSLARAGKVKGQTPKVDKQEKKKqKTGRAKRRMQYNRRFV 117
Cdd:COG4919     4 HGSLTKAGKVRSQTPKIPAKPRKN-PPPRVRNRREYRKRFV 43
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
11-71 4.84e-09

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.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 49.48  E-value: 4.84e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1981806245  11 HCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSSRL 71
Cdd:pfam00240  11 ITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQ 71
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
1-67 1.38e-08

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


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 48.41  E-value: 1.38e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1981806245    1 MQLFL--QAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDV 67
Cdd:smart00213   1 IELTVktLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHL 69
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
13-61 1.69e-05

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.


Pssm-ID: 340523 [Multi-domain]  Cd Length: 73  Bit Score: 40.31  E-value: 1.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1981806245  13 VEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQN 61
Cdd:cd16106    15 VEVEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKIQD 63
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
1-59 1.02e-04

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 38.31  E-value: 1.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1981806245   1 MQL---FLQAEQLHCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIED------ELSINDSDL 59
Cdd:cd01796     1 MKLtvtTEDDDRLFSLEVSPDMTLEDLKALCEAETGIPAAEQVLLHNGQPLTDdkktleALGLKDGDL 68
Ubl_ZFAND4 cd01802
ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar ...
1-65 2.21e-04

ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar proteins; ZFAND4, also termed AN1-type zinc finger and ubiquitin domain-containing protein-like 1 (ANUBL1), may function as an oncogene that promotes proliferation and regulates relevant tumor suppressor genes in gastric cancer, suggesting a role in gastric cancer initiation and progression. ZFAND4contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal AN1-type zinc finger. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal Ubl domain of ZFAND4 does not undergo proteolytic processing.


Pssm-ID: 340500 [Multi-domain]  Cd Length: 74  Bit Score: 37.31  E-value: 2.21e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1981806245   1 MQLFLQAEQLHCVE--VDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTL 65
Cdd:cd01802     1 MELFIETLTGTAFElrVSPFETVASVKAKIQRLEGIPVSQQHLIWSGRELEDDYCLHDYNITDGSTL 67
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
11-50 6.47e-04

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340573  Cd Length: 71  Bit Score: 36.17  E-value: 6.47e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1981806245  11 HCVEVDGHETVATLKHLIALREGISVDDQILTCGGRIIED 50
Cdd:cd17053    13 HTLQVSRSTTVAQVKAMIEDQSGVPPNEQILVYNGKRLED 52
Ubl_parkin cd01798
ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed ...
13-67 1.39e-03

ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed Parkinson juvenile disease protein 2, is a RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like (Ubl) domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction.


Pssm-ID: 340496  Cd Length: 74  Bit Score: 35.35  E-value: 1.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1981806245  13 VEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDV 67
Cdd:cd01798    13 VEVDSDWSILQLKEVVAKRQGVPPDQLRIIFAGKELSDDLTLQNCDLGQQSIVHA 67
Ubl1_FAF1 cd17129
ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; ...
13-69 1.44e-03

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.


Pssm-ID: 340649  Cd Length: 73  Bit Score: 34.93  E-value: 1.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1981806245  13 VEVDGHETVATLKHLIALREGISVDDQILtCGGRiiedelSINDSDLQNLCTLDVSS 69
Cdd:cd17129    15 VVLPDTETVGDIKQILENELGIPPCKQIL-KGWK------ARTVSDSTVLRSLHLPK 64
Ubl_RB1CC1 cd17060
ubiquitin-like (Ubl) domain found in retinoblastoma 1-inducible coiled-coil protein 1 (RB1CC1) ...
19-51 1.85e-03

ubiquitin-like (Ubl) domain found in retinoblastoma 1-inducible coiled-coil protein 1 (RB1CC1) and similar proteins; RB1CC1, also termed FAK family kinase-interacting protein of 200 kDa (FIP200), is the mammalian counterpart of the yeast Atg17 gene and functions as a component of the ULK1/Atg13/RB1CC1/Atg101 complex essential for induction of autophagy. RB1CC1 is a key signaling node to regulate cellular proliferation and differentiation. As a DNA-binding transcription factor, RB1CC1 has been implicated in the regulation of retinoblastoma 1 (RB1) expression. RB1CC1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, as well as a nuclear localization signal (KPRK), a leucine zipper motif and a coiled-coil structure.


Pssm-ID: 340580  Cd Length: 75  Bit Score: 34.85  E-value: 1.85e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1981806245  19 ETVATLKHLIALREGISVDDQILTC-GGRIIEDE 51
Cdd:cd17060    22 QSVSDLKEAIEEKTKIPVEKQVLLVsGGESLDPD 55
Ubl_AtUPL5_like cd16107
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) ...
13-69 5.78e-03

ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) and similar proteins; Arabidopsis thaliana AtUPL5, also termed HECT-type E3 ubiquitin transferase UPL5, is an E3 ubiquitin-protein ligase that contains a ubiquitin-like domain (Ubl), a C-type lectin-binding domain, a leucine zipper and a HECT domain. HECT domain containing-ubiquitin-protein ligases have more than one member in different genomes, these proteins have been classified into four sub-families (UPL1/2, UPL3/4, UPL5 and UPL6/7). AtUPL5 fUPL5 regulates leaf senescence in Arabidopsis through degradation of the transcription factor WRKY53.


Pssm-ID: 340524  Cd Length: 70  Bit Score: 33.63  E-value: 5.78e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1981806245  13 VEVDGHETVATLKHLIALREGISVDDQILTCGGRIIEDELSINDSDLQNLCTLDVSS 69
Cdd:cd16107    14 LHAKASDTVESLHQQIEARTGIPSLEQRLIFGGRQLQHSQSLESCKMENDATLFLVA 70
Ubl_IKKA_like cd17046
ubiquitin-like (Ubl) domain found in inhibitor of nuclear factor kappa-B kinases, IKK-alpha ...
9-42 6.59e-03

ubiquitin-like (Ubl) domain found in inhibitor of nuclear factor kappa-B kinases, IKK-alpha and IKK-beta, and similar proteins; IKK, also termed IkappaB kinase, is an enzyme complex involved in propagating the cellular response to inflammation. It is part of the upstream nuclear factor kappa-B kinase (NF-kappaB) signal transduction cascade, and plays an important role in regulating the NF-kappaB transcription factor. IKK is composed of three subunits, IKK-alpha/CHUK, IKK-beta/IKBKB, and IKK-gamma/NEMO. The IKK-alpha and IKK-beta subunits together are catalytically active whereas the IKK-gamma subunit serves a regulatory function. IKK-alpha and IKK-beta phosphorylate the IkappaB proteins, marking them for degradation via ubiquitination and allowing NF-kappaB transcription factors to go into the nucleus. IKK-alpha, also known as IKK-A, or IkappaB kinase A (IkBKA), or conserved helix-loop-helix ubiquitous kinase (CHUK), or I-kappa-B kinase 1 (IKK1), or nuclear factor NF-kappa-B inhibitor kinase alpha (NFKBIKA), or transcription factor 16 (TCF-16), belongs to the serine/threonine protein kinase family. In addition to NF-kappaB response, it has many additional cellular targets in an NF-kappaB-independent manner. For instance, it plays a role in epidermal differentiation, as well as in the regulation of the cell cycle protein cyclin D1. IKK-beta, also known as IKK-B, or IkappaB kinase B (IkBKB), or I-kappa-B kinase 2 (IKK2), or nuclear factor NF-kappa-B inhibitor kinase beta (NFKBIKB), belongs to the serine/threonine protein kinase family as well. It interacts with many different protein partners and has been implicated in the treatment of many inflammatory diseases and cancers. Both IKK-alpha and IKK-beta contain an N-terminal catalytic domain followed by a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340566  Cd Length: 75  Bit Score: 33.38  E-value: 6.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1981806245   9 QLHCVEVDGHETVATLKHLIALREGISVDDQILT 42
Cdd:cd17046    12 RILSYEVTEDTSLSTLQSWIERDTGIPVEDQELL 45
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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