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Conserved domains on  [gi|2497106|sp|Q04228|]
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RecName: Full=UBX domain-containing protein 2; AltName: Full=Secretion lowering protein 1

Protein Classification

UBA and UBX domain-containing protein( domain architecture ID 13862202)

UBA (ubiquitin-associated) and UBX domain-containing protein belongs to the ubiquitin family, a diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes; similar to Saccharomyces cerevisiae UBX domain-containing protein 2 (Ubx2p/Sel1p), an integral endoplasmic reticulum membrane protein that coordinates the assembly of the ER-associated protein degradation (ERAD) machinery at the ER membrane

Gene Ontology:  GO:0016567|GO:0043130
PubMed:  22201813|17495234|8871400

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 431-570 1.46e-11

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 smart00166:

Pssm-ID: 475130 [Multi-domain]  Cd Length: 77  Bit Score: 60.39  E-value: 1.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2497106     431 QATLQFRTSSGKRFVKKFPSMTTLYQIYQSIgchIYLAVYSSDPaewsnalqdkirqlsadddmlcfkegqletatatti 510
Cdd:smart00166   1 VCRLQIRLPDGSRLVRRFPSSDTLRTVYEFV---SAALGDGNDP------------------------------------ 41

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2497106     511 eelghiinneltsfdlergklefdFELVSPFPKYTVHPNE-HMSVDQVpQLWPNGSLLVEA 570
Cdd:smart00166  42 ------------------------FTLNSPFPRRTFTKDDySKKLLEL-ALLPSSTLVLEP 77
UBA_4 pfam14555
UBA-like domain;
18-58 9.26e-06

UBA-like domain;


:

Pssm-ID: 464207  Cd Length: 43  Bit Score: 42.82  E-value: 9.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2497106     18 EDKLNEFQVITNFPPEDlpdVVRLLRNHGWQLEPALSRYFD 58
Cdd:pfam14555   1 DELIAQFQAITGADEEV---ARQYLEAHNWDLEAAVNAFFD 38
 
Name Accession Description Interval E-value
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
 431-570 1.46e-11

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 60.39  E-value: 1.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2497106     431 QATLQFRTSSGKRFVKKFPSMTTLYQIYQSIgchIYLAVYSSDPaewsnalqdkirqlsadddmlcfkegqletatatti 510
Cdd:smart00166   1 VCRLQIRLPDGSRLVRRFPSSDTLRTVYEFV---SAALGDGNDP------------------------------------ 41

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2497106     511 eelghiinneltsfdlergklefdFELVSPFPKYTVHPNE-HMSVDQVpQLWPNGSLLVEA 570
Cdd:smart00166  42 ------------------------FTLNSPFPRRTFTKDDySKKLLEL-ALLPSSTLVLEP 77
UBA_4 pfam14555
UBA-like domain;
18-58 9.26e-06

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 42.82  E-value: 9.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2497106     18 EDKLNEFQVITNFPPEDlpdVVRLLRNHGWQLEPALSRYFD 58
Cdd:pfam14555   1 DELIAQFQAITGADEEV---ARQYLEAHNWDLEAAVNAFFD 38
UBA_TAP-C_like cd14273
UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; ...
 24-57 3.49e-03

UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. 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. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity.


Pssm-ID: 270459  Cd Length: 31  Bit Score: 35.07  E-value: 3.49e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 2497106   24 FQVITNFPPEDlpdVVRLLRNHGWQLEPALSRYF 57
Cdd:cd14273   1 FMEITGADPET---ARQYLESNNWDLEAAINLYF 31
 
Name Accession Description Interval E-value
UBX smart00166
Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.
 431-570 1.46e-11

Domain present in ubiquitin-regulatory proteins; Present in FAF1 and Shp1p.


Pssm-ID: 197552 [Multi-domain]  Cd Length: 77  Bit Score: 60.39  E-value: 1.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2497106     431 QATLQFRTSSGKRFVKKFPSMTTLYQIYQSIgchIYLAVYSSDPaewsnalqdkirqlsadddmlcfkegqletatatti 510
Cdd:smart00166   1 VCRLQIRLPDGSRLVRRFPSSDTLRTVYEFV---SAALGDGNDP------------------------------------ 41

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2497106     511 eelghiinneltsfdlergklefdFELVSPFPKYTVHPNE-HMSVDQVpQLWPNGSLLVEA 570
Cdd:smart00166  42 ------------------------FTLNSPFPRRTFTKDDySKKLLEL-ALLPSSTLVLEP 77
UBA_4 pfam14555
UBA-like domain;
18-58 9.26e-06

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 42.82  E-value: 9.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2497106     18 EDKLNEFQVITNFPPEDlpdVVRLLRNHGWQLEPALSRYFD 58
Cdd:pfam14555   1 DELIAQFQAITGADEEV---ARQYLEAHNWDLEAAVNAFFD 38
UBA_TAP-C_like cd14273
UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; ...
 24-57 3.49e-03

UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. 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. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity.


Pssm-ID: 270459  Cd Length: 31  Bit Score: 35.07  E-value: 3.49e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 2497106   24 FQVITNFPPEDlpdVVRLLRNHGWQLEPALSRYF 57
Cdd:cd14273   1 FMEITGADPET---ARQYLESNNWDLEAAINLYF 31
 
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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