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Conserved domains on  [gi|747811802|ref|NP_001291271|]
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ubiquilin-4 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ubl_PLICs cd01808
ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein ...
11-83 4.61e-45

ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein.


:

Pssm-ID: 340506 [Multi-domain]  Cd Length: 73  Bit Score: 153.55  E-value: 4.61e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 747811802  11 PPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd01808    1 SIIKVTVKTPKEKEDFEVPEDSSVKEFKEEISKKFKAPVEQLVLIFAGKILKDQDTLSQHGIKDGLTVHLVIK 73
UBA_PLICs cd14399
UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) ...
538-577 6.96e-20

UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the ubiquitin-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the ubiquitin-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UBQLN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is a ubiquitin-like nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and ubiquitin-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal ubiquitin-like (UBL) domain that is responsible for the binding of ubiquitin-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal ubiquitin-associated (UBA) domain that interacts with ubiquitin chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region which is absent in other PLIC proteins and the yeast Dsk2 protein.


:

Pssm-ID: 270582  Cd Length: 40  Bit Score: 82.96  E-value: 6.96e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 747811802 538 RFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLG 577
Cdd:cd14399    1 RYASQLEQLQAMGFVDRQANIQALIATGGNVNAAIERLLG 40
STI1 super family cl17974
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
202-246 9.14e-05

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


The actual alignment was detected with superfamily member pfam17830:

Pssm-ID: 450205  Cd Length: 55  Bit Score: 40.24  E-value: 9.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 747811802  202 NPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQD 246
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLQQIQKNPSSLQQYMQDPR 45
STI1 super family cl17974
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
172-220 1.29e-03

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


The actual alignment was detected with superfamily member pfam17830:

Pssm-ID: 450205  Cd Length: 55  Bit Score: 37.15  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  172 NPEMLSQIMENPLVQDMMSNPDLMRHM--IMANPQMQQLMERNPEISHMLN 220
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLqqIQKNPSSLQQYMQDPRVMTKLG 51
STI1 smart00727
Heat shock chaperonin-binding motif;
373-404 9.79e-03

Heat shock chaperonin-binding motif;


:

Pssm-ID: 128966  Cd Length: 41  Bit Score: 34.17  E-value: 9.79e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 747811802   373 NPQLMQNvISAPYMRSMMQTLAQNPDFAAQMM 404
Cdd:smart00727   1 DPEMALR-LQNPQVQSLLQDMQQNPDMLAQML 31
 
Name Accession Description Interval E-value
Ubl_PLICs cd01808
ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein ...
11-83 4.61e-45

ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein.


Pssm-ID: 340506 [Multi-domain]  Cd Length: 73  Bit Score: 153.55  E-value: 4.61e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 747811802  11 PPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd01808    1 SIIKVTVKTPKEKEDFEVPEDSSVKEFKEEISKKFKAPVEQLVLIFAGKILKDQDTLSQHGIKDGLTVHLVIK 73
UBA_PLICs cd14399
UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) ...
538-577 6.96e-20

UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the ubiquitin-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the ubiquitin-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UBQLN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is a ubiquitin-like nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and ubiquitin-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal ubiquitin-like (UBL) domain that is responsible for the binding of ubiquitin-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal ubiquitin-associated (UBA) domain that interacts with ubiquitin chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region which is absent in other PLIC proteins and the yeast Dsk2 protein.


Pssm-ID: 270582  Cd Length: 40  Bit Score: 82.96  E-value: 6.96e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 747811802 538 RFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLG 577
Cdd:cd14399    1 RYASQLEQLQAMGFVDRQANIQALIATGGNVNAAIERLLG 40
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
15-85 3.49e-15

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: 70.28  E-value: 3.49e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 747811802   15 VTVKTPKDKEEIVICDR-ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKTP 85
Cdd:pfam00240   1 ITVKTLDGKKITLEVDPtDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
13-83 2.33e-14

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: 68.05  E-value: 2.33e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 747811802    13 IRVTVKTPKDKEEIV-ICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:smart00213   1 IELTVKTLDGKTITLeVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
13-119 1.63e-07

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 53.75  E-value: 1.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802   13 IRVTVKT-PKDKEEIVICDRASVKEFKEEISR---RFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVI---KTP 85
Cdd:TIGR00601   1 MTLTFKTlQQQKFKIDMEPDETVKELKEKIEAeqgKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVskpKTG 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 747811802   86 QKAQDPAAATASSPSTPDPASAPSTTPASPATPA 119
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSAAPA 114
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
540-576 8.04e-07

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.


Pssm-ID: 197551 [Multi-domain]  Cd Length: 37  Bit Score: 45.56  E-value: 8.04e-07
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 747811802   540 QQQLEQLNSMGFiNREANLQALIATGGDINAAIERLL 576
Cdd:smart00165   2 EEKIDQLLEMGF-SREEALKALRAANGNVERAAEYLL 37
UBI4 COG5272
Ubiquitin [Posttranslational modification, protein turnover, chaperones];
32-84 2.47e-06

Ubiquitin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 444084 [Multi-domain]  Cd Length: 213  Bit Score: 48.63  E-value: 2.47e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 747811802  32 ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKT 84
Cdd:COG5272   21 DTIEAVKAKIQDKEGIPPDQQRLIFAGKQLEDDRTLADYNIQKESTLHLVTRT 73
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
540-575 7.47e-06

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 42.81  E-value: 7.47e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 747811802  540 QQQLEQLNSMGFiNREANLQALIATGGDINAAIERL 575
Cdd:pfam00627   3 EEAIQRLVEMGF-DREQVREALRATGNNVERAAEYL 37
STI1 pfam17830
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
202-246 9.14e-05

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


Pssm-ID: 436075  Cd Length: 55  Bit Score: 40.24  E-value: 9.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 747811802  202 NPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQD 246
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLQQIQKNPSSLQQYMQDPR 45
STI1 pfam17830
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
172-220 1.29e-03

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


Pssm-ID: 436075  Cd Length: 55  Bit Score: 37.15  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  172 NPEMLSQIMENPLVQDMMSNPDLMRHM--IMANPQMQQLMERNPEISHMLN 220
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLqqIQKNPSSLQQYMQDPRVMTKLG 51
STI1 smart00727
Heat shock chaperonin-binding motif;
172-209 2.54e-03

Heat shock chaperonin-binding motif;


Pssm-ID: 128966  Cd Length: 41  Bit Score: 35.71  E-value: 2.54e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 747811802   172 NPEMlSQIMENPLV----QDMMSNPDLMRHMIMANPQMQQLM 209
Cdd:smart00727   1 DPEM-ALRLQNPQVqsllQDMQQNPDMLAQMLQENPQLLQLI 41
PTZ00044 PTZ00044
ubiquitin; Provisional
33-83 3.56e-03

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 36.73  E-value: 3.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  33 SVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:PTZ00044  22 TVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQ 72
STI1 smart00727
Heat shock chaperonin-binding motif;
373-404 9.79e-03

Heat shock chaperonin-binding motif;


Pssm-ID: 128966  Cd Length: 41  Bit Score: 34.17  E-value: 9.79e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 747811802   373 NPQLMQNvISAPYMRSMMQTLAQNPDFAAQMM 404
Cdd:smart00727   1 DPEMALR-LQNPQVQSLLQDMQQNPDMLAQML 31
 
Name Accession Description Interval E-value
Ubl_PLICs cd01808
ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein ...
11-83 4.61e-45

ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein.


Pssm-ID: 340506 [Multi-domain]  Cd Length: 73  Bit Score: 153.55  E-value: 4.61e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 747811802  11 PPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd01808    1 SIIKVTVKTPKEKEDFEVPEDSSVKEFKEEISKKFKAPVEQLVLIFAGKILKDQDTLSQHGIKDGLTVHLVIK 73
UBA_PLICs cd14399
UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) ...
538-577 6.96e-20

UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the ubiquitin-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the ubiquitin-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UBQLN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is a ubiquitin-like nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and ubiquitin-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal ubiquitin-like (UBL) domain that is responsible for the binding of ubiquitin-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal ubiquitin-associated (UBA) domain that interacts with ubiquitin chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region which is absent in other PLIC proteins and the yeast Dsk2 protein.


Pssm-ID: 270582  Cd Length: 40  Bit Score: 82.96  E-value: 6.96e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 747811802 538 RFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLLG 577
Cdd:cd14399    1 RYASQLEQLQAMGFVDRQANIQALIATGGNVNAAIERLLG 40
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
13-81 1.06e-17

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: 77.68  E-value: 1.06e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802  13 IRVTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLV 81
Cdd:cd16106    1 IKVTVKCSNGKKfTVEVEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKIQDGHTVHLV 70
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
15-85 3.49e-15

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: 70.28  E-value: 3.49e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 747811802   15 VTVKTPKDKEEIVICDR-ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKTP 85
Cdd:pfam00240   1 ITVKTLDGKKITLEVDPtDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
15-81 3.63e-15

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: 70.32  E-value: 3.63e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 747811802  15 VTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLV 81
Cdd:cd17039    1 ITVKTLDGKTyTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
13-83 2.33e-14

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: 68.05  E-value: 2.33e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 747811802    13 IRVTVKTPKDKEEIV-ICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:smart00213   1 IELTVKTLDGKTITLeVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
UBA_PLCs_like cd14323
UBA domain of eukaryotic protein linking integrin-associated protein with cytoskeleton (PLIC) ...
538-576 4.95e-14

UBA domain of eukaryotic protein linking integrin-associated protein with cytoskeleton (PLIC) proteins, Saccharomyces cerevisiae proteins Dsk2p and Gts1p, and similar proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. Saccharomyces 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. Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture.


Pssm-ID: 270508  Cd Length: 39  Bit Score: 66.27  E-value: 4.95e-14
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 747811802 538 RFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLL 576
Cdd:cd14323    1 RYQQQLATLKEMGFNDTEKNLQALSATGGNINLAIERLF 39
UBA_Dsk2p_like cd14324
UBA domain of Saccharomyces cerevisiae proteasome interacting protein Dsk2p and its homologs ...
535-576 2.83e-10

UBA domain of Saccharomyces cerevisiae proteasome interacting protein Dsk2p and its homologs found in fungi; The family contains several fungal multi-ubiquitin 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 ubiquitin-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 a ubiquitin 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 ubiquitin chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 270509  Cd Length: 42  Bit Score: 55.54  E-value: 2.83e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 747811802 535 PEVRFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLL 576
Cdd:cd14324    1 PEERYEEQLRQLNEMGFFDFDRNVRALRRSGGSVQGAVESLL 42
UBA_Gts1p_like cd14400
UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins; Gts1p, ...
538-576 6.31e-10

UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins; Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture. Gts1p contains an N-terminal zinc finger motif similar to that of GATA-transcription factors, a ubiquitin-associated (UBA) domain and a C-terminal glutamine-rich strand. The zinc finger is responsible for the binding to the glycolytic enzyme glyceraldehydes-3-phosphate dehydrogenase (GAPDH) which is required for the maintenance of the metabolic oscillations of budding yeast. The polyglutamine sequence is indispensable for the pleiotropy and nuclear localization of Gts1p. It is essential for the transcriptional activation, whereas Gts1p lacks DNA binding activity.


Pssm-ID: 270583  Cd Length: 39  Bit Score: 54.56  E-value: 6.31e-10
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 747811802 538 RFQQQLEQLNSMGFINREANLQALIATGGDINAAIERLL 576
Cdd:cd14400    1 KYSRQLRFLKEMGFTNEDNNLEALSQANGNINRAIDILL 39
Ubl_BAG6 cd01809
ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; ...
13-81 1.81e-08

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.


Pssm-ID: 340507 [Multi-domain]  Cd Length: 71  Bit Score: 51.19  E-value: 1.81e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802  13 IRVTVKTPKDK-EEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIkDGLTVHLV 81
Cdd:cd01809    1 LEVTVKTLDSQnRTFTVPEEITVKEFKEHIASSVNIPAEKQRLIFQGRVLQDDKKLKEYDV-DGKVIHLV 69
Ubl_UBL4A_like cd01807
ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, ...
15-83 2.02e-08

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.


Pssm-ID: 340505 [Multi-domain]  Cd Length: 72  Bit Score: 51.21  E-value: 2.02e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802  15 VTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd01807    3 ITVKILQGKEcTIEVSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLVVK 72
Ubl_Rad23 cd01805
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ...
14-78 7.99e-08

ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins.


Pssm-ID: 340503 [Multi-domain]  Cd Length: 72  Bit Score: 49.48  E-value: 7.99e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 747811802  14 RVTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQ-DQLVLIFAGKILKDGDTLNQHGIKDGLTV 78
Cdd:cd01805    2 KITFKTLQQQTfEIEVEPSDTVLELKEKIEQEQGDFPaSGQKLIYSGKVLKDDKTLSEYNIKEKDFV 68
Ubl_NUB1 cd17062
ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, ...
32-84 1.31e-07

ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also termed negative regulator of ubiquitin-like proteins 1, or renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1), which may function in the regulation of cell cycle progression. NUB1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif.


Pssm-ID: 340582  Cd Length: 78  Bit Score: 49.06  E-value: 1.31e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 747811802  32 ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVhLVIKT 84
Cdd:cd17062   27 ITGSELREKIAEELGVPEDRIKLISNGKVLKDEKTLAEQGVKNNSQV-MVLVL 78
UBA_UBL7 cd14326
UBA domain found in ubiquitin-like protein 7 (UBL7) and similar proteins; UBL7, also called ...
539-576 1.61e-07

UBA domain found in ubiquitin-like protein 7 (UBL7) and similar proteins; UBL7, also called bone marrow stromal cell ubiquitin-like protein (BMSC-UbP), or ubiquitin-like protein SB132, is a novel ubiquitin-like protein that may play roles in regulation of bone marrow stromal cell (BMSC) function or cell differentiation via an evocator-associated and cell-specific pattern. UBL7 contains an N-terminal ubiquitin domain (UBQ) and a C-terminal ubiquitin-associated (UBA) domain. UBQ domain interacts with 26S proteasome-dependent degradation, and UBA domain links cellular processes and the ubiquitin system.


Pssm-ID: 270511  Cd Length: 38  Bit Score: 47.71  E-value: 1.61e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 747811802 539 FQQQLEQLNSMGFINREANLQALIATGGDINAAIERLL 576
Cdd:cd14326    1 LQSQLQQLREMGITDDSLSLRALQATGGDVQAALNLLF 38
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
13-119 1.63e-07

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 53.75  E-value: 1.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802   13 IRVTVKT-PKDKEEIVICDRASVKEFKEEISR---RFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVI---KTP 85
Cdd:TIGR00601   1 MTLTFKTlQQQKFKIDMEPDETVKELKEKIEAeqgKDAYPVAQQKLIYSGKILSDDKTVKEYKIKEKDFVVVMVskpKTG 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 747811802   86 QKAQDPAAATASSPSTPDPASAPSTTPASPATPA 119
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSAAPA 114
Ubl_TMUB1_like cd17057
ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing ...
13-82 5.42e-07

ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins; TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1.


Pssm-ID: 340577  Cd Length: 74  Bit Score: 47.22  E-value: 5.42e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 747811802  13 IRVTVKTPKDKEEIVICDRAS-VKEFKeeiSRRFKA--QQDQLV-LIFAGKILKD-GDTLNQHGIKDGLTVHLVI 82
Cdd:cd17057    2 ITIRLKFLNETERVVYARPEDtVGDFK---RRHFPDelAQGKRVrLIYQGQLLRDdSRTLSSYGIQDGSVIHCHI 73
Ubiquitin_like_fold cd00196
Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various ...
15-81 6.95e-07

Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises 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 proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily.


Pssm-ID: 340450  Cd Length: 68  Bit Score: 46.93  E-value: 6.95e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 747811802  15 VTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLV 81
Cdd:cd00196    1 VKVETPSLKKiVVAVPPSTTLRQVLEKVAKRIGLPPDVIRLLFNGQVLDDLMTAKQVGLEPGEELHFV 68
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
540-576 8.04e-07

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.


Pssm-ID: 197551 [Multi-domain]  Cd Length: 37  Bit Score: 45.56  E-value: 8.04e-07
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 747811802   540 QQQLEQLNSMGFiNREANLQALIATGGDINAAIERLL 576
Cdd:smart00165   2 EEKIDQLLEMGF-SREEALKALRAANGNVERAAEYLL 37
UBI4 COG5272
Ubiquitin [Posttranslational modification, protein turnover, chaperones];
32-84 2.47e-06

Ubiquitin [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 444084 [Multi-domain]  Cd Length: 213  Bit Score: 48.63  E-value: 2.47e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 747811802  32 ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKT 84
Cdd:COG5272   21 DTIEAVKAKIQDKEGIPPDQQRLIFAGKQLEDDRTLADYNIQKESTLHLVTRT 73
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
540-575 7.47e-06

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 42.81  E-value: 7.47e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 747811802  540 QQQLEQLNSMGFiNREANLQALIATGGDINAAIERL 575
Cdd:pfam00627   3 EEAIQRLVEMGF-DREQVREALRATGNNVERAAEYL 37
UBA cd14270
UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ...
543-573 8.43e-06

UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains.


Pssm-ID: 270456 [Multi-domain]  Cd Length: 30  Bit Score: 42.72  E-value: 8.43e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 747811802 543 LEQLNSMGFiNREANLQALIATGGDINAAIE 573
Cdd:cd14270    1 LAQLVEMGF-SREQARRALRATNGDVEAAVE 30
Ubl_midnolin cd01804
ubiquitin-like (Ubl) domain found in midnolin and similar proteins; Midnolin, also termed ...
32-81 1.51e-05

ubiquitin-like (Ubl) domain found in midnolin and similar proteins; Midnolin, also termed midbrain nucleolar protein, is a nucleolar protein that may be involved in regulation of genes related to neurogenesis in the nucleolus. It is strongly expressed at the mesencephalon (midbrain) of the embryo in day 12.5 (E12.5) mice and its expression is developmentally regulated. Midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells. It can also control development via regulation of mRNA transport in cells. Midnolin contains an N-terminal conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340502  Cd Length: 70  Bit Score: 43.02  E-value: 1.51e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 747811802  32 ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGdTLNQHGIKDGLTVHLV 81
Cdd:cd01804   21 ETVEGLKRRISKKLKVPKERITLLHKEKQLKDG-TLRENGIGDGSKLTLL 69
UBA_NBR1 cd14319
UBA domain of next to BRCA1 gene 1 protein (NBR1) and similar proteins; NBR1, also called cell ...
542-576 2.33e-05

UBA domain of next to BRCA1 gene 1 protein (NBR1) and similar proteins; NBR1, also called cell migration-inducing gene 19 protein, membrane component chromosome 17 surface marker 2, neighbor of BRCA1 gene 1 protein, or protein 1A1-3B, is a scaffold protein that may be involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Moreover, NBR1 functions as an autophagic receptor for ubiquitinated cargo. It interacts with ATG8-family proteins for its degradation by autophagy. NBR1 contains an N-terminal Phox and Bem1p (PB1) domain that plays a critical role in mediating protein-protein interactions with both titin kinase and with another scaffold protein, p62. NBR1 also has a LC3-interaction region (LIR) and a ubiquitin-associated (UBA) domain. The LIR is required for the autophagic clearance of NBR1. UBA domain is responsible for the ubiquitin binding which is necessary for the puromycin-induced formation of ubiquitinated protein aggregates.


Pssm-ID: 270504  Cd Length: 39  Bit Score: 41.65  E-value: 2.33e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 747811802 542 QLEQLNSMGFINREANLQALIATGGDINAAIERLL 576
Cdd:cd14319    5 ELEQLFEMGFTDRDLNQELLKKHNGDLDRVVDELL 39
Ubl_parkin cd01798
ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed ...
32-87 4.00e-05

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: 41.90  E-value: 4.00e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 747811802  32 ASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKTPQK 87
Cdd:cd01798   19 WSILQLKEVVAKRQGVPPDQLRIIFAGKELSDDLTLQNCDLGQQSIVHAVQGPKRK 74
STI1 pfam17830
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
202-246 9.14e-05

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


Pssm-ID: 436075  Cd Length: 55  Bit Score: 40.24  E-value: 9.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 747811802  202 NPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQD 246
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLQQIQKNPSSLQQYMQDPR 45
Ubl2_ISG15 cd01810
ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar ...
33-80 1.03e-04

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: 40.90  E-value: 1.03e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 747811802  33 SVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHL 80
Cdd:cd01810   22 TVDQLKQKVSGREGVHDDQFWLTFEGRPLEDQLPLGEYGLKPQSTIHM 69
Ubl_ubiquitin cd01803
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ...
33-83 1.19e-04

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.


Pssm-ID: 340501 [Multi-domain]  Cd Length: 76  Bit Score: 40.51  E-value: 1.19e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  33 SVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd01803   22 TIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
Ubl_HERP cd01790
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ...
13-81 1.54e-04

ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP; HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively.


Pssm-ID: 340488  Cd Length: 78  Bit Score: 40.31  E-value: 1.54e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 747811802  13 IRVTVKTPKDKEE--IVICDR-ASVKEFKEEISRRF--KAQQDQLVLIFAGKILKDGDTLNQ----HGIKDGLTVHLV 81
Cdd:cd01790    1 VTLVVKSPNQRIQdlTVNCTLgWTVLKLKEHLSEVYpsKPLPEDQKLIYSGKLLEDHQTLKDvlreDDPEQVHTVHLV 78
UBA1_NUB1_like cd14291
UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called ...
541-573 2.18e-04

UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain.


Pssm-ID: 270477 [Multi-domain]  Cd Length: 36  Bit Score: 38.58  E-value: 2.18e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 747811802 541 QQLEQLNSMGFINREANLqALIATGGDINAAIE 573
Cdd:cd14291    3 DKLQQLMEMGFSEAEARL-ALRACNGNVERAVD 34
Rad60-SLD pfam11976
Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl ...
13-82 3.25e-04

Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).


Pssm-ID: 403255 [Multi-domain]  Cd Length: 72  Bit Score: 39.47  E-value: 3.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 747811802   13 IRVTVKTPKDKE-EIVICDRASVKEFKEE-ISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVI 82
Cdd:pfam11976   1 IKIILKGKDGKEvFIKVKPTTTVSKLINAyRKKRGIPPSQQVRLIFDGERLDPNSTVEDLDIEDGDTIDVVI 72
Ubl_SUMO_like cd01763
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar ...
12-75 6.83e-04

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins, and the mechanism of ligation. 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 Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4, which all regulate different cellular functions by conjugating to different proteins. SUMO2-4 are more closely related to each other than to SUMO1.


Pssm-ID: 340462 [Multi-domain]  Cd Length: 72  Bit Score: 38.33  E-value: 6.83e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 747811802  12 PIRVTVKTPKDKEEIV--ICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDG 75
Cdd:cd01763    1 KITIKVRGQDGGKKVRfkVKKTTKLKKLFDAYAEKKGLDPDSLRFTFDGERISPNDTPESLGLEDG 66
YukD pfam08817
WXG100 protein secretion system (Wss), protein YukD; The YukD protein family members ...
13-80 7.15e-04

WXG100 protein secretion system (Wss), protein YukD; The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (pfam06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway.


Pssm-ID: 430235  Cd Length: 77  Bit Score: 38.35  E-value: 7.15e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 747811802   13 IRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQD-------QLVLIFAGKI-LKDGDTLNQHGIKDGLTVHL 80
Cdd:pfam08817   2 VRVTVLAPNRRVDLALPADVPVAELLPELLRLLGLPLTdpggapgGWVLARLGGRpLDGDRTLADAGVRDGDVLVL 77
UBA_II_E2_UBC27_like cd14312
UBA domain found in plant ubiquitin-conjugating enzyme E2 27 and similar proteins; UBC27, also ...
540-576 1.23e-03

UBA domain found in plant ubiquitin-conjugating enzyme E2 27 and similar proteins; UBC27, also called ubiquitin carrier protein 27, functions as a class II ubiquitin-conjugating (UBC) enzyme (E2). E2, together with E1 (ubiquitin-activating enzyme UBA) and E3 (ubiquitin ligase), is required in the multi-step reaction of ubiquitin conjugation. Unlike other Arabidopsis UBCs, in addition to an N-terminal ubiquitin-conjugating enzyme E2 catalytic domain (UBCc), UBC27 has an additional C-terminal ubiquitin-associated domain (UBA).


Pssm-ID: 270497  Cd Length: 36  Bit Score: 36.55  E-value: 1.23e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 747811802 540 QQQLEQLNSMGFiNREANLQALIATGGDINAAIERLL 576
Cdd:cd14312    1 EEKVQRLVEMGF-PRDQAVVALESAGGDENAALEKLL 36
STI1 pfam17830
STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 ...
172-220 1.29e-03

STI1 domain; This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein.


Pssm-ID: 436075  Cd Length: 55  Bit Score: 37.15  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  172 NPEMLSQIMENPLVQDMMSNPDLMRHM--IMANPQMQQLMERNPEISHMLN 220
Cdd:pfam17830   1 DPELLAKLAANPETRALLSDPEFVAKLqqIQKNPSSLQQYMQDPRVMTKLG 51
UBA_UBAC2 cd14305
UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar ...
542-576 1.37e-03

UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins; UBAC2, also called phosphoglycerate dehydrogenase-like protein 1, is a ubiquitin-associated domain (UBA)-domain containing protein encoded by gene UBAC2 (or PHGDHL1), a risk gene for Behcet's disease (BD). It may play an important role in the development of BD through its transcriptional modulation. Members in this family contain an N-terminal rhomboid-like domain and a C-terminal UBA domain.


Pssm-ID: 270490  Cd Length: 38  Bit Score: 36.55  E-value: 1.37e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 747811802 542 QLEQLNSMGFiNREANLQALIATGGDINAAIERLL 576
Cdd:cd14305    5 QVQQLVDMGF-SREDVLEALRQSNNDVNAATNLLL 38
Ubl_NEDD8 cd01806
ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally ...
15-82 1.49e-03

ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins; NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 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. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340504 [Multi-domain]  Cd Length: 74  Bit Score: 37.37  E-value: 1.49e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 747811802  15 VTVKTPKDKE-EIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVI 82
Cdd:cd01806    1 IKVKTLTGKEiEIDIEPTDKVERIKERVEEKEGIPPQQQRLIFSGKQMNDEKTAADYKIEGGSVLHLVL 69
Ubl_IQUB cd17061
ubiquitin-like (Ubl) domain found in IQ and ubiquitin-like domain-containing protein (IQUB) ...
15-80 1.96e-03

ubiquitin-like (Ubl) domain found in IQ and ubiquitin-like domain-containing protein (IQUB) and similar proteins; IQUB is an IQ motif and ubiquitin domain-containing protein that may play roles in cilia formation and/or maintenance. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340581  Cd Length: 79  Bit Score: 37.24  E-value: 1.96e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802  15 VTVKT--PKDKEEIVIC--DRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHL 80
Cdd:cd17061    3 ATVKFvlMPSGQVITLAftLGQTIGELKEHFSSELKIPPDVLQIMFDGKLVEDNTTLVDLGVRPNGTIQL 72
STI1 smart00727
Heat shock chaperonin-binding motif;
172-209 2.54e-03

Heat shock chaperonin-binding motif;


Pssm-ID: 128966  Cd Length: 41  Bit Score: 35.71  E-value: 2.54e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 747811802   172 NPEMlSQIMENPLV----QDMMSNPDLMRHMIMANPQMQQLM 209
Cdd:smart00727   1 DPEM-ALRLQNPQVqsllQDMQQNPDMLAQMLQENPQLLQLI 41
Ubl2_OASL cd16103
ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and ...
13-80 2.95e-03

ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and similar proteins; OASL, also termed 2'-5'-OAS-related protein (2'-5'-OAS-RP), or 59 kDa 2'-5'-oligoadenylate synthase-like protein, or thyroid receptor-interacting protein 14, or TR-interacting protein 14 (TRIP-14), or p59 OASL (p59OASL), is an interferon (IFN)-induced antiviral protein that plays an important role in the IFNs-mediated antiviral signaling pathway. It inhibits respiratory syncytial virus replication and is targeted by the viral nonstructural protein 1 (NS1). It also displays antiviral activity against encephalomyocarditis virus (EMCV) and hepatitis C virus (HCV) via an alternative antiviral pathway independent of RNase L. Moreover, OASL does not have 2'-5'-OAS activity, but can bind double-stranded RNA (dsRNA) to enhance RIG-I signaling. OASL belongs to the 2'-5' oligoadenylate synthase (OAS) family. While each member of this family has a conserved N-terminal OAS catalytic domain, only OASL has two tandem C-terminal ubiquitin-like (Ubl) repeats, which are required for its antiviral activity. This family corresponds to the second Ubl domain.


Pssm-ID: 340520 [Multi-domain]  Cd Length: 72  Bit Score: 36.50  E-value: 2.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 747811802  13 IRVTVKTPKDKEEIV-ICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHL 80
Cdd:cd16103    2 IQIFVKFPDGTSKPYaINPEDTILDLKEKIEEQGGPPVEDQILLFQGQELRDKKSLKYYGIKDGDTLQL 70
PTZ00044 PTZ00044
ubiquitin; Provisional
33-83 3.56e-03

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 36.73  E-value: 3.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 747811802  33 SVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:PTZ00044  22 TVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVLQ 72
Ubl1_FAT10 cd17052
ubiquitin-like (Ubl) domain 1 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
33-83 5.04e-03

ubiquitin-like (Ubl) domain 1 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 first Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340572 [Multi-domain]  Cd Length: 74  Bit Score: 36.09  E-value: 5.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 747811802  33 SVKEFKEEISRRFKAQ-QDQlVLIFAGKILKDGDTLNQHGIKDGLTVHLVIK 83
Cdd:cd17052   21 SVKKINEHVRSKTKVPvQDQ-VLLLGSKILKPRRRLSSYGIDKEKTIHLTLK 71
Ubl_SNRNP25 cd17058
ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 ...
13-81 5.31e-03

ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 (SNRNP25) and similar proteins; SNRNP25, also termed U11/U12 small nuclear ribonucleoprotein 25 kDa protein, U11/U12 snRNP 25 kDa protein (U11/U12-25K), or minus-99 protein, is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340578  Cd Length: 89  Bit Score: 36.34  E-value: 5.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 747811802  13 IRVTV-KTPKDKEEIVICDRASVKEFKEEISRRF--KAQQDQLV-------------LIFAGKILKDGDT-LNQHGIKDG 75
Cdd:cd17058    2 ITLSVlRLDGESLPVVVPQNATVLDLKKAIERYFtlKLKREGGTkkiswkyvwktycLCFDGQKLTDDKAkLKDYGIRNG 81

                 ....*.
gi 747811802  76 LTVHLV 81
Cdd:cd17058   82 DELTFV 87
STI1 smart00727
Heat shock chaperonin-binding motif;
373-404 9.79e-03

Heat shock chaperonin-binding motif;


Pssm-ID: 128966  Cd Length: 41  Bit Score: 34.17  E-value: 9.79e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 747811802   373 NPQLMQNvISAPYMRSMMQTLAQNPDFAAQMM 404
Cdd:smart00727   1 DPEMALR-LQNPQVQSLLQDMQQNPDMLAQML 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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