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Conserved domains on  [gi|1950227485|gb|KAG0578858|]
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hypothetical protein KC19_4G054900 [Ceratodon purpureus]

Protein Classification

Ubl5/Hub1 family ubiquitin-like protein( domain architecture ID 10110356)

Ubl5/Hub1 family ubiquitin-like protein similar to Saccharomyces cerevisiae Hub1 that plays a role in splice-site usage and alternative splicing

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl_UBL5 cd01791
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; ...
 85-155 1.53e-54

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; UBL5, known as Hub1 in yeast, is an atypical ubiquitin-like (Ubl) post-translational modifier that contains a conserved Ubl domain with a beta-grasp Ubl fold. At the C-terminal end of its Ubl fold is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other Ubl modifiers, and thus UBL5 does not form covalent conjugates with cellular proteins. The yeast Hub1p binds non-covalently to the HIND element of spliceosomal protein Snu66p (Snu66p is termed SART1 in mammals) and modifies the spliceosome by this unconventional Ubl modifier. In higher eukaryotes, UBL5/Hub1 plays a role in modulating pre-mRNA splicing. It also is required for signaling in the mitochondrial unfolded protein response, through interaction with the transcription factor DVE-1 and upregulation of chaperone genes in response to mitochondrial stress. Moreover, UBL5 functions as a factor that directly binds to and stabilizes FANCI, and promotes the functionality of the Fanconi anemia (FA) DNA repair pathway.


:

Pssm-ID: 340489  Cd Length: 71  Bit Score: 165.95  E-value: 1.53e-54
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1950227485  85 MIEVVLNDRLGKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIQKWYTIYKDHITLADYEIHDGMGLELY 155
Cdd:cd01791     1 MIEVICNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLEDYEIHDGMNLELY 71
 
Name Accession Description Interval E-value
Ubl_UBL5 cd01791
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; ...
 85-155 1.53e-54

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; UBL5, known as Hub1 in yeast, is an atypical ubiquitin-like (Ubl) post-translational modifier that contains a conserved Ubl domain with a beta-grasp Ubl fold. At the C-terminal end of its Ubl fold is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other Ubl modifiers, and thus UBL5 does not form covalent conjugates with cellular proteins. The yeast Hub1p binds non-covalently to the HIND element of spliceosomal protein Snu66p (Snu66p is termed SART1 in mammals) and modifies the spliceosome by this unconventional Ubl modifier. In higher eukaryotes, UBL5/Hub1 plays a role in modulating pre-mRNA splicing. It also is required for signaling in the mitochondrial unfolded protein response, through interaction with the transcription factor DVE-1 and upregulation of chaperone genes in response to mitochondrial stress. Moreover, UBL5 functions as a factor that directly binds to and stabilizes FANCI, and promotes the functionality of the Fanconi anemia (FA) DNA repair pathway.


Pssm-ID: 340489  Cd Length: 71  Bit Score: 165.95  E-value: 1.53e-54
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1950227485  85 MIEVVLNDRLGKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIQKWYTIYKDHITLADYEIHDGMGLELY 155
Cdd:cd01791     1 MIEVICNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLEDYEIHDGMNLELY 71
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 95-155 1.03e-07

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: 46.40  E-value: 1.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485  95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIqkwytIYK-----DHITLADYEIHDGMGLELY 155
Cdd:pfam00240   8 GKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRL-----IYSgkvleDDQTLGEYGIEDGSTIHLV 68
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 95-155 4.54e-05

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: 39.55  E-value: 4.54e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485   95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIqkwytIY-----KDHITLADYEIHDGMGLELY 155
Cdd:smart00213  10 GKTITLEVKPSDTVSELKEKIAELTGIPPEQQRL-----IYkgkvlEDDRTLADYGIQDGSTIHLV 70
 
Name Accession Description Interval E-value
Ubl_UBL5 cd01791
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; ...
 85-155 1.53e-54

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins; UBL5, known as Hub1 in yeast, is an atypical ubiquitin-like (Ubl) post-translational modifier that contains a conserved Ubl domain with a beta-grasp Ubl fold. At the C-terminal end of its Ubl fold is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other Ubl modifiers, and thus UBL5 does not form covalent conjugates with cellular proteins. The yeast Hub1p binds non-covalently to the HIND element of spliceosomal protein Snu66p (Snu66p is termed SART1 in mammals) and modifies the spliceosome by this unconventional Ubl modifier. In higher eukaryotes, UBL5/Hub1 plays a role in modulating pre-mRNA splicing. It also is required for signaling in the mitochondrial unfolded protein response, through interaction with the transcription factor DVE-1 and upregulation of chaperone genes in response to mitochondrial stress. Moreover, UBL5 functions as a factor that directly binds to and stabilizes FANCI, and promotes the functionality of the Fanconi anemia (FA) DNA repair pathway.


Pssm-ID: 340489  Cd Length: 71  Bit Score: 165.95  E-value: 1.53e-54
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1950227485  85 MIEVVLNDRLGKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIQKWYTIYKDHITLADYEIHDGMGLELY 155
Cdd:cd01791     1 MIEVICNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKWYTIFKDHITLEDYEIHDGMNLELY 71
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 88-149 1.29e-09

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: 51.44  E-value: 1.29e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1950227485  88 VVLNDRLGKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIQKWYTIYKDHITLADYEIHDG 149
Cdd:cd17039     1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDG 62
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 95-155 1.03e-07

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: 46.40  E-value: 1.03e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485  95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIqkwytIYK-----DHITLADYEIHDGMGLELY 155
Cdd:pfam00240   8 GKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRL-----IYSgkvleDDQTLGEYGIEDGSTIHLV 68
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
 97-149 3.21e-07

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: 45.32  E-value: 3.21e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1950227485  97 KVRVKCNQDD----------TIGDLKKLVAAQTGTRPEKIRIqkwytIYKDHI-----TLADYEIHDG 149
Cdd:cd16106     2 KVTVKCSNGKkftvevepdaTVLELKELIAEKSDIPAEQQRL-----IYKGKIlkdeeTLSSYKIQDG 64
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 95-155 4.54e-05

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: 39.55  E-value: 4.54e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485   95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIqkwytIY-----KDHITLADYEIHDGMGLELY 155
Cdd:smart00213  10 GKTITLEVKPSDTVSELKEKIAELTGIPPEQQRL-----IYkgkvlEDDRTLADYGIQDGSTIHLV 70
Ubl_SF3a120 cd01800
ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar ...
 106-154 1.86e-04

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


Pssm-ID: 340498  Cd Length: 84  Bit Score: 38.32  E-value: 1.86e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1950227485 106 DTIGDLKKLVAAQTGTRPEKIRIQ-KWYTIYKDHITLADYEIHDGMGLEL 154
Cdd:cd01800    32 DTISVLKEKIHEELGMPANKQKLQvEGGGFLKDSNSLAFYNLGSGTVLTL 81
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
 95-149 4.20e-04

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


Pssm-ID: 340573  Cd Length: 71  Bit Score: 36.94  E-value: 4.20e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485  95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKIRIQ-KWYTIYKDHITLADYEIHDG 149
Cdd:cd17053    10 GTVHTLQVSRSTTVAQVKAMIEDQSGVPPNEQILVyNGKRLEDGDKTLGEYGIKTG 65
Ubl2_OASL cd16103
ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and ...
 103-154 1.40e-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: 35.73  E-value: 1.40e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1950227485 103 NQDDTIGDLKKLVAAQTGTRPEK--IRIQKwyTIYKDHITLADYEIHDGMGLEL 154
Cdd:cd16103    19 NPEDTILDLKEKIEEQGGPPVEDqiLLFQG--QELRDKKSLKYYGIKDGDTLQL 70
Ubl_UBLCP1 cd01813
ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 ...
 95-130 1.51e-03

ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) and similar proteins; UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. It is localized in the nucleus and it contains conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which directly interacts with the proteasome. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. UBLCP1 may also play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain, a key event during mRNA metabolism.


Pssm-ID: 340511  Cd Length: 74  Bit Score: 35.63  E-value: 1.51e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1950227485  95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKiriQK 130
Cdd:cd01813     9 GKEYPVTVLSSDTVLDLKQRIFELTGVLPKR---QK 41
Ubiquitin_2 pfam14560
Ubiquitin-like domain; This entry contains ubiquitin-like domains.
 105-150 2.09e-03

Ubiquitin-like domain; This entry contains ubiquitin-like domains.


Pssm-ID: 405277  Cd Length: 83  Bit Score: 35.19  E-value: 2.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1950227485 105 DDTIGDLKKLVAAQTGTRPEKIRIQ-------KWYTIYKDHITLADYEIHDGM 150
Cdd:pfam14560  22 SLTIEELKEKLELITGTPPSSMRLQlyddddnLVAKLDDDDALLGSYGVRDGM 74
Ubl_UBTD1 cd17120
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is ...
 95-147 3.49e-03

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is the mammalian homolog of the mitochondrial Dc-UbP/UBTD2 protein, both of which contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. As a tumor suppressor, UBTD1 plays a pivotal role in in regulating cellular senescence that mediates p53 function. It is also involved in MDM2 ubiquitination and degradation.


Pssm-ID: 340640  Cd Length: 69  Bit Score: 34.52  E-value: 3.49e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1950227485  95 GKKVRVKCNQDDTIGDLKKLVAAQTGTRPEKiriQKWY---TIYKDHITLADYEIH 147
Cdd:cd17120     8 GKDVRLSASMSDTIGQLKKQLHAQEGIEPSW---QRWFfsgKLLTDKTRLQETKIQ 60
 
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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