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Conserved domains on  [gi|15234839|ref|NP_194229|]
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Ubiquitin family protein [Arabidopsis thaliana]

Protein Classification

Rad60-SLD_2 domain-containing protein( domain architecture ID 10620708)

Rad60-SLD_2 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rad60-SLD_2 pfam13881
Ubiquitin-2 like Rad60 SUMO-like;
5-116 1.08e-56

Ubiquitin-2 like Rad60 SUMO-like;


:

Pssm-ID: 372780  Cd Length: 111  Bit Score: 171.34  E-value: 1.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839     5 ESIDIKFRLYDGSDIGPFRYSAASTVDFLKQRVVSDWPKGKTVVPKGINEVKLISSGKILENNKTVGQCKTPFGDIAGGV 84
Cdd:pfam13881   1 DQIELKFRLVDGSDIGPFVFSPATTVADLKEKVIAQWPKDKENGPKTVNDVKLINAGKILENNKTLGECRLPVGETPGGV 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 15234839    85 IVMHVVVQPSLAKSKTEKKvDKAPKAVICTCT 116
Cdd:pfam13881  81 TTMHVVVRPNLPEPNSEKK-ANKPKQNGCGCC 111
 
Name Accession Description Interval E-value
Rad60-SLD_2 pfam13881
Ubiquitin-2 like Rad60 SUMO-like;
5-116 1.08e-56

Ubiquitin-2 like Rad60 SUMO-like;


Pssm-ID: 372780  Cd Length: 111  Bit Score: 171.34  E-value: 1.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839     5 ESIDIKFRLYDGSDIGPFRYSAASTVDFLKQRVVSDWPKGKTVVPKGINEVKLISSGKILENNKTVGQCKTPFGDIAGGV 84
Cdd:pfam13881   1 DQIELKFRLVDGSDIGPFVFSPATTVADLKEKVIAQWPKDKENGPKTVNDVKLINAGKILENNKTLGECRLPVGETPGGV 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 15234839    85 IVMHVVVQPSLAKSKTEKKvDKAPKAVICTCT 116
Cdd:pfam13881  81 TTMHVVVRPNLPEPNSEKK-ANKPKQNGCGCC 111
Ubl_MUBs_plant cd01814
ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); ...
 6-93 1.01e-47

ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold.


Pssm-ID: 340512  Cd Length: 89  Bit Score: 147.91  E-value: 1.01e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839   6 SIDIKFRLYDGSDIGPFRYSAASTVDFLKQRVVSDWPKGKTVVPKGINEVKLISSGKILENNKTVGQCKTPFGDIAGGVI 85
Cdd:cd01814   1 LIEIKFRLTDGSDIGPFRYSSATTVATLKEKVIAEWPKDKENGPKSINDVKLIYAGKVLENGKTLADSRTPGKVPPGGVI 80


                ....*...
gi 15234839  86 VMHVVVQP 93
Cdd:cd01814  81 TMHVVVRP 88
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 21-110 1.08e-05

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: 42.96  E-value: 1.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839    21 PFRYSAASTVDFLKQRVVSDwpKGKTVVPKGinEVKLISSGKILENNKTVGQCKTPFGDIaggVIVMhvvvqpsLAKSKT 100
Cdd:TIGR00601  14 KIDMEPDETVKELKEKIEAE--QGKDAYPVA--QQKLIYSGKILSDDKTVKEYKIKEKDF---VVVM-------VSKPKT 79

                          90
                  ....*....|
gi 15234839   101 EKKVDKAPKA 110
Cdd:TIGR00601  80 GTGKVAPPAA 89
 
Name Accession Description Interval E-value
Rad60-SLD_2 pfam13881
Ubiquitin-2 like Rad60 SUMO-like;
5-116 1.08e-56

Ubiquitin-2 like Rad60 SUMO-like;


Pssm-ID: 372780  Cd Length: 111  Bit Score: 171.34  E-value: 1.08e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839     5 ESIDIKFRLYDGSDIGPFRYSAASTVDFLKQRVVSDWPKGKTVVPKGINEVKLISSGKILENNKTVGQCKTPFGDIAGGV 84
Cdd:pfam13881   1 DQIELKFRLVDGSDIGPFVFSPATTVADLKEKVIAQWPKDKENGPKTVNDVKLINAGKILENNKTLGECRLPVGETPGGV 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 15234839    85 IVMHVVVQPSLAKSKTEKKvDKAPKAVICTCT 116
Cdd:pfam13881  81 TTMHVVVRPNLPEPNSEKK-ANKPKQNGCGCC 111
Ubl_MUBs_plant cd01814
ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); ...
 6-93 1.01e-47

ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold.


Pssm-ID: 340512  Cd Length: 89  Bit Score: 147.91  E-value: 1.01e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839   6 SIDIKFRLYDGSDIGPFRYSAASTVDFLKQRVVSDWPKGKTVVPKGINEVKLISSGKILENNKTVGQCKTPFGDIAGGVI 85
Cdd:cd01814   1 LIEIKFRLTDGSDIGPFRYSSATTVATLKEKVIAEWPKDKENGPKSINDVKLIYAGKVLENGKTLADSRTPGKVPPGGVI 80


                ....*...
gi 15234839  86 VMHVVVQP 93
Cdd:cd01814  81 TMHVVVRP 88
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 21-110 1.08e-05

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: 42.96  E-value: 1.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839    21 PFRYSAASTVDFLKQRVVSDwpKGKTVVPKGinEVKLISSGKILENNKTVGQCKTPFGDIaggVIVMhvvvqpsLAKSKT 100
Cdd:TIGR00601  14 KIDMEPDETVKELKEKIEAE--QGKDAYPVA--QQKLIYSGKILSDDKTVKEYKIKEKDF---VVVM-------VSKPKT 79

                          90
                  ....*....|
gi 15234839   101 EKKVDKAPKA 110
Cdd:TIGR00601  80 GTGKVAPPAA 89
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 9-91 1.14e-03

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: 34.84  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234839     9 IKFRLYDGSDIgPFRYSAASTVDFLKQRVVSdwpkgKTVVPkgINEVKLISSGKILENNKTVGQCktpfgDIAGGVIVmH 88
Cdd:pfam00240   1 ITVKTLDGKKI-TLEVDPTDTVLELKEKIAE-----KEGVP--PEQQRLIYSGKVLEDDQTLGEY-----GIEDGSTI-H 66


                  ...
gi 15234839    89 VVV 91
Cdd:pfam00240  67 LVL 69
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 9-80 1.79e-03

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: 34.49  E-value: 1.79e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15234839   9 IKFRLYDGSDIgPFRYSAASTVDFLKQRVvsdwpKGKTVVPkgINEVKLISSGKILENNKTVGQCKTPFGDI 80
Cdd:cd17039   1 ITVKTLDGKTY-TVEVDPDDTVADLKEKI-----EEKTGIP--VEQQRLIYNGKELKDDKTLSDYGIKDGST 64
Ubl_UBL3 cd17048
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; ...
 22-90 3.74e-03

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; UBL3, also termed membrane-anchored ubiquitin-fold protein (MUB), or protein HCG-1, belongs to a newly described MUB protein family with structural homology with ubiquitin. MUB proteins have a beta-grasp ubiquitin-like (Ubl) domain with longer N- and C-termini and extended loops. The Ubl domain contains a C-terminal CAAX-box, a canonical motif for protein prenylation, which is modified through protein lipidation with a hydrophobic membrane anchor. The lipidation and membrane localization inhibit attachment of MUBs to target proteins.


Pssm-ID: 340568  Cd Length: 82  Bit Score: 33.89  E-value: 3.74e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15234839  22 FRYSAASTVDFLKQRVVSDWPKG---KTVVPKGIneVKLISSGKILENNKTVGQCKTPFGDIAggviVMHVV 90
Cdd:cd17048  15 FLFSPNDSAADIAQHVFDNWPEDweeEQVSSANI--LRLIYQGRFLHGNVTLGALQLPLGKTT----VMHLV 80
 
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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