SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic ...
1158-1441
1.28e-92
SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic proteins found on vacuolar-sorting associated proteins towards the C-terminus. In plants, the domain is found to be the region which interacts with SHR or the SHORT-ROOT transcription factor, a regulator of root-growth and asymmetric cell division that separates ground tissue into endodermis and cortex. The plant protein containing the SHR-BD is named SHRUBBY or SHBY, UniProtKB:Q9FT44.
:
Pssm-ID: 461974 [Multi-domain] Cd Length: 275 Bit Score: 301.92 E-value: 1.28e-92
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated ...
1496-1656
1.82e-86
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated protein 13D (VPS13D) and similar proteins; VPS13D is a ubiquitin-binding protein that is required for the regulation of mitochondrial size and clearance. It promotes mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission. Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. VPS13D contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site.
:
Pssm-ID: 467331 Cd Length: 159 Bit Score: 279.20 E-value: 1.82e-86
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar ...
549-584
1.97e-13
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.
:
Pssm-ID: 270491 Cd Length: 36 Bit Score: 65.93 E-value: 1.97e-13
SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic ...
1158-1441
1.28e-92
SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic proteins found on vacuolar-sorting associated proteins towards the C-terminus. In plants, the domain is found to be the region which interacts with SHR or the SHORT-ROOT transcription factor, a regulator of root-growth and asymmetric cell division that separates ground tissue into endodermis and cortex. The plant protein containing the SHR-BD is named SHRUBBY or SHBY, UniProtKB:Q9FT44.
Pssm-ID: 461974 [Multi-domain] Cd Length: 275 Bit Score: 301.92 E-value: 1.28e-92
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated ...
1496-1656
1.82e-86
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated protein 13D (VPS13D) and similar proteins; VPS13D is a ubiquitin-binding protein that is required for the regulation of mitochondrial size and clearance. It promotes mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission. Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. VPS13D contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site.
Pssm-ID: 467331 Cd Length: 159 Bit Score: 279.20 E-value: 1.82e-86
Vacuolar-sorting-associated 13 protein C-terminal; VPS13_C is a family of eukaryotic vacuolar ...
1866-2011
2.98e-29
Vacuolar-sorting-associated 13 protein C-terminal; VPS13_C is a family of eukaryotic vacuolar sorting-associated 13 proteins that lies at the C-terminus of the members, The exact function of this domain is not known.
Pssm-ID: 465310 [Multi-domain] Cd Length: 175 Bit Score: 116.10 E-value: 2.98e-29
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar ...
549-584
1.97e-13
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.
Pssm-ID: 270491 Cd Length: 36 Bit Score: 65.93 E-value: 1.97e-13
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
546-580
4.98e-05
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: 42.04 E-value: 4.98e-05
SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic ...
1158-1441
1.28e-92
SHR-binding domain of vacuolar-sorting associated protein 13; SHR-BD is a family of eukaryotic proteins found on vacuolar-sorting associated proteins towards the C-terminus. In plants, the domain is found to be the region which interacts with SHR or the SHORT-ROOT transcription factor, a regulator of root-growth and asymmetric cell division that separates ground tissue into endodermis and cortex. The plant protein containing the SHR-BD is named SHRUBBY or SHBY, UniProtKB:Q9FT44.
Pssm-ID: 461974 [Multi-domain] Cd Length: 275 Bit Score: 301.92 E-value: 1.28e-92
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated ...
1496-1656
1.82e-86
ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated protein 13D (VPS13D) and similar proteins; VPS13D is a ubiquitin-binding protein that is required for the regulation of mitochondrial size and clearance. It promotes mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission. Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. VPS13D contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site.
Pssm-ID: 467331 Cd Length: 159 Bit Score: 279.20 E-value: 1.82e-86
Vacuolar-sorting-associated 13 protein C-terminal; VPS13_C is a family of eukaryotic vacuolar ...
1866-2011
2.98e-29
Vacuolar-sorting-associated 13 protein C-terminal; VPS13_C is a family of eukaryotic vacuolar sorting-associated 13 proteins that lies at the C-terminus of the members, The exact function of this domain is not known.
Pssm-ID: 465310 [Multi-domain] Cd Length: 175 Bit Score: 116.10 E-value: 2.98e-29
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar ...
549-584
1.97e-13
UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins; VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required.
Pssm-ID: 270491 Cd Length: 36 Bit Score: 65.93 E-value: 1.97e-13
UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called ...
548-580
4.33e-06
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: 45.13 E-value: 4.33e-06
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
546-580
4.98e-05
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: 42.04 E-value: 4.98e-05
UBA domain found in elongation factor Ts (EF-Ts) from bacteria, chloroplasts and mitochondria ...
556-582
7.62e-05
UBA domain found in elongation factor Ts (EF-Ts) from bacteria, chloroplasts and mitochondria of eukaryotes; EF-Ts functions as a nucleotide exchange factor in the functional cycle of EF-Tu, another translation elongation factor that facilitates the binding of aminoacylated transfer RNAs (aminoacyl-tRNA) to the ribosomal A site as a ternary complex with guanosine triphosphate during the elongation cycle of protein biosynthesis, and then catalyzes the hydrolysis of GTP and release itself in GDP-bound form. EF-Ts forms complex with EF-Tu and catalyzes the nucleotide exchange reaction promoting the formation of EF-Tu in GTP-bound form from EF-Tu in GDP-bound form. EF-Ts from Thermus thermophiles is shorter than EF-Ts from Escherichia coli, but it has higher thermostability. The mitochondrial translational EF-Ts from chloroplasts and mitochondria display high similarity to the bacterial EF-Ts. The majority of family members contain one ubiquitin-associated (UBA) domain, but some family members from plants harbor two tandem UBA domains.
Pssm-ID: 270461 [Multi-domain] Cd Length: 37 Bit Score: 41.61 E-value: 7.62e-05
UBA2 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 ...
546-583
2.26e-04
UBA2 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.
Pssm-ID: 270484 [Multi-domain] Cd Length: 38 Bit Score: 40.52 E-value: 2.26e-04
UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 ...
546-584
1.90e-03
UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.
Pssm-ID: 270483 [Multi-domain] Cd Length: 39 Bit Score: 37.85 E-value: 1.90e-03
UBA2 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) ...
552-583
4.46e-03
UBA2 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain which show a high level of sequence similarity with mammalian ubiquitin-associated and SH3 domain-containing protein A (UBS3A).
Pssm-ID: 270571 Cd Length: 38 Bit Score: 36.78 E-value: 4.46e-03
UBA2 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast ...
551-581
5.33e-03
UBA2 domain of Rad23 proteins found in eukaryotes; 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 a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain.
Pssm-ID: 270467 Cd Length: 38 Bit Score: 36.72 E-value: 5.33e-03
UBA domain found in proteins involved in ubiquitin-mediated proteolysis; The ...
549-578
8.77e-03
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: 35.79 E-value: 8.77e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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