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Conserved domains on  [gi|2008372123|ref|NP_001380815|]
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sequestosome-1 isoform 5 [Rattus norvegicus]

Protein Classification

sequestosome-1( domain architecture ID 10866440)

sequestosome-1 (SQSTM) functions as a bridge between polyubiquitinated cargo and autophagosomes

Gene Symbol:  SQSTM1
Gene Ontology:  GO:0006511|GO:0006914|GO:0008270|GO:0070530|GO:0043130
PubMed:  34414460|18083707|17726178|12062168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PB1_p62 cd06402
The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) ...
 4-100 5.75e-41

The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


:

Pssm-ID: 99723  Cd Length: 87  Bit Score: 139.01  E-value: 5.75e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123   4 LTVKAYLLGKEeAAREIRRFSFCfspepeaeaAAGPGPCERLLSRVAVLFPALRPGGFQAHYRDEDGDLVAFSSDEELTM 83
Cdd:cd06402     1 LTVKAYLLGKD-ANAEIRRFAID---------EDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVM 70

                          90
                  ....*....|....*..
gi 2008372123  84 AMSYVKDDIFRIYIKEK 100
Cdd:cd06402    71 ALGSLNDDTFRIYIKEK 87
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
 323-374 2.44e-33

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. 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 bind the 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. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.


The actual alignment was detected with superfamily member pfam16577:

Pssm-ID: 473871  Cd Length: 62  Bit Score: 118.61  E-value: 2.44e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2008372123 323 EADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 374
Cdd:pfam16577  11 DADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62
ZZ_NBR1_like cd02340
Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 ...
 123-163 1.11e-21

Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.


:

Pssm-ID: 239080  Cd Length: 43  Bit Score: 86.54  E-value: 1.11e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2008372123 123 VICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHREHSKL 163
Cdd:cd02340     1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEAKGVHPEHAML 41
 
Name Accession Description Interval E-value
PB1_p62 cd06402
The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) ...
 4-100 5.75e-41

The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


Pssm-ID: 99723  Cd Length: 87  Bit Score: 139.01  E-value: 5.75e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123   4 LTVKAYLLGKEeAAREIRRFSFCfspepeaeaAAGPGPCERLLSRVAVLFPALRPGGFQAHYRDEDGDLVAFSSDEELTM 83
Cdd:cd06402     1 LTVKAYLLGKD-ANAEIRRFAID---------EDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVM 70

                          90
                  ....*....|....*..
gi 2008372123  84 AMSYVKDDIFRIYIKEK 100
Cdd:cd06402    71 ALGSLNDDTFRIYIKEK 87
UBA_5 pfam16577
UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome ...
 323-374 2.44e-33

UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins.


Pssm-ID: 318725  Cd Length: 62  Bit Score: 118.61  E-value: 2.44e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2008372123 323 EADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 374
Cdd:pfam16577  11 DADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62
ZZ_NBR1_like cd02340
Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 ...
 123-163 1.11e-21

Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.


Pssm-ID: 239080  Cd Length: 43  Bit Score: 86.54  E-value: 1.11e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2008372123 123 VICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHREHSKL 163
Cdd:cd02340     1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEAKGVHPEHAML 41
UBA_SQSTM cd14320
UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated ...
 327-366 7.05e-21

UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role connected to the ubiquitin-proteasome pathway. It functions as a scaffolding protein that regulates a diverse range of signaling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors. It also plays a novel role in connecting receptor signals with the endosomal signaling network required for mediating TrkA-induced differentiation. SQSTM contains a PB1 dimerization domain, a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding site, and a C-terminal ubiquitin-associated (UBA) domain that mediates the recognition of polyubiquitin chains and ubiquitylated substrates.


Pssm-ID: 270505  Cd Length: 40  Bit Score: 84.55  E-value: 7.05e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2008372123 327 RLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ 366
Cdd:cd14320     1 KIEEALSQMLAMGFSNEGGWLTRLLEAKNGDIGKVLDVIQ 40
ZnF_ZZ smart00291
Zinc-binding domain, present in Dystrophin, CREB-binding protein; Putative zinc-binding domain ...
 119-161 4.63e-15

Zinc-binding domain, present in Dystrophin, CREB-binding protein; Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy.


Pssm-ID: 197633 [Multi-domain]  Cd Length: 44  Bit Score: 68.62  E-value: 4.63e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2008372123  119 VHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKG-LHREHS 161
Cdd:smart00291   1 VHHSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGsAGGEHS 44
PB1 smart00666
PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. ...
 3-97 5.68e-13

PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.


Pssm-ID: 214770  Cd Length: 81  Bit Score: 63.76  E-value: 5.68e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123    3 SLTVKAYLLGkeeaarEIRRFSFCfspepeaeaaaGPGPCERLLSRVAVLFPaLRPGGFQAHYRDEDGDLVAFSSDEELT 82
Cdd:smart00666   1 TVDVKLRYGG------ETRRLSVP-----------RDISFEDLRSKVAKRFG-LDNQSFTLKYQDEDGDLVSLTSDEDLE 62

                           90
                   ....*....|....*...
gi 2008372123   83 MAMSYVK---DDIFRIYI 97
Cdd:smart00666  63 EAIEEYDslgSKKLRLHV 80
PB1 pfam00564
PB1 domain;
21-100 5.83e-12

PB1 domain;


Pssm-ID: 395447  Cd Length: 84  Bit Score: 61.15  E-value: 5.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123  21 RRFSFCFSPEPEAEAAAGPG-PCERLLSRVAVLFPaLRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVK---DDIFRIY 96
Cdd:pfam00564   2 VRLKLRYGGGIRRFLSVSRGiSFEELRALVEQRFG-LDDVDFKLKYPDEDGDLVSLTSDEDLEEALEEARslgSKSLRLH 80


                  ....
gi 2008372123  97 IKEK 100
Cdd:pfam00564  81 VFPT 84
ZZ pfam00569
Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds ...
 120-160 2.23e-08

Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.


Pssm-ID: 395451  Cd Length: 45  Bit Score: 49.79  E-value: 2.23e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2008372123 120 HPNVICDGC-NGPVVGTRYKCSVCPDYDLCSVCEGKGLHREH 160
Cdd:pfam00569   2 HKVYTCNGCsNDPSIGVRYHCLRCSDYDLCQSCFQTHKGGNH 43
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
 328-365 8.55e-05

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: 39.39  E-value: 8.55e-05
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2008372123  328 LIESLSQMLSMGFSDEggWLTRLLQTKNYDIGAALDTI 365
Cdd:smart00165   1 DEEKIDQLLEMGFSRE--EALKALRAANGNVERAAEYL 36
 
Name Accession Description Interval E-value
PB1_p62 cd06402
The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) ...
 4-100 5.75e-41

The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


Pssm-ID: 99723  Cd Length: 87  Bit Score: 139.01  E-value: 5.75e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123   4 LTVKAYLLGKEeAAREIRRFSFCfspepeaeaAAGPGPCERLLSRVAVLFPALRPGGFQAHYRDEDGDLVAFSSDEELTM 83
Cdd:cd06402     1 LTVKAYLLGKD-ANAEIRRFAID---------EDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVM 70

                          90
                  ....*....|....*..
gi 2008372123  84 AMSYVKDDIFRIYIKEK 100
Cdd:cd06402    71 ALGSLNDDTFRIYIKEK 87
UBA_5 pfam16577
UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome ...
 323-374 2.44e-33

UBA domain; UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins.


Pssm-ID: 318725  Cd Length: 62  Bit Score: 118.61  E-value: 2.44e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2008372123 323 EADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL 374
Cdd:pfam16577  11 DADPRLIESLAQMLSMGFSDEGGWLTRLLHTKNFDIGAALDAIHFSKHPPPA 62
ZZ_NBR1_like cd02340
Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 ...
 123-163 1.11e-21

Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.


Pssm-ID: 239080  Cd Length: 43  Bit Score: 86.54  E-value: 1.11e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2008372123 123 VICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHREHSKL 163
Cdd:cd02340     1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEAKGVHPEHAML 41
UBA_SQSTM cd14320
UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated ...
 327-366 7.05e-21

UBA domain of sequestosome-1 (SQSTM) and similar proteins; SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role connected to the ubiquitin-proteasome pathway. It functions as a scaffolding protein that regulates a diverse range of signaling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors. It also plays a novel role in connecting receptor signals with the endosomal signaling network required for mediating TrkA-induced differentiation. SQSTM contains a PB1 dimerization domain, a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding site, and a C-terminal ubiquitin-associated (UBA) domain that mediates the recognition of polyubiquitin chains and ubiquitylated substrates.


Pssm-ID: 270505  Cd Length: 40  Bit Score: 84.55  E-value: 7.05e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2008372123 327 RLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQ 366
Cdd:cd14320     1 KIEEALSQMLAMGFSNEGGWLTRLLEAKNGDIGKVLDVIQ 40
ZnF_ZZ smart00291
Zinc-binding domain, present in Dystrophin, CREB-binding protein; Putative zinc-binding domain ...
 119-161 4.63e-15

Zinc-binding domain, present in Dystrophin, CREB-binding protein; Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy.


Pssm-ID: 197633 [Multi-domain]  Cd Length: 44  Bit Score: 68.62  E-value: 4.63e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2008372123  119 VHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKG-LHREHS 161
Cdd:smart00291   1 VHHSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGsAGGEHS 44
PB1 smart00666
PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. ...
 3-97 5.68e-13

PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.


Pssm-ID: 214770  Cd Length: 81  Bit Score: 63.76  E-value: 5.68e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123    3 SLTVKAYLLGkeeaarEIRRFSFCfspepeaeaaaGPGPCERLLSRVAVLFPaLRPGGFQAHYRDEDGDLVAFSSDEELT 82
Cdd:smart00666   1 TVDVKLRYGG------ETRRLSVP-----------RDISFEDLRSKVAKRFG-LDNQSFTLKYQDEDGDLVSLTSDEDLE 62

                           90
                   ....*....|....*...
gi 2008372123   83 MAMSYVK---DDIFRIYI 97
Cdd:smart00666  63 EAIEEYDslgSKKLRLHV 80
ZZ cd02249
Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ...
 123-161 2.26e-12

Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.


Pssm-ID: 239069 [Multi-domain]  Cd Length: 46  Bit Score: 60.91  E-value: 2.26e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2008372123 123 VICDGCNGPVVGTRYKCSVCPDYDLCSVC--EGKGLH-REHS 161
Cdd:cd02249     1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCyaKGKKGHpPDHS 42
PB1 pfam00564
PB1 domain;
21-100 5.83e-12

PB1 domain;


Pssm-ID: 395447  Cd Length: 84  Bit Score: 61.15  E-value: 5.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123  21 RRFSFCFSPEPEAEAAAGPG-PCERLLSRVAVLFPaLRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVK---DDIFRIY 96
Cdd:pfam00564   2 VRLKLRYGGGIRRFLSVSRGiSFEELRALVEQRFG-LDDVDFKLKYPDEDGDLVSLTSDEDLEEALEEARslgSKSLRLH 80


                  ....
gi 2008372123  97 IKEK 100
Cdd:pfam00564  81 VFPT 84
PB1 cd05992
The PB1 domain is a modular domain mediating specific protein-protein interactions which play ...
 4-98 7.38e-12

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


Pssm-ID: 99716 [Multi-domain]  Cd Length: 81  Bit Score: 60.75  E-value: 7.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2008372123   4 LTVKAYLLGkeeaarEIRRFSFCFSPEPeaeaaagpgpCERLLSRVAVLFPaLRPGGFQAHYRDEDGDLVAFSSDEELTM 83
Cdd:cd05992     1 VRVKVKYGG------EIRRFVVVSRSIS----------FEDLRSKIAEKFG-LDAVSFKLKYPDEDGDLVTISSDEDLEE 63

                          90
                  ....*....|....*...
gi 2008372123  84 AMSYVK---DDIFRIYIK 98
Cdd:cd05992    64 AIEEARrsgSKKLRLFVF 81
ZZ_Mind_bomb cd02339
Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. ...
 123-157 1.07e-10

Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.


Pssm-ID: 239079  Cd Length: 45  Bit Score: 56.31  E-value: 1.07e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2008372123 123 VICDGCNG-PVVGTRYKCSVCPDYDLCSVCEGKGLH 157
Cdd:cd02339     1 IICDTCRKqGIIGIRWKCAECPNYDLCTTCYHGDKH 36
ZZ pfam00569
Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds ...
 120-160 2.23e-08

Zinc finger, ZZ type; Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.


Pssm-ID: 395451  Cd Length: 45  Bit Score: 49.79  E-value: 2.23e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2008372123 120 HPNVICDGC-NGPVVGTRYKCSVCPDYDLCSVCEGKGLHREH 160
Cdd:pfam00569   2 HKVYTCNGCsNDPSIGVRYHCLRCSDYDLCQSCFQTHKGGNH 43
ZZ_CBP cd02337
Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif ...
 125-163 1.86e-05

Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.


Pssm-ID: 239077  Cd Length: 41  Bit Score: 41.39  E-value: 1.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2008372123 125 CDGCNGpVVGTRYKCSVCPDYDLCSVC-EGKGLHREHSKL 163
Cdd:cd02337     3 CNECKH-HVETRWHCTVCEDYDLCITCyNTKNHPHKMEKL 41
ZZ_PCMF_like cd02338
Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and ...
 123-151 2.49e-05

Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.


Pssm-ID: 239078  Cd Length: 49  Bit Score: 41.18  E-value: 2.49e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 2008372123 123 VICDGC-NGPVVGTRYKCSVCPDYDLCSVC 151
Cdd:cd02338     1 VSCDGCgKSNFTGRRYKCLICYDYDLCADC 30
ZZ_ZZZ3 cd02341
Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related ...
 125-164 4.55e-05

Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.


Pssm-ID: 239081  Cd Length: 48  Bit Score: 40.49  E-value: 4.55e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2008372123 125 CDGCN-GPVVGTRYKCSVCP--DYDLCSVC-EGKGLHREHSKLI 164
Cdd:cd02341     3 CDSCGiEPIPGTRYHCSECDdgDFDLCQDCvVKGESHQEDHWLV 46
ZZ_UBA_plant cd02342
Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ ...
 125-151 6.31e-05

Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.


Pssm-ID: 239082  Cd Length: 43  Bit Score: 39.87  E-value: 6.31e-05
                          10        20
                  ....*....|....*....|....*...
gi 2008372123 125 CDGCN-GPVVGTRYKCSVCPDYDLCSVC 151
Cdd:cd02342     3 CDGCGvLPITGPRYKSKVKEDYDLCTIC 30
UBA smart00165
Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 ...
 328-365 8.55e-05

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: 39.39  E-value: 8.55e-05
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2008372123  328 LIESLSQMLSMGFSDEggWLTRLLQTKNYDIGAALDTI 365
Cdd:smart00165   1 DEEKIDQLLEMGFSRE--EALKALRAANGNVERAAEYL 36
ZZ_HERC2 cd02344
Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential ...
 123-151 1.15e-04

Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.


Pssm-ID: 239084  Cd Length: 45  Bit Score: 39.10  E-value: 1.15e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 2008372123 123 VICDGCNG-PVVGTRYKCSVCPDYDLCSVC 151
Cdd:cd02344     1 VTCDGCQMfPINGPRFKCRNCDDFDFCENC 30
PB1_Joka2 cd06398
The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with ...
 21-87 5.02e-04

The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


Pssm-ID: 99720  Cd Length: 91  Bit Score: 38.93  E-value: 5.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2008372123  21 RRFSFCF-SPEPEAEAAAgpgpcerLLSRVAVLFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSY 87
Cdd:cd06398    12 RRFTFPVaENQLDLNMDG-------LREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72
ZZ_ADA2 cd02335
Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and ...
 125-151 6.37e-04

Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.


Pssm-ID: 239075 [Multi-domain]  Cd Length: 49  Bit Score: 37.27  E-value: 6.37e-04
                          10        20
                  ....*....|....*....|....*...
gi 2008372123 125 CDGCNGPVVGT-RYKCSVCPDYDLCSVC 151
Cdd:cd02335     3 CDYCSKDITGTiRIKCAECPDFDLCLEC 30
ZZ_dystrophin cd02334
Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif ...
 123-162 3.60e-03

Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.


Pssm-ID: 239074  Cd Length: 49  Bit Score: 35.02  E-value: 3.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2008372123 123 VICDGCNG-PVVGTRYKCSVCPDYDLCSVCEGKGLH-REHSK 162
Cdd:cd02334     1 AKCNICKEfPITGFRYRCLKCFNYDLCQSCFFSGRTsKSHKN 42
ZZ_dah cd02345
Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif ...
 125-155 5.69e-03

Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.


Pssm-ID: 239085  Cd Length: 49  Bit Score: 34.49  E-value: 5.69e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2008372123 125 CDGCN-GPVVGTRYKCSVCPDYDLCSVCEGKG 155
Cdd:cd02345     3 CSACRkQDISGIRFPCQVCRDYSLCLGCYTKG 34
 
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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