NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|20544151|ref|NP_057671|]
View 

chromobox protein homolog 3 isoform a [Homo sapiens]

Protein Classification

chromo domain-containing protein( domain architecture ID 13036253)

chromo (chromatin organization modifier) domain-containing protein such as mammalian chromobox protein homologs 1, 3, and 5, which are components of heterochromatin; also contains a chromo shadow domain

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
CSD_HP1gamma_Cbx3 cd18656
chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain ...
116-173 3.25e-33

chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


:

Pssm-ID: 349303  Cd Length: 58  Bit Score: 112.86  E-value: 3.25e-33
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 20544151 116 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
Cdd:cd18656   1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 58
CD_HP1gamma_Cbx3 cd18652
chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier ...
29-78 3.87e-30

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma.


:

Pssm-ID: 349299  Cd Length: 50  Bit Score: 104.70  E-value: 3.87e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18652   1 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 50
 
Name Accession Description Interval E-value
CSD_HP1gamma_Cbx3 cd18656
chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain ...
116-173 3.25e-33

chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349303  Cd Length: 58  Bit Score: 112.86  E-value: 3.25e-33
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 20544151 116 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
Cdd:cd18656   1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 58
Chromo_shadow pfam01393
Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always ...
123-174 2.66e-30

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.


Pssm-ID: 460191  Cd Length: 52  Bit Score: 104.94  E-value: 2.66e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 20544151   123 PERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTW 174
Cdd:pfam01393   1 PEKIIGATDTRGELMFLMKWKNGEEADLVPSKEANQKCPQKVIKFYEERLTW 52
CD_HP1gamma_Cbx3 cd18652
chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier ...
29-78 3.87e-30

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma.


Pssm-ID: 349299  Cd Length: 50  Bit Score: 104.70  E-value: 3.87e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18652   1 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 50
ChSh smart00300
Chromo Shadow Domain;
115-176 1.83e-28

Chromo Shadow Domain;


Pssm-ID: 197638  Cd Length: 61  Bit Score: 100.52  E-value: 1.83e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 20544151    115 RGFARGLDPERIIGATDSSGELMFLMKWKDsDEADLVLAKEANMKCPQIVIAFYEERLTWHS 176
Cdd:smart00300   1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQS 61
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
30-79 1.05e-14

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 64.91  E-value: 1.05e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 20544151    30 FVVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAFLNS 79
Cdd:pfam00385   1 YEVERILDHRKDkGGKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKDR 52
CHROMO smart00298
Chromatin organization modifier domain;
29-81 9.85e-12

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 57.22  E-value: 9.85e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 20544151     29 EFVVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENLD-CPELIEAFLNSQK 81
Cdd:smart00298   1 EYEVEKILDHRWKkKGELEYLVKWKGYSYSEDTWEPEENLLnCSKKLDNYKKKER 55
 
Name Accession Description Interval E-value
CSD_HP1gamma_Cbx3 cd18656
chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain ...
116-173 3.25e-33

chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349303  Cd Length: 58  Bit Score: 112.86  E-value: 3.25e-33
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 20544151 116 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
Cdd:cd18656   1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 58
CSD_HP1beta_Cbx1 cd18654
chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 ...
116-173 1.61e-32

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3


Pssm-ID: 349301  Cd Length: 58  Bit Score: 110.95  E-value: 1.61e-32
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 20544151 116 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
Cdd:cd18654   1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58
Chromo_shadow pfam01393
Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always ...
123-174 2.66e-30

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.


Pssm-ID: 460191  Cd Length: 52  Bit Score: 104.94  E-value: 2.66e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 20544151   123 PERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTW 174
Cdd:pfam01393   1 PEKIIGATDTRGELMFLMKWKNGEEADLVPSKEANQKCPQKVIKFYEERLTW 52
CD_HP1gamma_Cbx3 cd18652
chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier ...
29-78 3.87e-30

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma.


Pssm-ID: 349299  Cd Length: 50  Bit Score: 104.70  E-value: 3.87e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18652   1 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 50
CSD_HP1alpha_Cbx5 cd18655
chromo shadow domain of heterochromatin protein 1 homolog alpha; Chromo shadow domain (CSD) of ...
116-173 7.09e-30

chromo shadow domain of heterochromatin protein 1 homolog alpha; Chromo shadow domain (CSD) of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349302  Cd Length: 58  Bit Score: 104.32  E-value: 7.09e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 20544151 116 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 173
Cdd:cd18655   1 GFERGLEPEKIIGATDSCGDLMFLMKWKDSDEADLVLAKEANVKCPQIVIAFYEERLT 58
CSD cd00034
chromo shadow domain; The chromo shadow domain (CSD) is always found in association with a ...
121-172 3.82e-29

chromo shadow domain; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349275  Cd Length: 52  Bit Score: 101.90  E-value: 3.82e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151 121 LDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
Cdd:cd00034   1 LEVEKILGATDSDGELMFLIKWKGSDEADLVPAKEANEKCPQIVIQFYESRL 52
ChSh smart00300
Chromo Shadow Domain;
115-176 1.83e-28

Chromo Shadow Domain;


Pssm-ID: 197638  Cd Length: 61  Bit Score: 100.52  E-value: 1.83e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 20544151    115 RGFARGLDPERIIGATDSSGELMFLMKWKDsDEADLVLAKEANMKCPQIVIAFYEERLTWHS 176
Cdd:smart00300   1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQS 61
CD_HP1_like cd18631
chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; ...
29-78 7.69e-26

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349281  Cd Length: 50  Bit Score: 93.66  E-value: 7.69e-26
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18631   1 EYVVEKVLDRRVVKGKVEYLLKWKGYPDEDNTWEPEENLDCPDLIAEFEE 50
CD_HP1beta_Cbx1 cd18650
chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier ...
29-77 8.59e-26

chromodomain of heterochromatin protein 1 homolog beta; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3).


Pssm-ID: 349297  Cd Length: 50  Bit Score: 93.47  E-value: 8.59e-26
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFL 77
Cdd:cd18650   1 EYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFL 49
CD_HP1alpha_Cbx5 cd18651
chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier ...
29-77 4.98e-23

chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349298  Cd Length: 50  Bit Score: 86.58  E-value: 4.98e-23
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFL 77
Cdd:cd18651   1 EYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFM 49
CD_HP1a_insect cd18653
chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. ...
29-76 2.73e-20

chromodomain of insect HP1a; CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a.


Pssm-ID: 349300  Cd Length: 50  Bit Score: 79.31  E-value: 2.73e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18653   1 EYAVEKICDRRVRKGKVEYYLKWKGYPETENTWEPEENLDCQDLIQQY 48
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
30-77 4.98e-19

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274 [Multi-domain]  Cd Length: 50  Bit Score: 75.98  E-value: 4.98e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAFL 77
Cdd:cd00024   1 YEVEKILDHRVRKGKLEYLVKWKGYPPEENTWEPEENLtNAPELIKEYE 49
CSD_HP1a_insect cd18658
chromo shadow domain of insect heterochromatin protein 1a; The chromo shadow domain (CSD) is ...
120-172 1.75e-16

chromo shadow domain of insect heterochromatin protein 1a; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CSD of Drosophila melanogaster HP1a.


Pssm-ID: 349305  Cd Length: 53  Bit Score: 69.64  E-value: 1.75e-16
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 20544151 120 GLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
Cdd:cd18658   1 GLEAEKILGASDSNGGLTFLIQFKGVDQAEMVPASVANVKIPQMVIKFYEERL 53
Chromo pfam00385
Chromo (CHRromatin organization MOdifier) domain;
30-79 1.05e-14

Chromo (CHRromatin organization MOdifier) domain;


Pssm-ID: 459793 [Multi-domain]  Cd Length: 52  Bit Score: 64.91  E-value: 1.05e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 20544151    30 FVVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAFLNS 79
Cdd:pfam00385   1 YEVERILDHRKDkGGKEEYLVKWKGYPYDENTWEPEENLsKCPELIEEFKDR 52
CD_polycomb_like cd18627
chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier ...
30-78 9.03e-14

chromodomain of polycomb and chromobox family proteins; CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349277  Cd Length: 49  Bit Score: 62.41  E-value: 9.03e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18627   1 FAAECILKKRIRKGKVEYLVKWKGWSQKYNTWEPEENILDPRLLAAFES 49
CD_HP1_like cd18960
chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; ...
30-76 2.17e-13

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; uncharacterized subgroup; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).


Pssm-ID: 349316  Cd Length: 51  Bit Score: 61.42  E-value: 2.17e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 20544151  30 FVVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18960   2 FVVERILDKRLGrNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEF 49
CD_polycomb cd18644
chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG ...
30-76 2.25e-13

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.


Pssm-ID: 349291  Cd Length: 54  Bit Score: 61.71  E-value: 2.25e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18644   4 YAAEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIF 50
CD_POL_like cd18976
chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup ...
30-76 1.89e-12

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349332  Cd Length: 51  Bit Score: 59.12  E-value: 1.89e-12
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD--CPELIEAF 76
Cdd:cd18976   1 YIVESLLDRRKVRGQVQYLVKWRGFPRSEATWEPREELMrrCAELVAAY 49
chromodomain cd18968
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
29-76 2.16e-12

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349324  Cd Length: 57  Bit Score: 58.90  E-value: 2.16e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 20544151  29 EFVVEKVLDRRVV------NGKVEYFLKWKGFTDADNTWEPEENLD-CPELIEAF 76
Cdd:cd18968   1 EYEVEVILAARVVkdaesrKKGWKYLVKWAGYPDEENTWEPEESFDgCDDLLERF 55
CD_SUV39H1_like cd18639
chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin ...
30-78 8.08e-12

chromodomain of histone methyltransferase SUV39H1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of human SUV39H1, a histone lysine methyltransferase (HMT) which catalyzes di- and tri-methylation of lysine 9 of histone H3 (H3K9me2/3), leading to heterochromatin formation and gene silencing. H3K9me2/3 represents a specific mark for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3, and/or CBX5) proteins to methylated histones. SUV39H1 mainly functions in heterochromatin regions. The human SUV39H1/2, histone H3K9 methyltransferases, are the mammalian homologs of Drosophila Su(var)3-9 and Schizosaccharomyces pombe Clr4. SUV39H1 contains a chromodomain at its N-terminus and a SET domain at its C-terminus. Although the SET domain performs the catalytic activity, the chromodomain of SUV39H1 is essential for the catalytic activity of SUV39H1. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349289  Cd Length: 49  Bit Score: 57.53  E-value: 8.08e-12
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18639   1 YEVEYLCDYKKIREQEYYLVKWKGYPDSENTWEPRQNLKCSRLLKQFHK 49
CHROMO smart00298
Chromatin organization modifier domain;
29-81 9.85e-12

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 57.22  E-value: 9.85e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 20544151     29 EFVVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENLD-CPELIEAFLNSQK 81
Cdd:smart00298   1 EYEVEKILDHRWKkKGELEYLVKWKGYSYSEDTWEPEENLLnCSKKLDNYKKKER 55
CD_MT_like cd18962
chromodomain of a putative Coemansia reversa NRRL 1564 methyltransferase, and similar proteins; ...
29-76 1.98e-11

chromodomain of a putative Coemansia reversa NRRL 1564 methyltransferase, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Coemansia reversa NRRL 1564 SET (Su(var)3-9, enhancer-of-zeste, trithorax) domain-containing protein, and similar proteins. The SU(VAR)3-9 protein is the main chromocenter-specific histone H3-K9 methyltransferase (HMTase) in Drosophila where it plays a role in heterochromatic gene silencing. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349318  Cd Length: 52  Bit Score: 56.42  E-value: 1.98e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18962   3 HYVVEAIVNDVLIDGKHMYEVKWEGYPSDHNNWVAEWDLNDKEILRKY 50
CD_MarY1_POL_like cd18975
chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes ...
30-76 3.59e-11

chromodomain of Tricholoma matsutake polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349331  Cd Length: 49  Bit Score: 55.63  E-value: 3.59e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18975   1 YEVESILNSRLHRGKLQYLIQWKGYPLEEASWELEDNIKNPRLIEEF 47
CD_Rhino cd18630
chromodomain of Drosophila melanogaster Rhino, and similar proteins; N-terminal CHRomatin ...
29-76 5.70e-11

chromodomain of Drosophila melanogaster Rhino, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of Drosophila melanogaster Rhino (also known as heterochromatin protein 1-like), and similar proteins. Rhino is a female-specific protein that affects chromosome structure and egg polarity that is required for germline PIWI-interacting RNA (piRNA) production. In Drosophila the RDC (rhino, deadlock, and cutoff) complex, composed of rhino, the protein deadlock (Del) and the Rai1-like transcription termination cofactor cutoff (Cuff) binds to chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is anchored to H3K9me3-marked chromatin in part via the H3K9me3-binding activity of Rhino, and is required for transcription of piRNA precursors. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349280  Cd Length: 51  Bit Score: 55.22  E-value: 5.70e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  29 EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18630   1 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENLgNCMKLVADY 49
CD_MMP8 cd18633
chromodomain of M-phase phosphoprotein 8; The chromodomain of M-phase phosphoprotein 8 (MPP8), ...
30-76 1.18e-10

chromodomain of M-phase phosphoprotein 8; The chromodomain of M-phase phosphoprotein 8 (MPP8), a component of the RanBPM-containing large protein complex, binds methylated H3K9. This may in turn recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promoting tumor cell motility and invasion. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349283  Cd Length: 51  Bit Score: 54.60  E-value: 1.18e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18633   2 FEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEVHLeDCKEVLLEF 49
chromodomain cd18966
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
30-75 1.27e-10

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349322  Cd Length: 49  Bit Score: 54.21  E-value: 1.27e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEA 75
Cdd:cd18966   1 YEVERILAERRDDGGKRYLVKWEGYPLEEATWEPEENIGDEELLKE 46
CD_Cbx4 cd18645
chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of ...
30-81 2.20e-10

chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 4 (CBX4), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. In addition to a chromodomain with H3K27me3-binding activity, Cbx4 contains two SUMO-interacting motifs responsible for its small ubiquitin-related modifier (SUMO) E3 ligase activity. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX4 may serve as a tumor suppressor in colorectal carcinoma, and has been shown to be an oncogene in osteosarcoma and breast cancer.


Pssm-ID: 349292  Cd Length: 55  Bit Score: 53.91  E-value: 2.20e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK 81
Cdd:cd18645   4 FAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRER 55
CD_Cbx2 cd18647
chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of ...
30-76 2.73e-10

chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 2 (CBX2), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349294  Cd Length: 53  Bit Score: 53.52  E-value: 2.73e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18647   4 FAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAF 50
CD_EhHp1_like cd18638
chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins; This ...
30-76 3.55e-10

chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins; This subgroup includes the N-terminal CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 (HP1)-like protein from Entamoeba histolytica, and similar proteins. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349288  Cd Length: 52  Bit Score: 53.03  E-value: 3.55e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD--CPELIEAF 76
Cdd:cd18638   2 FEVEKIVKKKTVKGGTEYFVKWKGYSAKENTWETEDNLEksYKEMIDEF 50
CD_Swi6_like cd18637
chromodomain of fission yeast Swi6, and similar proteins; Fission yeast Swi6 protein is a ...
29-78 8.12e-09

chromodomain of fission yeast Swi6, and similar proteins; Fission yeast Swi6 protein is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromeres, telomeres, and the silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. chromodomains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2). CSDs have only been found in proteins that also possess a chromodomain.


Pssm-ID: 349287  Cd Length: 54  Bit Score: 49.43  E-value: 8.12e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 20544151  29 EFVVEKVLDRRVV--NGKVEYFLKWKGFTDA-DNTWEPEENLD-CPELIEAFLN 78
Cdd:cd18637   1 EYVVEKILKHRMArkGGGYEYLLKWEGYDDPsDNTWSSEADCAgCKDLIEAYWE 54
CD_DDE_transposase_like cd18978
chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins; This ...
27-78 8.97e-09

chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizopus microsporus putative DDE transposases, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349334  Cd Length: 52  Bit Score: 49.24  E-value: 8.97e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151  27 PEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLN 78
Cdd:cd18978   1 DESYEVEKIINHRGEKNRRKYLVKWKGYDDTDNSWVTQEDFNDKDMIDEYEN 52
CD_CDY cd18634
chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain ...
29-76 1.47e-08

chromodomain of the Chromodomain Y-like protein family; This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development).


Pssm-ID: 349284  Cd Length: 52  Bit Score: 48.98  E-value: 1.47e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  29 EFVVEKVLDRRV-VNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18634   1 LYEVERIVDKRKnKKGKTEYLVRWKGYDSEDDTWEPEQHLlNCEEFIHDF 50
CD_Cbx7 cd18646
chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of ...
30-76 2.10e-08

chromodomain of chromobox homolog 7; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 7 (CBX7), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX7 has been shown to function as a tumor suppressor in lung carcinoma and an oncogene in gastric cancer and lymphoma.


Pssm-ID: 349293  Cd Length: 56  Bit Score: 48.55  E-value: 2.10e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18646   5 FAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAY 51
CD_Cbx8 cd18649
chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of ...
30-76 2.16e-08

chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 8 (CBX8), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, CBX8 for example promotes proliferation while suppressing metastasis, in colorectal carcinoma progression.


Pssm-ID: 349296  Cd Length: 55  Bit Score: 48.56  E-value: 2.16e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 76
Cdd:cd18649   5 FAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAF 51
CD_Cbx6 cd18648
chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of ...
30-81 3.52e-08

chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 6 (CBX6), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.


Pssm-ID: 349295  Cd Length: 58  Bit Score: 48.13  E-value: 3.52e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQK 81
Cdd:cd18648   4 FAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKER 55
CD_Tf2-1_POL_like cd18973
chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type ...
30-68 3.76e-08

chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349329  Cd Length: 50  Bit Score: 47.63  E-value: 3.76e-08
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD 68
Cdd:cd18973   1 YVVEAILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENLE 39
chromodomain cd18964
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
30-76 3.91e-08

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349320  Cd Length: 54  Bit Score: 47.71  E-value: 3.91e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151  30 FVVEKVLDRR----VVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18964   1 FFVERIIGRRpsarDGPGKFLWLVKWDGYPIEDATWEPPENLgEHAKLIEDF 52
chromodomain cd18965
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain ...
30-67 1.24e-07

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.


Pssm-ID: 349321  Cd Length: 53  Bit Score: 46.32  E-value: 1.24e-07
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL 67
Cdd:cd18965   1 YIIEALLKKRQFNRKLEYLVKWHGLPESENTWEREKDI 38
CD_CMT3_like cd18635
chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier ...
29-76 2.83e-07

chromodomain of chromomethylase 3, and similar proteins; CHRomatin Organization Modifier (chromo) domain of DNA (cytosine-5)-methyltransferase chromomethylase 3 (CMT3, EC:2.1.1.37), and similar proteins. CMT3 is primarily a CHG (where H is either A, T or C) methyltransferase and is predominantly expressed in actively replicating cells. The protein is involved in preferentially methylating transposon-related sequences, reducing their mobility. Studies suggest that in order to target DNA methylation, CMT3 associates with H3K9me2-containing nucleosomes through binding of its BAH- and chromo-domains to H3K9me2. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349285  Cd Length: 57  Bit Score: 45.38  E-value: 2.83e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 20544151  29 EFVVEKVLDRRVVNGK------VEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18635   1 EFEVEKLVGICYGDPKktgergLYFKVRWKGYGPEEDTWEPIEGLsNCPEKIKEF 55
CD_Chp1_like cd18636
chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin ...
30-67 5.31e-07

chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of chromodomain-containing protein 1 (CHp1), and similar proteins. Chp1 is needed for RNA interference-dependent heterochromatin formation in fission yeast. Chp1 is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions. The chromodomain of the Chp1 component binds the histone H3 lysine 9 methylated tail (H3K9me) and the core of the nucleosome. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349286  Cd Length: 52  Bit Score: 44.75  E-value: 5.31e-07
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRV-VNGKVEYFLKWKGFTDADNTWEPEENL 67
Cdd:cd18636   2 YEVEDILADRVnKNGINEYYIKWAGYDWYDNTWEPEQNL 40
CSD_Swi6 cd18657
chromo shadow domain of chromatin-associated protein Swi6; Chromo shadow domain (CSD) of ...
130-172 5.48e-07

chromo shadow domain of chromatin-associated protein Swi6; Chromo shadow domain (CSD) of fission yeast Swi6 protein. Swi6 is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromere, telomere and silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation.


Pssm-ID: 349304  Cd Length: 55  Bit Score: 44.59  E-value: 5.48e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 20544151 130 TDSSGELMFLMKWKDSDEAdLVLAKEANMKCPQIVIAFYEERL 172
Cdd:cd18657  14 RDKDGKLLVYLTWKNGKKS-QHPSSVVYKKCPQKMLQFYESHL 55
CD_CEC-4_like cd18961
chromodomain of Caenorhabditis elegans chromodomain protein 4, and similar proteins; CHRomatin ...
30-76 5.61e-07

chromodomain of Caenorhabditis elegans chromodomain protein 4, and similar proteins; CHRomatin Organization Modifier (chromo) domain of Caenorhabditis elegans CEC-4, and similar proteins. CEC-4 is a perinuclear heterochromatin anchor, it mediates the anchoring of H3K9 methylation-bearing chromatin at the nuclear periphery in early to mid-stage embryos. It is necessary for anchoring, but does not affect transcriptional repression. CEC-4 contributes to the efficiency with which muscle differentiation is induced following ectopic expression of the master regulator, HLH-1 (MyoD in mammals). A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349317  Cd Length: 51  Bit Score: 44.78  E-value: 5.61e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTD-ADNTWEPEENL-DCPELIEAF 76
Cdd:cd18961   1 YEVEKILSHRIVNGKPLYLVMWVGYPGpVENSEMWEEDLkNCGELLKAY 49
CD_POL_like cd18974
chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the ...
32-76 1.18e-06

chromodomain of Penicillium solitum protein PENSOL_c198G03123; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349330  Cd Length: 50  Bit Score: 43.62  E-value: 1.18e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 20544151  32 VEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18974   3 VEEIVDEKMIDDELHYLVKWKGWPAEYNQWEPEDDMeNAPKAIQSY 48
CD2_tandem cd18659
repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier ...
31-78 2.08e-06

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349306 [Multi-domain]  Cd Length: 54  Bit Score: 42.95  E-value: 2.08e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 20544151  31 VVEKVLDRRVV-NGKVEYFLKWKGFTDADNTWEPEENL--DCPELIEAFLN 78
Cdd:cd18659   4 IVERIIAHREDdEGVTEYLVKWKGLPYDECTWESEEDIsdIFQEAIDEYKK 54
CSD_HP1e_insect cd18981
chromo shadow domain of insect heterochromatin protein 1E; The chromo shadow domain (CSD) is ...
120-172 2.21e-06

chromo shadow domain of insect heterochromatin protein 1E; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349337  Cd Length: 53  Bit Score: 42.92  E-value: 2.21e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 20544151 120 GLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERL 172
Cdd:cd18981   1 GFTAQEILKGINNNGEISFLIRFKHLDQPQVVPSDMAYVEIPQMVLKFYENHC 53
CD_Chro-like cd18640
chromodomain of Drosophila melanogaster chromator chromodomain protein, and similar proteins; ...
30-76 1.60e-05

chromodomain of Drosophila melanogaster chromator chromodomain protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in chromodomain of Drosophila melanogaster chromator (also known as Chriz/Chro) chromodomain protein, and similar proteins. Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349290  Cd Length: 52  Bit Score: 40.74  E-value: 1.60e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  30 FVVEKVLDRRVVNGKV--EYFLKWKGFTDADNTWEPEENLD-CPELIEAF 76
Cdd:cd18640   1 EPVEKIVAKRFNPRKKtwEYLVKWENRSHHENTWEPMANLErCKYLLQMF 50
CD_Clr4_like cd18632
N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar ...
29-77 2.98e-05

N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of cryptic loci regulator 4 (Clr4), a histone H3 lysine methyltransferase which targets H3K9. Clr4 regulates silencing and switching at the mating-type loci and affects chromatin structure at centromeres. Clr4 is a catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349282  Cd Length: 55  Bit Score: 40.18  E-value: 2.98e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 20544151  29 EFVVEKVLD-RRVVNGKVE-YFLKWKGFTDADNTWEPEENL-DCPELIEAFL 77
Cdd:cd18632   1 EYEVEKIVDeKTDRNTAEPlYLVRWKNYSKNHDTWEPAENLsGCQAVLEKWK 52
chromodomain cd18969
CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members ...
28-76 6.95e-05

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members of this subgroup, the chromodomain is followed by a chromo shadow domain; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. For the majority of members of this subgroup, the chromodomain is followed by a chromo shadow domain (CSD).


Pssm-ID: 349325  Cd Length: 56  Bit Score: 39.04  E-value: 6.95e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 20544151  28 EEFVVEKVLD---RRVVNGKVEYFLKWKGFTDADNTWEPEENL-DCPELIEAF 76
Cdd:cd18969   2 EEYEIEEILDvkkGGFEDGKLAYFVKWKGYPSSENSWVTEEDAaNAQEMIEEY 54
CD_POL_like cd18971
chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar ...
30-67 2.21e-04

chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Magnaporthe grisea putative retrotransposon polyprotein which includes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349327  Cd Length: 50  Bit Score: 37.37  E-value: 2.21e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 20544151  30 FVVEKVLD---RRVVNGKVEYFLKWKGFtdADNTWEPEENL 67
Cdd:cd18971   1 YEVEEILAarrRRIRGKGREVLVKWVGY--AEPTWEPLDNL 39
CD1_tandem cd18660
repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier ...
28-67 2.58e-04

repeat 1 of paired tandem chromodomains; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349307 [Multi-domain]  Cd Length: 70  Bit Score: 37.73  E-value: 2.58e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 20544151  28 EEFVVEKVLDRRVVNGKV----------------EYFLKWKGFTDADNTWEPEENL 67
Cdd:cd18660   1 DEDKIEKILDHRPKGPVEeasldltdpdepwderEFLVKWKGKSYLHCTWVTEETL 56
CD3_cpSRP43_like cd18628
chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; ...
31-76 5.87e-04

chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 3 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.


Pssm-ID: 349278  Cd Length: 51  Bit Score: 36.59  E-value: 5.87e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 20544151  31 VVEKVLDRRVVNG--KVEYFLKWkgFTDADNTWEPEENLDcPELIEAF 76
Cdd:cd18628   5 VAESVIGKRVGDDgkTIEYLVKW--TDMSDATWEPQDNVD-STLVLLY 49
CD_NC-like cd18980
chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and ...
29-68 8.04e-04

chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Trichosporon asahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349336  Cd Length: 56  Bit Score: 36.01  E-value: 8.04e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 20544151  29 EFVVEKVLDRRVVNGKVE---YFLKWKGFTDADNTWEPEENLD 68
Cdd:cd18980   3 EYEVEAILDHKVDRRYRDpnfYLVRWRGYGPSHDSWEPTSALE 45
CD_POL_like cd18972
chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and ...
30-77 2.54e-03

chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Moniliophthora perniciosa FA553 putative retrotelement polyprotein, which includes domains in the following order: a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related "chromo shadow" domain


Pssm-ID: 349328  Cd Length: 50  Bit Score: 34.80  E-value: 2.54e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD-CPELIEAFL 77
Cdd:cd18972   1 YEVEAIVGHKPKKKPRQFLVSWLGYDSSHNEWKQKEELEnARELLQDYL 49
CD2_cpSRP43_like cd18629
chromodomain 2 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; ...
32-67 3.19e-03

chromodomain 2 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 2 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.


Pssm-ID: 349279  Cd Length: 48  Bit Score: 34.40  E-value: 3.19e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 20544151  32 VEKVLDRRVVNGKVEYFLKWKgfTDADNTWEPEENL 67
Cdd:cd18629   5 VNEILESRGKGKDMEYLIEWK--DGGDCEWVKGVHV 38
CD_eEF3 cd18626
chromodomain-like insertion in an ATPase domain of elongation factor eEF3; Eukaryotic ...
30-68 7.31e-03

chromodomain-like insertion in an ATPase domain of elongation factor eEF3; Eukaryotic elongation factor eEF3 (also known as EF-3, YEF3, and TEF3), a member of the ATP-binding cassette (ABC) family of proteins, is a ribosomal binding ATPase essential for fungal translation machinery. Until recently it was considered fungal-specific and therefore an attractive target for antifungal therapy; however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes, and translation elongation factor 3 activity has been demonstrated from a non-fungal species, Phytophthora infestans. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain. Chromodomain mutations in the ABC2 domain of eEF3 have been shown to reduce ATPase activity, but not ribosome binding. Thus, the chromodomain-like insertion is critical to eEF3 function. In addition to its elongation function, eEF3 has been shown to interact with mRNA in a translation independent manner, suggesting an additional, non-elongation function for this factor.


Pssm-ID: 349276 [Multi-domain]  Cd Length: 56  Bit Score: 33.34  E-value: 7.31e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 20544151  30 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLD 68
Cdd:cd18626   2 RVIEKIVGRRKLKKSYEYEVKWKGMSSKDNSWIPREELE 40
CD2_tandem_CHD3-4_like cd18662
repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and ...
27-75 9.45e-03

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.


Pssm-ID: 349309 [Multi-domain]  Cd Length: 55  Bit Score: 33.01  E-value: 9.45e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 20544151  27 PEEFVVEKVLDRRVVN-GKVEYFLKWKGFTDADNTWEPEEnLDCPELIEA 75
Cdd:cd18662   1 PEWLQIHRIINHRVDKdGNTWYLVKWRDLPYDQSTWESED-DDIPDYEKH 49
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH