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Conserved domains on  [gi|564345942|ref|XP_006236202|]
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inhibitor of growth protein 3 isoform X1 [Rattus norvegicus]

Protein Classification

ING3 family PHD finger domain-containing protein( domain architecture ID 13801036)

ING3 (inhibitor of growth protein 3) family PHD (plant homeodomain) finger domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ING pfam12998
Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous ...
3-102 1.22e-39

Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.


:

Pssm-ID: 463768  Cd Length: 100  Bit Score: 136.89  E-value: 1.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942    3 YLEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQL 82
Cdd:pfam12998   1 YLEDYLDDLENLPLELQRNFTELREIDAKVQELLKEIDSQIQKFIKQNGSLTPNPKEEELSKIQEELKKAQELQDEKIQL 80
                          90       100
                  ....*....|....*....|
gi 564345942   83 ANQIYDLVDRHLRKLDQELA 102
Cdd:pfam12998  81 ANQALELVDKHIRRLDLDLE 100
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
354-398 3.01e-35

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


:

Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 123.72  E-value: 3.01e-35
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15585    1 YCICNQVSYGEMVGCDNDDCPIEWFHYGCVGLTEAPKGKWYCPQC 45
TNG2 super family cl34876
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
4-402 1.80e-29

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


The actual alignment was detected with superfamily member COG5034:

Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 115.42  E-value: 1.80e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   4 LEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVS--EFFMNAKKNKPEWREEQMASIKKDYY-KALEDADEKV 80
Cdd:COG5034    7 LNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISilKKIIDLDSQTYEEVEDGLLKEIRELLlKAIYIQKEKS 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  81 QLANQIYDLVDRHLRKLDQELAKfkMELEADNAGITEIleRRSLELDAPSQpvnnhhahshtpvettdhipekkfKSEAL 160
Cdd:COG5034   87 DLADRAEKLLRRHRKLLDDRIAK--RPHEKVAARIENC--HDAVSRLERNS------------------------YSSAA 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 161 LSTLTSDASKENTLGCRNNNSTASCNNAYNVNSSQPLAS-----YNIGSLSSGAGAGAItmaaaqavqataqmKEGRRTS 235
Cdd:COG5034  139 RRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkrevsFTLESPSVPDTATRV--------------KEGNNGG 204
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 236 SLKasyeafknndfqlgkefsmpretagyssssalmttltqnasssaadsrsgrksknntksssqqssssssssssssls 315
Cdd:COG5034  205 STK----------------------------------------------------------------------------- 207
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 316 lcsssstvvqevsqqttvvpeSDSNSQVDWTYDpnEPRYCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFC 395
Cdd:COG5034  208 ---------------------SRGVSSEDNSEG--EELYCFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYC 264

                 ....*..
gi 564345942 396 PQCTAAM 402
Cdd:COG5034  265 PECKKAA 271
 
Name Accession Description Interval E-value
ING pfam12998
Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous ...
3-102 1.22e-39

Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.


Pssm-ID: 463768  Cd Length: 100  Bit Score: 136.89  E-value: 1.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942    3 YLEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQL 82
Cdd:pfam12998   1 YLEDYLDDLENLPLELQRNFTELREIDAKVQELLKEIDSQIQKFIKQNGSLTPNPKEEELSKIQEELKKAQELQDEKIQL 80
                          90       100
                  ....*....|....*....|
gi 564345942   83 ANQIYDLVDRHLRKLDQELA 102
Cdd:pfam12998  81 ANQALELVDKHIRRLDLDLE 100
ING_ING3_Yng2p cd16858
Inhibitor of growth (ING) domain of inhibitor of growth protein 3 (ING3), Yng2p and similar ...
11-98 5.03e-36

Inhibitor of growth (ING) domain of inhibitor of growth protein 3 (ING3), Yng2p and similar proteins; ING3, also termed p47ING3, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). Yeast chromatin modification-related protein Yng2p, also termed ESA1-associated factor 4 or ING1 homolog 2, is a subunit of the NuA4 histone acetyltransferase (HAT) complex. It plays a critical role in intra-S-phase DNA damage response. Members of this family contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341091  Cd Length: 92  Bit Score: 127.32  E-value: 5.03e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNK----PEWREEQMASIKKDYYKALEDADEKVQLANQI 86
Cdd:cd16858    1 LENLPSELRHLLTEIREKDLQVQELLDRIQQRDAKLFKHIKKNGsltpNPKEEELYEKIREDYDKALELADEKVELANRL 80
                         90
                 ....*....|..
gi 564345942  87 YDLVDRHLRKLD 98
Cdd:cd16858   81 LDLVDRHLRRLD 92
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
354-398 3.01e-35

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 123.72  E-value: 3.01e-35
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15585    1 YCICNQVSYGEMVGCDNDDCPIEWFHYGCVGLTEAPKGKWYCPQC 45
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
4-402 1.80e-29

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 115.42  E-value: 1.80e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   4 LEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVS--EFFMNAKKNKPEWREEQMASIKKDYY-KALEDADEKV 80
Cdd:COG5034    7 LNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISilKKIIDLDSQTYEEVEDGLLKEIRELLlKAIYIQKEKS 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  81 QLANQIYDLVDRHLRKLDQELAKfkMELEADNAGITEIleRRSLELDAPSQpvnnhhahshtpvettdhipekkfKSEAL 160
Cdd:COG5034   87 DLADRAEKLLRRHRKLLDDRIAK--RPHEKVAARIENC--HDAVSRLERNS------------------------YSSAA 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 161 LSTLTSDASKENTLGCRNNNSTASCNNAYNVNSSQPLAS-----YNIGSLSSGAGAGAItmaaaqavqataqmKEGRRTS 235
Cdd:COG5034  139 RRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkrevsFTLESPSVPDTATRV--------------KEGNNGG 204
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 236 SLKasyeafknndfqlgkefsmpretagyssssalmttltqnasssaadsrsgrksknntksssqqssssssssssssls 315
Cdd:COG5034  205 STK----------------------------------------------------------------------------- 207
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 316 lcsssstvvqevsqqttvvpeSDSNSQVDWTYDpnEPRYCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFC 395
Cdd:COG5034  208 ---------------------SRGVSSEDNSEG--EELYCFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYC 264

                 ....*..
gi 564345942 396 PQCTAAM 402
Cdd:COG5034  265 PECKKAA 271
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
354-401 5.40e-09

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 51.72  E-value: 5.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 564345942  354 YC-ICNQVSY-GEMVGCDnqDCPiEWFHYGCVGLT----EAPKGKWFCPQCTAA 401
Cdd:pfam00628   1 YCaVCGKSDDgGELVQCD--GCD-DWFHLACLGPPldpaEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
354-398 1.06e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 50.67  E-value: 1.06e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 564345942   354 YC-ICNQV-SYGEMVGCDNqdCPiEWFHYGCVGLT---EAPKGKWFCPQC 398
Cdd:smart00249   1 YCsVCGKPdDGGELLQCDG--CD-RWYHQTCLGPPlleEEPDGKWYCPKC 47
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
4-122 9.56e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 41.59  E-value: 9.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942     4 LEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKpEWREEQmasikKDYYKALEDADEKVQLA 83
Cdd:TIGR02169  331 IDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFA-ETRDEL-----KDYREKLEKLKREINEL 404
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 564345942    84 NQIYDLVDRHLRKLDQELAKFKMELEADNAGITEILERR 122
Cdd:TIGR02169  405 KRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEK 443
 
Name Accession Description Interval E-value
ING pfam12998
Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous ...
3-102 1.22e-39

Inhibitor of growth proteins N-terminal histone-binding; Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.


Pssm-ID: 463768  Cd Length: 100  Bit Score: 136.89  E-value: 1.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942    3 YLEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQL 82
Cdd:pfam12998   1 YLEDYLDDLENLPLELQRNFTELREIDAKVQELLKEIDSQIQKFIKQNGSLTPNPKEEELSKIQEELKKAQELQDEKIQL 80
                          90       100
                  ....*....|....*....|
gi 564345942   83 ANQIYDLVDRHLRKLDQELA 102
Cdd:pfam12998  81 ANQALELVDKHIRRLDLDLE 100
ING_ING3_Yng2p cd16858
Inhibitor of growth (ING) domain of inhibitor of growth protein 3 (ING3), Yng2p and similar ...
11-98 5.03e-36

Inhibitor of growth (ING) domain of inhibitor of growth protein 3 (ING3), Yng2p and similar proteins; ING3, also termed p47ING3, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). Yeast chromatin modification-related protein Yng2p, also termed ESA1-associated factor 4 or ING1 homolog 2, is a subunit of the NuA4 histone acetyltransferase (HAT) complex. It plays a critical role in intra-S-phase DNA damage response. Members of this family contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341091  Cd Length: 92  Bit Score: 127.32  E-value: 5.03e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNK----PEWREEQMASIKKDYYKALEDADEKVQLANQI 86
Cdd:cd16858    1 LENLPSELRHLLTEIREKDLQVQELLDRIQQRDAKLFKHIKKNGsltpNPKEEELYEKIREDYDKALELADEKVELANRL 80
                         90
                 ....*....|..
gi 564345942  87 YDLVDRHLRKLD 98
Cdd:cd16858   81 LDLVDRHLRRLD 92
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
354-398 3.01e-35

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 123.72  E-value: 3.01e-35
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15585    1 YCICNQVSYGEMVGCDNDDCPIEWFHYGCVGLTEAPKGKWYCPQC 45
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
354-398 2.59e-31

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 113.16  E-value: 2.59e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15505    1 YCICNQVSYGEMVACDNPNCPIEWFHFECVGLTAKPKGKWYCPEC 45
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
4-402 1.80e-29

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 115.42  E-value: 1.80e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   4 LEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVS--EFFMNAKKNKPEWREEQMASIKKDYY-KALEDADEKV 80
Cdd:COG5034    7 LNDITDHLANVPSETDIRFTELSEIDAKVCDIIKNLRQMISilKKIIDLDSQTYEEVEDGLLKEIRELLlKAIYIQKEKS 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  81 QLANQIYDLVDRHLRKLDQELAKfkMELEADNAGITEIleRRSLELDAPSQpvnnhhahshtpvettdhipekkfKSEAL 160
Cdd:COG5034   87 DLADRAEKLLRRHRKLLDDRIAK--RPHEKVAARIENC--HDAVSRLERNS------------------------YSSAA 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 161 LSTLTSDASKENTLGCRNNNSTASCNNAYNVNSSQPLAS-----YNIGSLSSGAGAGAItmaaaqavqataqmKEGRRTS 235
Cdd:COG5034  139 RRSSGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSkrevsFTLESPSVPDTATRV--------------KEGNNGG 204
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 236 SLKasyeafknndfqlgkefsmpretagyssssalmttltqnasssaadsrsgrksknntksssqqssssssssssssls 315
Cdd:COG5034  205 STK----------------------------------------------------------------------------- 207
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942 316 lcsssstvvqevsqqttvvpeSDSNSQVDWTYDpnEPRYCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFC 395
Cdd:COG5034  208 ---------------------SRGVSSEDNSEG--EELYCFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYC 264

                 ....*..
gi 564345942 396 PQCTAAM 402
Cdd:COG5034  265 PECKKAA 271
PHD_Yng1p_like cd15587
PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the ...
354-400 2.06e-29

PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger.


Pssm-ID: 277062 [Multi-domain]  Cd Length: 47  Bit Score: 108.27  E-value: 2.06e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQCTA 400
Cdd:cd15587    1 YCYCRRVSFGEMVACDNPDCKIEWFHFECVGLTETPKGKWYCSDCKV 47
PHD_ING4_5 cd15586
PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed ...
354-398 5.50e-29

PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.


Pssm-ID: 277061 [Multi-domain]  Cd Length: 45  Bit Score: 106.89  E-value: 5.50e-29
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15586    1 YCLCHQVSYGEMIGCDNPDCPIEWFHFACVGLTTKPKGKWFCPRC 45
ING_ING4_5 cd16859
Inhibitor of growth (ING) domain of inhibitor of growth protein ING4, ING5, and similar ...
11-101 6.34e-27

Inhibitor of growth (ING) domain of inhibitor of growth protein ING4, ING5, and similar proteins; ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53, and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with Inhibitor of cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.


Pssm-ID: 341092  Cd Length: 91  Bit Score: 103.05  E-value: 6.34e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIYDLV 90
Cdd:cd16859    1 LESLPLELQRNFSLMRELDARVQDLLAEIEKLLREYLKTVKSLSKEERRELLKEIQDLFAKAKELSEEKVQLATQTYETV 80
                         90
                 ....*....|.
gi 564345942  91 DRHLRKLDQEL 101
Cdd:cd16859   81 DKHIRRLDADL 91
PHD_ING1_2 cd15584
PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic ...
354-398 6.90e-27

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277059 [Multi-domain]  Cd Length: 45  Bit Score: 101.37  E-value: 6.90e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15584    1 YCLCNQVSYGEMIGCDNDECPIEWFHFSCVGLTHKPKGKWYCPKC 45
PHD_ING5 cd15685
PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one ...
354-400 4.09e-26

PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277155 [Multi-domain]  Cd Length: 49  Bit Score: 99.35  E-value: 4.09e-26
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQCTA 400
Cdd:cd15685    2 YCLCHQVSYGEMIGCDNPDCPIEWFHFACVDLTTKPKGKWFCPRCTQ 48
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
354-398 5.64e-25

PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 96.23  E-value: 5.64e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15682    2 YCLCNQVSYGEMIGCDNDECPIEWFHFSCVGLNHKPKGKWYCPKC 46
PHD_ING4 cd15684
PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one ...
354-399 1.43e-24

PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277154 [Multi-domain]  Cd Length: 48  Bit Score: 95.14  E-value: 1.43e-24
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQCT 399
Cdd:cd15684    2 YCLCHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCS 47
PHD_ING2 cd15683
PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of ...
354-398 2.88e-24

PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277153 [Multi-domain]  Cd Length: 49  Bit Score: 94.32  E-value: 2.88e-24
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 354 YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15683    2 YCLCNQVSYGEMIGCDNEQCPIEWFHFSCVGLTYKPKGKWYCPKC 46
ING_ING4 cd16862
Inhibitor of growth (ING) domain of inhibitor of growth protein 4 (ING4); ING4, also termed ...
8-101 3.39e-17

Inhibitor of growth (ING) domain of inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341095  Cd Length: 94  Bit Score: 76.15  E-value: 3.39e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   8 LEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIY 87
Cdd:cd16862    1 LDSIENLPFELQRNFQLMRDLDQRTEDLKVEIDKLATEYVSNARSLSSEEKLKLLKQIQEAYGKCKEFGDDKVQLAMQTY 80
                         90
                 ....*....|....
gi 564345942  88 DLVDRHLRKLDQEL 101
Cdd:cd16862   81 EMVDKHIRRLDTDL 94
ING_ING5 cd16863
Inhibitor of growth (ING) domain of inhibitor of growth protein 5 (ING5); ING5, also termed ...
11-101 1.34e-16

Inhibitor of growth (ING) domain of inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with Inhibitor of cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341096  Cd Length: 93  Bit Score: 74.58  E-value: 1.34e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIYDLV 90
Cdd:cd16863    3 IENLPCELQRNFQLMRDLDQRTEDKKAEIDKLASEYIANVKNLSPEQRVEHLKKIQSAYSKCKEYSDDKVQLAMQTYEMV 82
                         90
                 ....*....|.
gi 564345942  91 DRHLRKLDQEL 101
Cdd:cd16863   83 DKHIRRLDADL 93
ING_ING1_2 cd16857
Inhibitor of growth (ING) domain of inhibitor of growth protein ING1, ING2, and similar ...
8-98 2.44e-14

Inhibitor of growth (ING) domain of inhibitor of growth protein ING1, ING2, and similar proteins; ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341090  Cd Length: 89  Bit Score: 68.04  E-value: 2.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   8 LEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKpeWREEQMASIKKDYYKALEDADEKVQLANQIY 87
Cdd:cd16857    1 LDCVENLPGDVQRNLSLMRELDKRYQEILNELEELYEEYLREDDESH--AKKRLLARIQKLLIRSQELGDEKLQIVSQIL 78
                         90
                 ....*....|.
gi 564345942  88 DLVDRHLRKLD 98
Cdd:cd16857   79 DLIENRNRQLE 89
ING_plant cd17015
Inhibitor of growth (ING) domain of plant inhibitor of growth proteins; This subfamily is ...
14-101 3.20e-14

Inhibitor of growth (ING) domain of plant inhibitor of growth proteins; This subfamily is composed of mainly plant inhibitor of growth proteins such as Arabidopsis thaliana ING1 (AtING1 or PHD finger protein ING1) and ING2 (AtING2 or PHD finger protein ING2). They are histone-binding components that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. The related mammalian ING proteins act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation, and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, which binds lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING domain for the H3 tail.


Pssm-ID: 341097 [Multi-domain]  Cd Length: 98  Bit Score: 68.09  E-value: 3.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  14 LPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAK---KNKPEWREEQMASIKKDYYKALED----ADEKVQLANQI 86
Cdd:cd17015    4 LPAELQRNLSLIRDLDERSQALQDQVEQKCERCLEEPSqssESASSSDDTAAAALREEIESAQKDclqlADEKVALAQQA 83
                         90
                 ....*....|....*
gi 564345942  87 YDLVDRHLRKLDQEL 101
Cdd:cd17015   84 YDLVDGHIQRLDKDL 98
ING cd16101
Inhibitor of growth (ING) domain family; The Inhibitor of growth (ING) family includes a group ...
11-98 1.97e-12

Inhibitor of growth (ING) domain family; The Inhibitor of growth (ING) family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation, and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, which binds lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING domain for the H3 tail. The ING family also includes three yeast orthologs, chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect.


Pssm-ID: 341089  Cd Length: 88  Bit Score: 62.73  E-value: 1.97e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIYDLV 90
Cdd:cd16101    1 LSHLPFELRRLLTLIRELDEKKTELQKEIDELAKELLKSARIESHQQKRRLLDEIRQLYEKSIELSDEKVQLSSQAYELV 80

                 ....*...
gi 564345942  91 DRHLRKLD 98
Cdd:cd16101   81 DNHIRKLD 88
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
354-398 3.51e-10

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 54.99  E-value: 3.51e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564345942 354 YC-ICNQVSYG-EMVGCDNQDcpiEWFHYGCVGLTEAPKG--KWFCPQC 398
Cdd:cd15522    1 ICpICKKPDDGsPMIGCDECD---DWYHWECVGITDEPPEedDWFCPKC 46
ING_Pho23p_like cd17016
Inhibitor of growth (ING) domain of yeast Pho23p and similar proteins; This family is composed ...
11-98 2.51e-09

Inhibitor of growth (ING) domain of yeast Pho23p and similar proteins; This family is composed of Saccharomyces cerevisiae transcriptional regulatory protein PHO23 (Pho23p), Schizosaccharomyces pombe chromatin modification-related protein png2 (also called ING1 homolog 2), and similar proteins. Pho23p is part of Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Pho23p inhibits p53-dependent transcription. The related mammalian ING proteins act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.


Pssm-ID: 341098  Cd Length: 89  Bit Score: 53.85  E-value: 2.51e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942  11 IEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMN-AKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIYDL 89
Cdd:cd17016    1 IEALPLEVMRYFTLLKEVDAKCRNPEPELNDLIDEFLKNpVEEQDKLERRELLSRLRKKLQEILPSLDEKMHVASDANDN 80

                 ....*....
gi 564345942  90 VDRHLRKLD 98
Cdd:cd17016   81 LDKQLKRID 89
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
354-401 5.40e-09

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 51.72  E-value: 5.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 564345942  354 YC-ICNQVSY-GEMVGCDnqDCPiEWFHYGCVGLT----EAPKGKWFCPQCTAA 401
Cdd:pfam00628   1 YCaVCGKSDDgGELVQCD--GCD-DWFHLACLGPPldpaEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
354-398 1.06e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 50.67  E-value: 1.06e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 564345942   354 YC-ICNQV-SYGEMVGCDNqdCPiEWFHYGCVGLT---EAPKGKWFCPQC 398
Cdd:smart00249   1 YCsVCGKPdDGGELLQCDG--CD-RWYHQTCLGPPlleEEPDGKWYCPKC 47
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
363-396 1.24e-08

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 50.41  E-value: 1.24e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564345942 363 GEMVGCDNQDCPiEWFHYGCVGLTEAPKGKWFCP 396
Cdd:cd15568    9 GDLVLCDFKGCP-KVYHLSCLGLEKPPGGKWICP 41
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
354-398 3.38e-08

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 49.40  E-value: 3.38e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564345942 354 YCICNQVSYGE-MVGCDNQDcpiEWFHYGCVGLTEAPKG---KWFCPQC 398
Cdd:cd16039    1 YCICQKPDDGRwMIACDGCD---EWYHFTCVNIPEADVElvdSFFCPPC 46
PHD2_3_BPTF cd15560
PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); ...
354-398 4.98e-08

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.


Pssm-ID: 277035  Cd Length: 47  Bit Score: 48.88  E-value: 4.98e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564345942 354 YCICNQvSYGE---MVGCDNQDcpiEWFHYGCVGLT--EAPKG-KWFCPQC 398
Cdd:cd15560    1 YCICRT-PYDEsqfYIGCDRCQ---DWFHGRCVGILqsEAEKIdEYVCPQC 47
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
354-398 9.38e-08

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 48.14  E-value: 9.38e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564345942 354 YCICNQVSYGE-MVGCDNqdCPiEWFHYGCVGLTE-APKG--KWFCPQC 398
Cdd:cd15553    1 YCICRSSDISRfMIGCDN--CE-EWYHGDCINITEkEAKAikEWYCQQC 46
PHD5_NSD3 cd15661
PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
354-396 2.38e-07

PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277131  Cd Length: 43  Bit Score: 46.88  E-value: 2.38e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564345942 354 YCICNQVSyGEMVGCDNQDCPiEWFHYGCVGLTEAPKGKWFCP 396
Cdd:cd15661    1 YCFQCGDG-GELVMCDKKDCP-KAYHLLCLNLTQPPYGKWECP 41
ING_ING1 cd16860
Inhibitor of growth (ING) domain of inhibitor of growth protein 1 (ING1); ING1 is an ...
8-98 2.87e-07

Inhibitor of growth (ING) domain of inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341093  Cd Length: 88  Bit Score: 47.98  E-value: 2.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   8 LEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFfmnAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIY 87
Cdd:cd16860    1 LDSIESLPFDLQRNVSLMREIDAKYQEILKELDEYYEKF---KRETDAVQKRRLLHCIQRALIRSQELGDEKIQIVSQMV 77
                         90
                 ....*....|.
gi 564345942  88 DLVDRHLRKLD 98
Cdd:cd16860   78 ELVENRTRQVD 88
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
355-398 1.47e-06

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 45.00  E-value: 1.47e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564345942 355 CICNQVSY--GEMVGCDNqdCPIeWFHYGCVGLTE---APKGKWFCPQC 398
Cdd:cd15489    3 IVCGKGGDlgGELLQCDG--CGK-WFHADCLGPPLssfVPNGKWICPVC 48
PHD_PHF3_like cd15552
PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, ...
354-398 4.05e-06

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.


Pssm-ID: 277027  Cd Length: 50  Bit Score: 43.54  E-value: 4.05e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564345942 354 YCICNQV-SYGEMVGCDNQDcpiEWFHYGCVGLTEApKGK--------WFCPQC 398
Cdd:cd15552    1 YCICRKPhNNRFMICCDRCE---EWFHGDCVGITEA-QGKemeenieeYVCPKC 50
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
355-398 6.58e-06

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 42.68  E-value: 6.58e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 564345942 355 CICNQVSY-GEMVGCDNQDcpiEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15529    3 TKCGDPHDeDKMMFCDQCD---RGYHTFCVGLRSIPDGRWICPLC 44
PHD_AF10_AF17 cd15574
PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. ...
355-398 1.77e-05

PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277049 [Multi-domain]  Cd Length: 48  Bit Score: 41.73  E-value: 1.77e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 355 CIC-NQVSYGE--MVGCDNQDCPIEwFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15574    3 CVCsDERGWAEnpLVYCDGHGCNVA-VHQACYGIVQVPTGPWFCRKC 48
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
354-398 4.09e-05

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 40.66  E-value: 4.09e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564345942 354 YC-ICNQvsYGEMVGCDNqdCPiEWFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15531    1 YCeVCQQ--GGEIILCDT--CP-RAYHLVCLDpeLEKAPEGKWSCPHC 43
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
354-398 4.15e-05

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 40.31  E-value: 4.15e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 354 YC-ICNQVsyGEMVGCDNqdCPIEwFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15567    1 WCfICSEG--GSLICCES--CPAS-FHPECLGLEPPPEGKFYCEDC 41
PHD5_NSD2 cd15660
PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed ...
363-396 4.47e-05

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.


Pssm-ID: 277130  Cd Length: 43  Bit Score: 40.69  E-value: 4.47e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564345942 363 GEMVGCDNQDCpIEWFHYGCVGLTEAPKGKWFCP 396
Cdd:cd15660    9 GQLVLCDRKSC-TKAYHLSCLGLTKRPFGKWECP 41
PHD1_NSD1_2 cd15648
PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; ...
356-399 4.65e-05

PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2; NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger.


Pssm-ID: 277118  Cd Length: 43  Bit Score: 40.53  E-value: 4.65e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 564345942 356 ICNQVsyGEMVGCDNQDCPIewFHYGCVGLTEAPKGKWFCPQCT 399
Cdd:cd15648    4 VCEKP--GELLLCEGQCCGA--FHLDCIGLSEMPSGKFICDECI 43
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
354-398 4.96e-05

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 40.34  E-value: 4.96e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564345942 354 YC-ICNQVsyGEMVGCDNqdCPiEWFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15532    1 FCrVCKDG--GELLCCDG--CP-SSYHLHCLNppLAEIPDGDWFCPRC 43
ING_ING2 cd16861
Inhibitor of growth (ING) domain of inhibitor of growth protein 2 (ING2); ING2, also termed ...
8-98 4.98e-05

Inhibitor of growth (ING) domain of inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain.


Pssm-ID: 341094  Cd Length: 88  Bit Score: 41.75  E-value: 4.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942   8 LEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFfmnAKKNKPEWREEQMASIKKDYYKALEDADEKVQLANQIY 87
Cdd:cd16861    1 LECVESLPLEIQRNVSLLREIDTKYQEALKEVDEVYEKY---KKETDPSQKKRLQQQLQRALINSQELGDEKIQIVTQML 77
                         90
                 ....*....|.
gi 564345942  88 DLVDRHLRKLD 98
Cdd:cd16861   78 ELVENRARQME 88
PHD5_NSD1 cd15659
PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
363-396 7.79e-05

PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277129  Cd Length: 43  Bit Score: 39.93  E-value: 7.79e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564345942 363 GEMVGCDNQDCPiEWFHYGCVGLTEAPKGKWFCP 396
Cdd:cd15659    9 GQLVSCKKPGCP-KVYHADCLNLTKRPAGKWECP 41
PHD2_KDM5A cd15606
PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
354-398 1.20e-04

PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277079  Cd Length: 56  Bit Score: 39.73  E-value: 1.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 564345942 354 YCICNQVSYGEMVGCdnQDCPiEWFHYGCVGL---TEAPKG-----------KWFCPQC 398
Cdd:cd15606    1 YCICRKPFSGFMLQC--ELCK-DWFHSSCVPLpksSSQKKGgngsgqgakelKFLCPLC 56
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
354-398 1.65e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 38.85  E-value: 1.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 354 YC-ICNQVsyGEMVGCDNqdCPiEWFHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15538    1 FCwRCHKE--GQVLCCSL--CP-RVYHKKCLKLTSEPDEDWVCPEC 41
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
354-398 2.06e-04

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 38.55  E-value: 2.06e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 564345942 354 YC-ICNQvsYGEMVGCDNqdCPiEWFHYGCVGL----TEAPKGKWFCPQC 398
Cdd:cd15535    1 FCsACGG--YGSFLCCDG--CP-RSFHFSCLDPpleeDNLPDDEWFCNEC 45
PHD_Ecm5p_Lid2p_like cd15518
PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), ...
354-398 2.27e-04

PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins; The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p.


Pssm-ID: 276993  Cd Length: 45  Bit Score: 38.48  E-value: 2.27e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 564345942 354 YCICNQVSYGEMVGCDNqdCPiEWFHYGCVGLTE---APKGKWFCPQC 398
Cdd:cd15518    1 YCFCRQGEGGTMIECEI--CK-EWYHVKCIKNGRwklDDDDKFVCPIC 45
PHD_DIDO1_like cd15639
PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family ...
354-398 2.50e-04

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.


Pssm-ID: 277109  Cd Length: 54  Bit Score: 38.79  E-value: 2.50e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564345942 354 YCICNQVSYGE-MVGCDNQDcpiEWFHYGCVGLTEApKGK--------WFCPQC 398
Cdd:cd15639    5 YCICRQPHNNRfMICCDRCE---EWFHGDCVGITEA-RGRllerngedYICPNC 54
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
355-398 2.91e-04

PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), or PLU-1) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277080  Cd Length: 44  Bit Score: 38.28  E-value: 2.91e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 355 CICNQVSYGEMVGCD-NQDCpiewFHYGCVGLTEAPKGK--WFCPQC 398
Cdd:cd15607    2 CVCQKAPMAPMIQCElCRDA----FHSGCVTAPSDPQGPqaWLCPQC 44
PHD2_KDM5A_like cd15516
PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar ...
354-398 6.10e-04

PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog protein, little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 276991  Cd Length: 53  Bit Score: 37.68  E-value: 6.10e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564345942 354 YCICNQVSYGEMVGCD-NQDcpieWFHYGCVGL---TEAPKG--------KWFCPQC 398
Cdd:cd15516    1 ICLCGKALAAGMLQCElCQD----WFHGSCVAVpriSSSPRPlawwegdrKFLCPLC 53
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
354-398 6.21e-04

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 37.36  E-value: 6.21e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564345942 354 YCICNQVsYGE---MVGCDnqdCPIEWFHYGCVGLTEAPKG---KWFCPQC 398
Cdd:cd15554    1 YCICRQP-YDVtrfMIECD---VCKDWFHGSCVGVEEHQANdieRYHCPNC 47
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
363-398 6.40e-04

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 37.04  E-value: 6.40e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564345942 363 GEMVGCDNqdCPiEWFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15539    9 GELLCCDG--CP-RAFHLACLVppLTLIPSGTWRCSSC 43
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
363-398 8.01e-04

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 37.06  E-value: 8.01e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564345942 363 GEMVGCDNqdCPIEwFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15519   12 GEVLLCDG--CDAE-YHTSCLDppLGEIPPGTWFCPSC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
355-398 8.40e-04

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 36.86  E-value: 8.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 355 CICNQVSYGE-MVGCDNQDcpiEWFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15543    3 RKCGLSDHPEwILLCDRCD---AGYHTACLRppLMIIPDGNWFCPPC 46
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
4-122 9.56e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 41.59  E-value: 9.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564345942     4 LEDYLEMIEQLPMDLRDRFTEMREMDLQVQNAMDQLEQRVSEFFMNAKKNKpEWREEQmasikKDYYKALEDADEKVQLA 83
Cdd:TIGR02169  331 IDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFA-ETRDEL-----KDYREKLEKLKREINEL 404
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 564345942    84 NQIYDLVDRHLRKLDQELAKFKMELEADNAGITEILERR 122
Cdd:TIGR02169  405 KRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEK 443
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
355-398 1.28e-03

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 36.44  E-value: 1.28e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 564345942 355 CICNQ-VSYG--EMVGCDNQDCPIewfHYGCVGLTEAPKGKWFCPQC 398
Cdd:cd15492    3 DVCLDgESEDdnEIVFCDGCNVAV---HQSCYGIPLIPEGDWFCRKC 46
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
356-398 1.65e-03

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 36.37  E-value: 1.65e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 564345942 356 ICNQVSY---GEMVGCDNqdCPiEWFHYGCVGLT---EAPKGKWFCPQC 398
Cdd:cd15517    4 ICNLETAavdELWVQCDG--CD-KWFHQFCLGLSnerYADEDKFKCPNC 49
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
356-398 2.19e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 35.83  E-value: 2.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 356 ICNQVSYGE-MVGCDNQDcpiEWFHYGCV--GLTEAPKGKWFCPQC 398
Cdd:cd15627    4 ICRRKGDAEkMLLCDGCD---RGHHMYCLrpPLKKVPEGDWFCPDC 46
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
355-398 4.82e-03

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 34.68  E-value: 4.82e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 355 CICNQVsyGEMVGCDNqdCPIEwFHYGCVG--LTEAPKGKWFCPQC 398
Cdd:cd15523    3 SVCRKS--GELLMCDT--CSLV-YHLDCLDppLKTIPKGMWICPKC 43
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
356-398 5.98e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 34.69  E-value: 5.98e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 564345942 356 ICNQVSYGE-MVGCDNQDCPiewFHYGCV--GLTEAPKGKWFCPQC 398
Cdd:cd15544    4 VCRKKGDPDnMILCDGCDKA---FHLYCLrpALREVPSGDWFCPAC 46
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
363-398 7.68e-03

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 34.25  E-value: 7.68e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 564345942 363 GEMVGCDNqdCPIEwFHYGC----VGLTEAPKGKWFCPQC 398
Cdd:cd15533    9 GDLLCCDR--CPAS-FHLQCcnppLDEEDLPPGEWLCHRC 45
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
367-398 8.30e-03

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 34.29  E-value: 8.30e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 564345942 367 GCDNQdcpiewFHYGCV--GLTEAPKGKWFCPQC 398
Cdd:cd15515   19 GCDDS------YHTFCLipPLPDIPPGDWRCPKC 46
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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